College Level Biology by AudioLearn

College-Level Biology

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TABLE OF CONTENTS Preface........................................................................................................ 1 Chapter 1: Biochemistry of Living Organisms .............................................. 4 Characteristics of Life ...................................................................................................... 4 Organic molecules ........................................................................................................... 11 Four Classifications of Organic Molecules .................................................................... 13 Carbohydrates ............................................................................................................ 13 Lipids .......................................................................................................................... 14 Proteins ....................................................................................................................... 16 Nucleic Acids .............................................................................................................. 18 Water and Biology.......................................................................................................... 19 Key Takeaways ............................................................................................................... 22 Quiz ................................................................................................................................ 23 Chapter 2: Viruses .................................................................................... 27 Virus Classification ........................................................................................................ 27 What is a Virus? ............................................................................................................. 29 Origins of Viruses........................................................................................................... 30 Viral Structure................................................................................................................ 31 The Virome ..................................................................................................................... 35 Virus Replication ........................................................................................................... 36 The Replication of the Viral Genome ............................................................................ 38 Viruses and Disease ....................................................................................................... 39

Epidemics from Viruses ................................................................................................. 40 Viruses and Cancer ........................................................................................................ 41 Vaccinations and Antiviral Drugs against Viral Infections ........................................... 41 Non-Human Viral Infections ......................................................................................... 42 Key Takeaways ............................................................................................................... 44 Quiz ................................................................................................................................ 45 Chapter 3: Bacteria ................................................................................... 48 Prokaryote versus Eukaryote ......................................................................................... 48 Prokaryote Structure...................................................................................................... 49 Bacterial Physiology ....................................................................................................... 53 Bacterial Genetics .......................................................................................................... 54 Bacterial Communication .............................................................................................. 55 Classifying Bacteria ........................................................................................................ 56 Prokaryote Cell Division ................................................................................................ 57 Bacterial Motility ........................................................................................................... 58 Key Takeaways ............................................................................................................... 59 Quiz ................................................................................................................................ 60 Chapter 4: Animal Cell Biology.................................................................. 64 Animal Cell Structure .................................................................................................... 64 Plasma Membrane ...................................................................................................... 64 Organelles ................................................................................................................... 66 Cytoskeleton ............................................................................................................... 67 Nucleus ....................................................................................................................... 68 Endoplasmic Reticulum ............................................................................................. 69

Golgi Apparatus .......................................................................................................... 70 Mitochondria .............................................................................................................. 70 Ribosomes ...................................................................................................................71 Lysosome .....................................................................................................................71 Vacuoles .......................................................................................................................71 Peroxisomes ................................................................................................................ 72 Animal Cell Physiology .................................................................................................. 72 Cell Membrane Physiology ......................................................................................... 72 Mitochondrial Physiology .......................................................................................... 74 Nucleus Physiology ........................................................................................................ 75 Ribosomes .................................................................................................................. 75 The Cell Cycle ................................................................................................................. 76 Mitosis ........................................................................................................................ 77 Meiosis ........................................................................................................................ 78 Key Takeaways ............................................................................................................... 81 Quiz ................................................................................................................................ 82 Chapter 5: Cellular Metabolism ................................................................. 85 Cellular Respiration ....................................................................................................... 85 Glycolysis ....................................................................................................................... 86 Krebs Cycle or Citric Acid Cycle .................................................................................... 90 Oxidative Phosphorylation ............................................................................................ 91 Fermentation ................................................................................................................. 94 Photosynthesis ............................................................................................................... 97 Chloroplasts ................................................................................................................. 100

Key Takeaways ............................................................................................................. 103 Quiz .............................................................................................................................. 104 Chapter 6: Genetics ................................................................................. 108 Mendelian Genetics ..................................................................................................... 108 Dominant Inheritance .................................................................................................. 112 Recessive Inheritance ................................................................................................... 113 X-linked Recessive Inheritance .................................................................................... 113 DNA and Genetics ......................................................................................................... 114 Chromosomes and Genes ............................................................................................. 116 Gene Mutations ............................................................................................................. 118 Genome ......................................................................................................................... 119 Regulation of Gene Expression.................................................................................... 120 Key Takeaways ............................................................................................................. 123 Quiz .............................................................................................................................. 124 Chapter 7: Evolution ............................................................................... 128 Darwinian Evolution .................................................................................................... 128 Natural Selection ......................................................................................................... 129 Modern Synthesis in Evolution ................................................................................... 133 History of Evolution on Earth and Origin of Species .................................................. 135 Key Takeaways ............................................................................................................. 143 Quiz .............................................................................................................................. 144 Chapter 8: Biological Diversity ................................................................ 148 The Three Domains...................................................................................................... 148 Archaea Domain .......................................................................................................... 149

Bacteria Domain .......................................................................................................... 149 Eukarya Domain .......................................................................................................... 150 The Six Kingdoms ........................................................................................................ 150 Archaea......................................................................................................................... 152 Protista ......................................................................................................................... 156 The Different Animal Phyla .......................................................................................... 161 Key Takeaways ............................................................................................................. 164 Quiz .............................................................................................................................. 165 Chapter 9: Plant Form and Function ....................................................... 169 Plant Cell Structure ...................................................................................................... 169 Plant Morphology .........................................................................................................172 Reproduction of Plants ................................................................................................. 175 Flowers ......................................................................................................................... 176 Pollination ..................................................................................................................... 177 Fruits ............................................................................................................................ 179 Soil Utilization and Plant Nutrition............................................................................. 180 Transpiration ................................................................................................................ 181 Plant Biotechnology ..................................................................................................... 183 Key Takeaways ............................................................................................................. 184 Quiz .............................................................................................................................. 185 Chapter 10: Fungi Form and Function ..................................................... 189 Fungal Diversity ........................................................................................................... 189 Fungal Anatomy ........................................................................................................... 190 Fungal Physiology ........................................................................................................ 194

Fungal Reproduction ................................................................................................... 195 Ecology of Fungi........................................................................................................... 197 Key Takeaways ............................................................................................................ 200 Quiz .............................................................................................................................. 201 Chapter 11: Animal Form and Function ................................................... 204 Circulatory Systems .....................................................................................................204 Nervous Systems .......................................................................................................... 207 Digestive Systems ........................................................................................................209 Respiratory Systems .................................................................................................... 210 Immune Systems ......................................................................................................... 213 Endocrine Systems........................................................................................................217 Reproductive Systems .................................................................................................. 219 Key Takeaways ............................................................................................................. 223 Quiz .............................................................................................................................. 224 Chapter 12: Ecology ................................................................................. 228 Nitrogen Cycle .............................................................................................................. 228 Ecosystems ................................................................................................................... 231 Population Ecology ...................................................................................................... 233 The Biosphere .............................................................................................................. 235 Global Ecological Changes ........................................................................................... 235 Key Takeaways ............................................................................................................. 237 Quiz .............................................................................................................................. 238 Summary of the Course ........................................................................... 242 Course Test Questions............................................................................. 245

PREFACE The purpose of this course is to open up the world of biology to the inquiring student. Biology is simply the study of living things. In this course, you will learn about what constitutes a “living thing” versus nonliving organisms. Each of the main categories of living things will be covered, including the biology of viruses, bacteria, protists (including fungi), animals, and plants. Biology is also concerned with genetics, evolution, and ecology—each of which is important to the way that biological organisms appear to us in today’s time and in the future. Chapter one in the course will begin the discussion of living things by explaining what constitutes a living thing. There are certain characteristics that make humans, plants, and even viral particles called living things. The biochemistry of life is something that unifies life and involves molecules that are only seen, at least in concert, in things that are considered living organisms. Life exists, for the most part, in an aqueous environment and so the physiology of life in relation to water is covered in this chapter. Virus anatomy and function are the focus of chapter two in the course. Viruses are the most basic structures in life and, some would argue, they barely qualify as truly representing life. As you have seen in the first chapter, however, viruses are basic living things that have structure and that replicate. The way viruses multiply and cause disease in other living things is covered as part of this chapter. Chapter three covers the topic of bacteria. Bacteria are single-celled organisms that, compared to viruses, are remarkably complex. These are prokaryotes as opposed to the typical animal and plant eukaryotic cells with the ability to divide and grow independently of other organisms. There are many types of bacteria, some of which are motile. The physiology of bacteria, particularly the way they can become motile, is discussed in this chapter. Chapter four in the course explains animal cells and their biology. These are the cells and cell types people are more familiar with, with multiple organelles that unite to create basic animal cell physiology. The structure and function or “physiology” of the

animal cell are presented in detail in this chapter along with the ways that genetic material divide. Both mitosis and meiosis, important in cellular and animal reproduction, are covered as part of this chapter. Chapter five describes the inner workings of cellular metabolism. Animal cell metabolism involves primarily cellular respiration and the use of oxygen to break down nutrients for use as fuel or energy, usually resulting in the making of ATP, the universal energy currency of the cell. There are processes in place for anaerobic respiration and fermentation, which will be covered in this chapter. Plants use their cellular machinery to participate in photosynthesis, which yields oxygen and utilizes carbon dioxide. This process is also discussed as part of this chapter. Genetics is the topic of discussion in chapter six in the course. It is the study of how traits are passed from one generation to the next, which involves the building blocks of genetics, DNA and RNA. These are divided into chromosomes and genes that together write the code that determines the offspring’s genotype (or genetic code) and phenotype (or physical appearance). Genes are tightly regulated so that some genes are expressed, while others are suppressed. This process of gene regulation is also covered in this chapter. The focus of chapter seven in the course is the evolutionary process, whereby individual species and populations gradually change over time because of the natural selection of the species that have inherited advantages over other species. Much of this involves Darwinian evolutionary principles, which is covered in this chapter. The history of evolution on earth and the origin of species has been largely uncovered and these are important topics of discussion in this chapter. The eighth chapter in the course covers the main divisions in nature and living things, outlining the six major kingdoms and their subdivisions. The way that biological species are defined is discussed in this chapter. The major features of each kingdom and how kingdoms and their subdivisions are determined are important topics of this chapter. Because archaea and Protista haven’t yet been covered, they are also discussed in separate sections.

Chapter nine in the course involves an extensive discussion of the cellular structures, basic anatomy, and reproductive functions of plants. Plants use much different nutrients when compared to animals and use these nutrients to participate in photosynthesis and in making nutritional substances used by many animal species. Plants are the subject of a great deal of discussion when it comes to biotechnology and genetic modification. This hot topic is covered in this chapter. Chapter ten in the course discusses fungi, their anatomy and physiology. Fungi are a broad category of organisms, ranging from microscopic organisms to the commonlyknown fungi, such as mushrooms. What they have in common and how they differ from one another are covered in this chapter. Fungi have their own unique way of reproducing themselves, which will be explained as part of this chapter. The focus of chapter eleven is the various systems that make up complex animals. All animals must have some way of obtaining nutrients through digestive systems, must circulate nutrients, and need to use respiration to have oxygen for energy. These will be different, depending on the animal species. Animal cells will have nervous systems of some sort and need strong immune systems to defend against pathogens. These systems as well as the endocrine systems and hormones in animal systems are discussed in this chapter. Ecology is the subject of chapter twelve in the course. This is the study of ecosystems in the world as well as the biosphere, which are the regions of the earth inhabited by living organisms. The ecology of populations is covered in this chapter as well as the important and timely topic of global ecological changes that have happened, are happening, and will happen to the earth as a planet.

CHAPTER 1: BIOCHEMISTRY OF LIVING ORGANISMS This chapter will begin the discussion of living things by explaining what constitutes a living thing. There are certain characteristics that make humans, plants, and even viral particles called living things. The biochemistry of life is something that unifies life and involves molecules that are only seen, at least in concert, in things that are considered living organisms. Life exists, for the most part, in an aqueous environment and so the physiology of life in relation to water is covered in this chapter.

CHARACTERISTICS OF LIFE In order to start any discussion of biology or the “study of life”, we need to define exactly what is meant by “life”. With the advent of artificial intelligence and computers, which are very complex but don’t represent life, we need to have definitions of what we really mean when we talk about living things. What makes a living thing truly life? It turns out that there are characteristics unique to life that simply aren’t present in nonliving organisms. Let’s look at these characteristics: •

Complex organization—there are many things that are complex but aren’t life and many living things that aren’t particularly complex. Computers are complex but they are not living. Remember that being complex is just one characteristic of living things to consider. Most living things are made from at least one cell. An exception to this is viruses, which are very important to life but are not made from cells. These are called “particles” rather than cells because they lack true cellular structure. However, as you’ll see, there are characteristics of virus particles that qualify them as being life. In general, though, living things are cellular; some are not just cellular but are multicellular—organized into tissues, organs, and whole multicellular living beings.

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Metabolic processes—living things will make use of organic molecules and will turn them over in order to make cellular structures and energy for the cell. Metabolism basically involves the exchange of organic molecules from the 4

exterior of the organism and transformation of organic matter inside the organism, releasing heat or chemical energy. Nonliving things do not use organic molecules and do not transform them in any meaningful way. The key feature of metabolism is the use of organic, carbon-based reactions and not inorganic reactions. •

Responsiveness to the environment—this feature of living things involves their ability to respond significantly to changes in sound, chemistry, mechanical contact, light, and heat in the environment. There must be the ability to detect stimuli, receive information, and respond to them in meaningful ways. Larger organisms have chemical-detecting taste buds, ears for hearing, and vision sensation. There are advanced nervous systems in complex living things. There are hormonal systems in place for the large-scale incorporation and coordination of responses to stimuli. Even simple living things have receptors for the detection of the environment, even though their ability to detect and react is rudimentary compared to multicellular organisms. As you can see, this ability to be responsive is very different, depending on the type of organism. This is why the study of biology is so all-encompassing of many types of organisms. Responsiveness can be thought of as the predictable behavior of an organism to respond to various external stimuli. It should be noted that, while a rock responds predictably to being rolled down a hill because of gravity, it is not living because it is simply following the laws of gravity and does not, in and of itself, have responsiveness to the environment. Responsiveness takes energy out of the organism in order to happen. There is no energy taken from the rock itself when it reacts to gravity.

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Growth—all living things have the ability to grow. They take in material from outside of themselves and organize that material in a meaningful way in order to make its own structures. Energy must be expended in order for growth to occur and the energy must come from within the organism. A building, for example, does indeed grow when built, but the energy does not come from within the structure itself. Growth involves the transformation of organic carbon-based molecules to make parts of the organism. In complex organisms, nutrients are digested, absorbed, and transformed into meaningful structural molecules or 5

energy necessary to build and grow things. But, do bacterial organisms digest and grow? As you’ll see in later chapters, they do in fact digest in simple ways and do use what they digest to grow and divide. This makes them just as “living” as complex organisms. •

Reproduction—living things have both simple and complex ways of reproducing themselves. Even viral particles reproduce themselves, albeit with machinery and energy derived from other organisms. Asexual reproduction involves the production of cells (or particles) that are basically identical to the parent cell, although things like differentiation are possible. Bacteria multiply through binary fission, in which one cell splits into two identical “daughter cells”. More complex organisms participate in sexual reproduction. This involves the presence of two separate parents that together create a new organism that combines the genetic material of both parents. New traits can be produced in the new organism. Both plants and animals participate in sexual reproduction as well as asexual reproduction, the latter of which usually involves reproduction within complex organisms; however, some species of organisms can create whole new organisms through asexual reproduction.

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Evolution—evolution is basically the ability of a living organism or species to adapt to changes in the environment. In evolution, the population has the potential to change as certain aspects of the organism become more efficient in metabolism, reproduction, or response to their environment. In that sense, the progeny develops features that either make it more adapted to the environment (and thus better able to reproduce and multiply), or less adapted, meaning that it does not succeed as time passes. This evolutionary process takes time and usually involves specific changes within a species, although some evolutionary processes will create new species. It is through this process that there are so many species on earth. Non-living things cannot undergo the kind of population-based evolutionary changes that happen in living things.

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Ecology—this is the study of relationships between organisms and their environment. There are biotic factors (or living factors) and abiotic (non-living)

factors, such as the sun, rain, and wind, that affect the environment but it is only living things that can fundamentally interact with the environment through things like hibernation and migration. Nonliving things can change because of the environment but they do not intentionally react and interact with the environment other than that which is predicted by the laws of physics. To put it simply, living things seem to defy the rule of entropy in physics (although this is physically impossible to do indefinitely). What is entropy? The American Heritage Dictionary gives as a definition of entropy as "a measure of disorder or randomness in a closed system”. Organisms take disordered things (nutrients) and make more ordered things out of them (structure). This takes energy and must cause other things to become disordered in order to create structure within the organism. While living organisms do not reverse entropy indefinitely (as they do die off and reverse the entropy direction toward greater disorder), they do use their energy to defy entropy for as long as energy can be utilized to do so. Hierarchy and Living Things A hierarchy involves the classification of things in a particular order. As it relates to living things, the hierarchy we will talk about goes from the smallest particle of living things to the largest aspect of living things. How it works is like this: •

Subatomic particles—these are the smallest thing that life can be broken into. The smallest atomic particle in life (and outside of life) is hydrogen, which is broken down into one proton and one electron. Protons and electrons are charged subatomic particles that together make an atom. There are also neutrons, which are not charged particles. There are much larger atoms but even these are made of increasing numbers of protons, neutrons, and electrons. The natural state of these subatomic particles is that the electrical charge be neutral. Protons are electrically positively charged and electrons are electrically negatively charged. Within living things (and outside of living things), the natural order is to have a balance between the positive and the negative. Biochemical reactions, by necessity, strive to create an electrical balance between these oppositely charged subatomic particles.

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Atoms—these are what subatomic particles come together to make. In the case of hydrogen atoms, one proton and one electron together make the hydrogen ion. In the case of carbon, 6 protons and 6 electrons together make a single carbon molecule. As you will see, there is not a solid and absolute connection between these neutrons and electrons so that electrical bonds can be made between different atoms.

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Molecule—this is a group of atoms that have bound together through covalent bonds. A covalent bond is a chemical link between two atoms in which the electron pairs are shared between them. This is also called a molecular bond. As mentioned, this tight connection of one electron needing one proton to bind to it is not as strong as one would think. If it were so strong, molecules could not be made and atoms would stay separate. A molecule is made when atoms share electrons so that a whole, usually electrically neutral, molecule can be created.

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Organelle—these are small structural groupings of organic molecules of different types that function within a cell to help in the inner workings of the cell. These apply only to eukaryotic cells, which are cells that have their genetic material within a nucleus, which is considered an organelle. As you will see, there are many different types of organelles within a single cell.

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Cell—this is the basic unit of biological organisms such that there can be singlecelled organisms called “unicellular” organisms and multicellular organisms; however, anything smaller on the hierarchy scale does not constitute a living organism. Again, we get into the gray area of viruses which, by some accounts, are not living because they aren’t truly cellular in the strictest sense of the word. We will discuss this further in the chapter on viruses. For all living organisms, on the other hand, the cell is the smallest independently-functioning aspect of life. Cells have their own metabolism and their own unique structure. Even very large organisms are basically collections of cells.

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Tissue—this involves a group of cells, usually of the same type, that work together within a multicellular organism. Only multicellular organisms have the tissue level of hierarchy. It requires physical connections to take place that hold

the cells together so they can function basically in the same direction, although many will interact with one another so that neighboring cells in a tissue know what the others are doing. This involves a relatively complex system of cell-to-cell communication. •

Organ—this involves a grouping of different tissues that collectively form a structure that has a particular function within the organism. Some examples of organs include the heart, lungs, and liver. These are made from different cell types (including connective tissue and epithelial tissue) that form a specific structure. The structure has its own function within a multicellular organism.

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Organ system—these are organs that work together to perform a unique function in a multi-cellular organism. An example is the heart and arteries—two organs that together form the cardiovascular system. Neither of these can function without the other. While there are different possible groupings that can be made for a given organism and while it can be argued that all organs in the body need each other to function as a whole, there are definitely subdivisions like the digestive system, the cardiorespiratory system, and the endocrine system, that involve different organs that interact toward the same goal.

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Organism—while we sometimes use the word organism to apply to both singlecelled and multicellular living things, this definition of organism applies to multicellular organisms that have different organ systems that function to create a whole and unique structural being. It is separate from other organisms within a population.

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Population—this is the next largest step in the hierarchy of living things and implies that the organisms within the population are of the same species. As part of the species, Homo sapiens, humans interact with one another but, from a metabolic standpoint, each is unique. Even so, populations basically act as a unit, having similar behaviors and similar goals. In some cases, we can refer to populations as being made of different species; however, from a biological standpoint, a population is said to be of a single species and in the same location

(even a large location), such that they can interact with one another when it comes to language, shared goals, and similar features. •

Community—this is where we get different populations that can interact with one another. As humans, we are part of smaller populations (such as our family or neighborhood) and larger communities (such as our country and the world in general). It still implies that the members of a community are basically components belonging to the same species.

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Ecosystem—this is where we get into different populations of different species that are in relationship to one another because of their physical proximity to one another. There are definable ecosystems, such as the ocean, a desert ecosystem, or the tundra. These are mainly defined by the general environment type in which the populations live. Different populations and communities interact by virtue of the fact that they share the same general environment.

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Biosphere—this is the largest hierarchy of living things and, when it comes to practical purposes, this involves the earth itself. Within it, there are numerous different ecosystems that interact with one another to make up the entirety of life as we know it. We do not yet know of life existing elsewhere so the earth is the largest biosphere we know.

ORGANIC MOLECULES There are so many molecules possible in nature—from individual atomic molecules (which are as numerous as the number of elements in the periodic table) to very large macromolecules made from at least a thousand different atoms that have somehow found themselves together in not only the same vicinity but connected to one another in a very specific way. There are thousands of possible combinations of atoms in nature; the vast majority of the molecules in nature have only four different atoms in them: these are carbon, hydrogen, oxygen, and nitrogen. In fact, it can easily be said that, of these, it is carbon that defines life as being life and that defines a given molecule as being “organic” or belonging to life. Of course, there are other atoms in life, such as sulfur, phosphorus, and minerals like magnesium, iron, and zinc. These arguably are necessary for life but, at least here on earth, they do not define life. (As you’ll see, water is necessary for life as well but in a different way). Organic molecules are completely built upon chains of carbon atoms. These chains, at least in life forms as we know them, are extremely long. You may ask, why carbon and what’s so special about it? Without getting deep into biochemistry, suffice it to say that carbon has the unique ability to bind to four other atoms at the same time. This leads to chains of carbon atoms that can combine to connect to other carbon atoms as well as to other molecules. Carbon has the unique property of also being able to form rings rather than lining up in single file. This ability to combine with other atoms as well as to form rings makes for an incredible variety of different molecules that can be made from it. You should know that organic molecules aren’t confined to living things. There are many carbon-based things in nature, such as fossil fuels, which are actually the remains of living organisms that once survived on earth. Manmade molecules, such as pesticides, medicines, and plastic substances are considered organic because of their molecular structure. There are organic components to much of what we see in life around us, such as cologne, shampoo, rayon fabric, nylon fabric, cotton, detergent, and cleaning products.

There are some inorganic molecules that are intimately connected to life but aren’t in themselves organic. These include carbon dioxide (CO2), oxygen (O2), and water (H2O). Life would not exist without these molecules and yet, because they do not involve a chain of carbon atoms, they are inorganic. These can be considered, however, to be the building blocks of life. Plants use carbon dioxide and water to make carbon-based molecules called carbohydrates. Carbon has six protons and six electrons. Four of these six electrons are available for bonding. When it comes to biochemical life forms, carbon can form four “single bonds”, two single bonds and a “double bond” or two double bonds. It depends on the demands of the other atoms in the molecule. For example, oxygen has two “spots” to connect with other atoms. It can connect with two carbon atoms with two single bonds or with one carbon atom in a double bond (which means the sharing of 2 electron pairs at once). This is why oxygen, which is unstable by itself, is generally seen in living things as O2 (two molecules together). One of the more basic carbon-based molecules is CO2. This involves carbon simultaneously “double-bonding” with two oxygen molecules. This is a completely stable molecule in that it uses up free electron pairing spots for both carbon and oxygen. Another simple carbon-based molecule is methane, which is CH4. This involves hydrogen, which has just one electron to share and carbon, which has four free electrons to share. The result is the stable molecule of methane. While we’re on the subject of pairing, you should know that nitrogen has three extra electrons available for pairing. This leads to a simple molecule of ammonia, which is NH3. This isn’t an organic molecule but it gives you an idea of what nitrogen needs as part of a molecular structure.

FOUR CLASSIFICATIONS OF ORGANIC MOLECULES With all of the different possibilities involved in carbon-based molecules, there really are just four major macromolecules involved in the making of living things. These are carbohydrates, lipids, proteins, and nucleic acids.

CARBOHYDRATES Carbohydrates are basically sugar molecules of varying lengths. A sugar molecule is a combination of carbon, hydrogen, and oxygen in a ratio of one carbon to two hydrogens to one oxygen atoms. The most basic sugar molecule is considered to be C6:H12:O6. A monomer or “single-unit” of sugar is made from these three atoms in the previously mentioned ratios. A sugar monomer is called a monosaccharide and these sugars are referred to as “hexoses” because they have six carbon atoms. Figure 1 shows the chemical structure of monosaccharide hexoses and disaccharides:

There are three monosaccharides in living things, each of which follows the hexose ring structure but has different placements of hydrogen atoms and oxygen atoms. These are glucose, galactose, and fructose. Disaccharides are two sugar molecules linked together. Three major disaccharides are lactose (a combination of glucose and galactose), sucrose (a combination of glucose and fructose), and maltose (a combination of 2 glucose molecules). A polysaccharide is any grouping of monosaccharides that is greater than 2 in a row. Cellulose is a plant-based polysaccharide that is not digested by humans but is digested by other organisms. Starch is another polysaccharide that is used in plants for their cellular energy. The same molecule comparable to starch in animals is glycogen, the energy storage molecule in animals.

LIPIDS Lipids are a little bit more complex in their diversity when compared to carbohydrates. What they share in common is that they are insoluble in water and in other polar solvents. You’ll hear more about polarity when it comes to water in the next major section. There are three major types of lipids in living systems: •

Triglycerides—these are basically fatty acid chains (three of them) attached to a glycerol molecule. A fatty acid is just chains of carbon and hydrogen atoms with a carboxyl group attached at the end. A carboxyl group is basically a -COOH grouping. Figure 2 is an illustration of a triglyceride:

You’ve probably heard about polyunsaturated fats, trans fats, monounsaturated fats, and saturated fats. Saturation, when it comes to fatty acids, involves the number of hydrogen atoms that are attached to the fatty acid. Saturated means the carbon atoms are all saturated with hydrogen atoms and that it is a straight molecule. Monounsaturated and polyunsaturated fats have some hydrogen atoms missing, making the molecule “kinky”. Trans fats have a bend in the fatty acid but the “kink” goes in the wrong way, making it more likely to block arteries in a more intense way than even saturated fats. •

Phospholipids—these look like triglycerides because they have fatty acid chains; however, one of the fatty acids has been replaced with a phosphate group, with the chemical symbol of PO4. These are highly important molecules in living things because they have hydrophobic tails and a hydrophilic phosphate group. This makes them great for the making of membranes because the phosphate groups are on the outside of the membrane and the fatty acid (hydrophobic) groups are on the inside of the membrane. It takes two sheets of phospholipids sandwiching the hydrophobic tails in between to make a membrane. This is how membranes are made all over cells and cell structures. Figure 3 illustrates what a lipid bilayer looks like:

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Steroids—these are completely different from triglycerides and phospholipids. They involve four carbon rings that are linked together. Figure 4 shows what cholesterol, a common steroid lipid, looks like:

The hormones estrogen and testosterone are also steroids. What these have in common is that they are made with the same four carbon rings but have different side chains. Cholesterol, in particular, is part of the cell membrane of many animal cells.

PROTEINS Proteins are chains of amino acids, which involves a wide variety of different “nitrogenous” molecules, which contain nitrogen. There are peptides, which are short chains of amino acids, also referred to as oligopeptide chains. There are also polypeptides, which are also just called “proteins”, having very long chains. There are 22 amino acids on earth with only 20 actually encoded for by the genetic code. The remaining two, selenocysteine and pyrrolysine are incorporated into proteins by synthetic mechanisms. Some are considered essential to humans because they must be taken in through food and are not encoded by the human genetic code. There are

different amino acids essential to different organisms. Amino acids are specific molecules characterized by having a side chain, an amine group (NH2), and a carboxyl group (COOH). Figure 5 shows the 22 amino acids on earth:

As you can see, the side chain, referred to by the letter “R” is simplest in glycine, in which R is just a hydrogen atom. Some R side chains, such as cysteine, have sulfur in them, while others, such as phenylalanine, will have a carbon ring. Proteins, as mentioned, are chains of amino acids. They have four different levels of organization as they are very complex molecules. There is a primary structure, which involves just the order of the amino acids. There are so many different combinations of amino acids, making even the primary structure complex and unique. Then there is the secondary structure. This is the three-dimensional shape of the protein. Some amino acids are attracted to one another, linked by hydrogen bonds (a mild type of bonding between molecules, less strong than covalent bonding) giving a 3D shape to the peptide. The tertiary structure is also a 3D organization of a protein made from the fact that some R side chains are hydrophobic, staying deep inside the protein, while others are hydrophilic, staying on the outside of the protein structure. There are also disulfide bonds between two cystine amino acids that twist the protein even further. The quaternary structure of a protein is that which comes from the combination of two

separate peptide chains. An example is hemoglobin, which is actually a combined 4peptide chain structure, held together by connections between the different amino acids.

NUCLEIC ACIDS Nucleic acids are unique molecules that make up the genetic code of a cell and of an organism. There are two types of nucleic acids. These are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). They differ in a couple of ways as will be described. DNA is a polymer (meaning it is a chain of monomers), consisting of three different parts. The first is a nitrogenous base, which is a nitrogen-containing ring, of which there are five types (but only four types in DNA, making this one difference between RNA and DNA). The different nitrogenous bases are adenine, guanine, thymine, and cytosine. Any one of these can be attached to a pentose sugar which, in the case of DNA is deoxyribose. Unlike the typical hexose sugar with six carbon atoms, a pentose sugar has five carbon atoms. Together, the combination of a nitrogenous base and a pentose sugar is called a nucleoside. When these molecules are added to a phosphate group, it is called a nucleotide. These nucleotides are chained together to make DNA. As you probably have learned, DNA has a unique structure, which is called a “double helix”. Basically, it looks like a spiral staircase. Two chains of nucleotides are connected to each other in a spiral, which are connected to each other through the different nitrogenous bases. The adenine (A) molecule always connects to a thymine (T) molecule, while the cytosine (C) molecule always connects to a guanine (G) molecule. Figure 6 shows what these molecules look like as they bind:

RNA is also a nucleic acid but is different from the DNA molecule. The sugar is a ribose sugar and not a deoxyribose sugar. The thymine nucleotide is not seen in the RNA molecule. Instead, there is guanine, which has a base pair with adenine in doublestranded RNA. Most RNA, however, is single stranded and does not have a base pair situation happening with it.

WATER AND BIOLOGY Water is extremely important to life because it has a number of features that make it an excellent medium in which to have the biochemical reactions necessary for life occur. It is also very abundant in the earth; in humans, it involves 70 percent of the body. Perhaps there are life forms on other planets that do not contain water as part of their structure; however, life as we know it on earth is entirely dependent on it. What features make water so good when it comes to life? As mentioned, water is a polar substance, which means that it is a molecule with a positive end electrically and a negative end electrically. This causes it to connect to or bind easily to other polar 19

molecules. What it doesn’t bind well to are fat-soluble molecules, like lipids. Fortunately, using certain biochemical “tricks” like carrier proteins, lipids can survive in an aqueous or water-containing solution. Molecules that can easily dissolve in water are called hydrophilic; molecules that cannot do this easily are called hydrophobic. The formula for water is H2O. This means that two hydrogen atoms are covalently bonded to one oxygen atom. This is a bent molecule with a negative oxygen side and a positive hydrogen side (and thus its polarity as a molecule). Hydrogen bonds will connect water molecules together in solution; however, a hydrogen bond is considered ten times weaker than a covalent bond so it can be easily broken when necessary. Water is a solvent that takes things up in solution. The compounds that are ionic (such as sodium chloride and other metal salts) will easily dissolve and break their bonding so they can be surrounded by water molecules, hydrating the ions. Both positive ions, like sodium, potassium, and calcium, and negative ions, like phosphate and chloride, have the ability to be hydrated by water. In fact, any polar molecule will dissolve easily in water, even larger molecules, such as polysaccharides, polypeptides, and nucleic acids. Water is also a good temperature buffer. This is important because many enzymatic reactions in biochemistry require a specific temperature and cannot work outside of that temperature. Water has a high specific heat capacity, which is the heat required to raise a kilogram of water by one degree Celsius. This means that those reactions that give of heat as energy are also protected by the heat buffering capacity of water from raising the surrounding temperature too much. Water acts as a metabolite in many enzymatic reactions involving metabolism. Metabolism is basically all of the chemical and physical processes within a cell, both those that build up molecules and those that break down molecules to form energy. Water is necessary for photosynthesis, aerobic respiration in the cells, and digestion of nutrients. It participates in hydrolysis (the breakdown of molecules) and condensation (the joining of two molecules together in a reaction). Water participates in pH phenomena in its environment. The pH of a substance depends on whether it has a predominance of acids or a predominance of bases or alkaline substances. Solutions like stomach acid have a predominance of hydrogen ions,

which are highly acidic solutions like lye have a predominance of hydroxide (OH) ions, which are highly alkaline. The pH scale ranges from 1 (which is highly acidic) to 14 (which is highly alkaline). The pH considered to be neutral is in the middle at 7. In living things, the pH tends toward being neutral, with the pH of the blood in humans being strictly controlled at 7.35-7.45. This allows for most enzymatic reactions to take place and water is a part of what makes this environment hospitable for enzymatic reactions in most biochemical processes. There are chemical buffers operating in cells and in the circulatory system that keep the pH within a narrow therapeutic range. This is necessary because, as mentioned, enzymes are tricky and don’t function outside of a certain pH range. In humans, there are protein buffers, bicarbonate buffer systems, and phosphate buffer systems. These will help maintain a pH balance in water so that there are not very large changes in the pH of body systems.

KEY TAKEAWAYS •

There are certain qualities of living things that separate them from nonliving things.

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There is a hierarchy of life that starts with subatomic particles as the smallest part and that ends with the biosphere, which represents all ecosystems put together.

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Life on earth is carbon-based so that living things (and many nonliving things) are made with this atom.

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There are four major organic macromolecules, such as proteins, carbohydrates, lipids, and nucleic acids.

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Water is essential for life and has molecular characteristics that make it an excellent solvent and temperature-regulator. It also participates in the pH of solutions that is strictly regulated in living systems for the purpose of enzymes and enzymatic reactions.

QUIZ 1. Which living thing defies one of the properties of living things by not being cellular in nature? a. Bacteria b. Fungi c. Viruses d. Prokaryotes Answer: c. Viruses, strictly speaking, are not cellular, being called viral particles instead of cells. They still, however, have many other properties of life. 2. What is not a feature of metabolism in living things? a. Inorganic chemical reactions b. The uptake of organic material from outside the organism c. The internal processing of organic material d. The production of energy in the form of chemical energy or heat Answer: a. Inorganic chemical reactions can happen outside of life and are not considered “metabolic reactions”. 3. A classification that applies to a group of the same type of cell that are connected to one another and communicate with one another is called what? a. Ecosystem b. Organ system c. Tissue d. Organelle Answer: c. A tissue is a group of the same type of cells that collectively interact and perform the same function toward the same end. They collectively contribute to an organ, along with other cell types.

4. What most defines the features and living things in an ecosystem? a. The cell type of the organism b. The environmental conditions c. The nutrients available d. The number of predators Answer: b. The environmental conditions dictate what organisms live in an ecosystem. The same organisms in the ocean cannot live in a desert ecosystem, and vice versa. What this means is that the environment plays a big role in which organisms (such as plants, animals, etcetera) live and interact with one another there. 5. Which inorganic molecule is not closely connected to most living things? a. Oxygen b. Carbon dioxide c. Methane d. Water Answer: c. Although there are rare organisms that use methane instead of oxygen, these are not representative of most life forms as most use oxygen along with carbon dioxide and water to make the building blocks or framework of organic molecules. 6. Which is a stable form of oxygen in living systems? a. O3 b. O2 c. O4 d. O Answer: b. In nature, there exists unstable oxygen formulations, such as ozone, which is O3, but it quickly breaks down into its stable form, which is O2. This balances out the binding needs of two oxygen molecules together.

7. What is the major energy-storing carbohydrate in plants? a. Starch b. Glycogen c. Maltose d. Cellulose Answer: a. Starch is the major energy-storing carbohydrate in plants. The same thing is true of glycogen in animal organisms. 8. Which triglyceride has the greatest number of hydrogen atoms in it? a. Polyunsaturated fats b. Trans fats c. Monounsaturated fats d. Saturated fats Answer: d. Saturated fats have the most hydrogen atoms associated with it because they have completely saturated all of the carbon atoms with hydrogen. The others have double bonds between carbon atoms that make for fewer electrons available for hydrogen bonding. 9. Amino acids contain several different side chains. What atom type is seen in some amino acids that is different from most other carbon-based organic molecules? a. Magnesium b. Sulfur c. Iron d. Zinc Answer: b. Sulfur is an added atom to some amino acids that make it different from most carbon-based organic molecules.

10. What atom is seen in amino acids that isn’t seen in the organic molecules, lipids and carbohydrates? a. Iron b. Oxygen c. Phosphorus d. Nitrogen Answer: d. All amino acids are nitrogen-based molecules, having an amine group as part of every amino acid molecule.

CHAPTER 2: VIRUSES Virus anatomy and function are the focus of this chapter. Viruses are the most basic structures in life and, some would argue, they barely qualify as truly representing life. As you have seen in the first chapter, however, viruses are basic living things that have structure and that replicate. The way viruses multiply and cause disease in other living things is covered as part of this chapter.

VIRUS CLASSIFICATION As you’ll come to find out, there are different ways to classify all organisms. Historically, classifications were based on what different organisms looked like. Now, in the era past the discovery of DNA and genomes, genetic classifications have changed the face of taxonomy, which is the branch of science concerned with the classification of organisms, also referred to as “systematics”. With regard to viruses, there are a couple of ways to classify them. One way is the Baltimore classification, which is based on what their genome is made of. There are seven different groups under this classification system: •

dsDNA viruses—these are viral particles with double stranded DNA and include Herpesviruses, Poxviruses, and Adenoviruses

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ssDNA viruses—these are single-stranded DNA viruses with a “positive strand”, meaning the strand is “read” by RNA to make protein directly. These include Parvoviruses.

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dsRNA viruses—these are unique in that they involve double-stranded RNA and include Reovirus particles.

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(+) ssRNA viruses—these are single-stranded RNA viruses that are also “positive strands” that get directly turned into proteins. They include Togaviruses and Picornaviruses.

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(-) ssRNA viruses—these are single stranded “negative strand” RNA viruses. A positive strand needs to be made in order to read the RNA to make protein. These include Orthomyxoviruses and Rhabdoviruses.

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ssRNA-RT viruses—these are positive strand viruses that use reverse transcriptase, an enzyme that has a DNA intermediate before making proteins as part of their life cycle. These include Retroviruses.

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dsDNA-RT viruses—these are double stranded DNA viruses with an RNA intermediate in the life cycle, including the Hepadnaviruses.

When we talk about the nucleic acids of the viral particle, we are talking about the viral “virome” rather than the “genome”, which is what the nucleic acid structure of cellular structures are called. There is also the ICTV classification, or the International Committee on Taxonomy of Viruses classification. The classification uses the same classification you will learn more about later on. What you need to know is that only a small number of virus types have been completely identified and characterized. There is a greater diversity in viruses that just hasn’t been studied yet. This is the classification: •

Order: It is identified by the suffix “-virales”.

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Family: It is identified by the suffix “viridae”.

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Subfamily: It is identified by the suffix “-virinae”.

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Genus: It is identified by the suffix “-virus”, such as “Adenovirus”.

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Species: It is also identified with the suffix “-virus”.

Things are changing all the time when it comes to classification of viruses, there are currently nine different orders, 131 families, 46 subfamilies, 803 genera, and nearly 5,000 different species of viruses. It is believed that, in reality, there are millions of different types. This is why it has been so difficult to study them.

WHAT IS A VIRUS? Viruses are infectious agents that do not have the typical cellular structure of all other forms of life. By the end of the chapter, you will be able to decide for yourself if they represent life or not. They have been known about since about the 1900s, when the tobacco mosaic virus was discovered. These are the most numerous types of biological organisms on Earth and are found in every ecosystem. Viruses can be independent but cannot replicate without infecting a cell of some type. Virus particles are referred to as virions. The three components of these particles are the following: •

Genetic material—these are long nucleic acids, which you’ve already discovered can be RNA or DNA, and can be double-stranded or single stranded. These contain the particle’s genetic information.

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Protein coat—this is referred to as the capsid and is what protects and surrounds the genetic material of the virus particle.

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Lipid envelope—not all viruses will have these but, if seen, it will surround the protein coat.

It is unclear how viruses came to be evolutionarily. They may be evolving structures that came from plasmids, which are stray pieces of DNA that travel from cell to cell. Some may have evolved from bacterial species. Interestingly, they may be involved in the evolution of other species by having their genes or the genes of one organism transferred to other organisms, causing a genetic change in the species receiving the nucleic acid through a viral infection. Viruses carry genetic material, evolve through natural selection, and reproduce, making them living in some scientists’ eyes, even though they are not cellular.

ORIGINS OF VIRUSES Viruses are found in all ecosystems and probably have existed since the origins of cellular life. They don’t form fossils so this cannot be proven. They are passed vertically (which means through the offspring of organisms) by inserting their DNA into organisms that then divide, allowing the virus to be in the offspring of an organism. This is how virologists have determined that viruses have existed for millions of years. There are three main hypotheses of how viruses originated, including these: •

Viruses may have once been smaller cells that were parasites of larger cell but lost all of the genes except those involved in parasitism. There are examples of “middle ground” bacteria, such as chlamydia and rickettsia, which are living things that can only reproduce inside cells (but, unlike viruses, these are cellular). Viruses may have degenerated from organisms like this. This is referred to as the “reduction hypothesis” or “degeneracy hypothesis”.

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Viruses may have evolved from escaped bits of nucleic acids that “escaped” from nucleic acids in larger organisms. This can happen when plasmids (which are pieces of DNA that escape from cells) or transposons (which are pieces of DNA that move to a different part of the same cell) get out of the cell. This is called the “escape hypothesis” or the “vagrancy hypothesis”.

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They may have evolved from pieces of DNA and RNA at the beginning of time and may have been dependent on cellular life for billions of years on earth. This is called the “virus first hypothesis” and means that viruses have always been around. People who propose this idea point to viroids, which are molecules of RNA that have no protein coat, commonly infecting plants. These are called subviral particles. There are also “satellite viruses” that are also in-between viruses. They have a protein coat that isn’t technically their own but belong another virus that they need to infect the cell before they can be released. These defective viruses include the hepatitis D virus that needs a coinfection with hepatitis B before it can become infective.

There are problems with these three hypotheses and it is currently believed that virus particles are extremely ancient and pre-date the divergence of life into the three domains we use to define living things. Genetic analyses of virus particles have so far indicated that there is probably no single ancestral virus particle and that they sprung up several times in order to have multiple ancestral organisms, rather than just one. Prions are related to viruses but are not life at all because they don’t contain RNA or DNA. These are infectious protein molecules. There are many protein-prion diseases, such as “mad cow disease” or bovine spongiform encephalopathy, scrapie in sheep, chronic wasting disease in deer, kuru in humans, and Creutzfeldt-Jakob disease in humans. Whether or not viruses can be considered life is a matter of debate. They have genetic material and genes, they are known to evolve through natural selection, and can reproduce by creating multiple viral particles. They don’t, however, have a cellular structure or their own metabolism. They also don’t divide through mitosis and cell division but through the building up of their structure within a cell. They don’t, however, grow like crystal structures because they can inherit genetic mutations (and undergo natural selection).

VIRAL STRUCTURE Viruses have many different viral structures. Most are extremely small and cannot be seen via typical light microscopy. Many are between 20 and 300 nanometers in diameter; however, some are long and thin. As mentioned, they have a capsid or protein coat, which is made by different capsomeres or individual protein subunits. These capsomeres are made by the genetic material of the virus but require the protein-making structures of the cells that they infect. Some viruses will make proteins that assist in the making of their protein coat and other structures.

There are several different virus shapes, including the following: •

Helical—these are viruses made from a single capsomere that are stacked around a central axis in order to form the structure of a helix. There may or may not be a central cavity (or tube). These can be short and roughly cylindrical or very long and filamentous. These are made often from single-stranded RNA but can be single-stranded DNA. The nucleic acids are negatively charged and are attracted to the capsid by the fact that the capsid is positively charged. The length of the virus depends on how long the nucleic acid chain necessarily must be covered. Figure 7 shows what a helical virus particle looks like:

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Icosahedral—these are roughly spherical, closing the virus particle within a closed structure. These have multiple triangular faces, many with more than sixty capsomeres per triangular face (with the minimum number of capsomeres per face being three). Those with large triangular faces appear spherical. Figure 8 shows a viral particle that is icosahedral in shape:

Viruses that have icosahedral structures are only released into the environment when the infected cells die off and release viral particles only when the cell itself breaks down. Examples of this include the adenovirus, poliovirus, and rhinovirus. •

Prolate—this is an elongated icosahedral viral particle that is commonly seen as part of bacteriophage heads. This is basically a cylinder that has a cap at either end. It is still icosahedral but is elongated with faces that are not the same size.

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Envelope—Certain viruses have membranes around them. These could be envelopes that come from the cell membranes of the cells they have infected, from the nuclear envelope (the lipid layer around cellular DNA) or from the lipid making up the endoplasmic reticulum (an organelle inside cells). This will create a viral envelope that has proteins on it that come from the host and from the virus itself; this same viral envelope will contain carbohydrates that come from the host. The envelope, used in the influenza virus and the HIV virus, is needed for the virus to infect the cells they get inside.

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Complex—these are complicated viral particles that have extra structures on them or a complex outer wall. These include many bacteriophages that have an icosahedral head, a helical tail and protein-containing tail fibers. The tail is

responsible for injecting the viral genome into the cell. Figure 9 shows a complex-type bacteriophage:

Poxviruses are complex, having a centralized disc structure called a nucleoid. It is a membrane-bound virus that has two lateral bodies (paired bodies) that have no known function. This is a pleomorphic virus that is roughly ovoid in shape. Figure 10 shows what the poxvirus particle looks like:

THE VIROME As you remember, the virome is the viral genome. There is more genomic diversity among viruses in nature than there are in archaea, bacteria, animals, and plants. More than 75,000 out of millions of different types of bacteria have had their genomes determined, although only 5000 viruses have been fully identified. We have also talked about the contents of the genome, with RNA or DNA making up the different viral particles. Most viruses have RNA genomes with plant viruses mostly being singlestranded RNA genomes and bacteriophages having mostly double-stranded DNA genomes. Viral genomes can be circular or linear in nature. The genome is segmented in many cases. Each segment codes for a single protein, similar to genes in cellular DNA. Most are found in a single capsid; however, a few situations exist in which different infectious segments are found in different but interdependent viral particles. This is seen, for example, in the brome mosaic virus particles, which is a plant virus. It is also seen in other plant virus infections. The viral genome is can be single-stranded or double-stranded DNA or RNA. Remember that most DNA comes double-stranded as a twisted helix that has two outer ladder poles and multiple rungs made up of base pairs. In single-stranded DNA and RNA, it is as though a ladder was cut vertically in half. The virus particles in Hepadnaviridae species have partially double-stranded and partially single-stranded nucleic acids. Single strands can be positive sense or negative sense, called plus strands and minus strands, respectively. Plus-strand RNA can be directly translated into proteins, while negative strand RNA is like a photo negative. It needs to be turned into a positive by RNAdependent RNA polymerase, an enzyme that makes a positive strand RNA, which can be read. DNA in a virus particle can be double-stranded or single-stranded. A single strand can be positive or negative, with the possibility of what’s called ambisense nucleic acidsituation, which involves reading of the strand from both ends of the strand. This can happen with either ssDNA or ssRNA.

The smallest genome known so far for viral particles is the ssDNA structure of Circoviridae, which codes for only two proteins. The largest genome known so far codes for 2500 proteins, which is the case with pandoraviruses. Many of the genes in viruses will overlap and have nucleic acid segments that code for more than one protein; there are only rarely-seen segments of nucleic acid that don’t code for anything at all. RNA viruses have smaller genome sizes than DNA viruses (in general). Because of this, viruses have segmented genomes that are split into smaller molecules in order to reduce the chances of errors in reading the genome. Errors, as you can imagine, can lead to a virus that is completely ineffective and not competitive. Viruses have a great capacity to mutate into other forms. This is why viruses like the influenza virus can continue to infect people year after year. It undergoes “antigenic drift” in which there are changes in the DNA or RNA of the virus particle that, while they might not affect the virus particle, they can change the proteins on the surface of the virus, essentially making a “new” virus of the same type, except that it isn’t recognized by the immune system of the host anymore and will infect the host again. There is an advantage to having segmented genomes or genes on two different molecules. These gene segments can “mix and match” with each other in order to create offspring virus particles that are uniquely different to the original virus particle. In addition, viruses can have their DNA broken up and put together in different ways to make a new viral particle. This is called “genetic recombination” and has been found to be a common way in which viruses evolve. Not every virus particle will evolve in a good way but it takes just one to be advantageous in order to start a new infection or potentially a new species.

VIRUS REPLICATION As you know, viruses must replicate in order to make new viral particles but they do not do this by means of cell division. They also do not do this themselves. They require the metabolic processes and machinery of the host cell in order to produce copies of themselves. In that sense, they do not divide or truly replicate; instead, they assemble

copies of themselves inside the cell. Figure 11 shows the replication cycle of viral particles:

The viral life cycle is different, depending on the viral species. Suffice it to say, however, that there are six different steps involved in the viral replication cycle. These include the following: •

Attachment—this is the binding of the capsid or envelope on the viral particle to the cell surface of the host. This attachment must be specific to a certain host cell. An example of this is that plant viruses bind to specific plant cells but not to other plant cells and not to animal cells. Even with the HIV virus, it only binds to the CD4 molecule on human T helper cells (types of white blood cells). This makes this a virus that only decreases the T helper cell count in humans, which is dangerous to humans because it affects the entire immune system functioning. The attachment of an enveloped virus causes the envelope to fuse with host cell.

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Penetration—this involves receptor-mediated endocytosis or membrane fusion. Endocytosis involves taking in the viral particle that has attached, while membrane fusion happens with enveloped viruses. The virus can enter the cell either way. Plants, animals, and bacteria are completely different in how they are

penetrated. Because plant and fungal cells have thick cell walls, they can often only get in when the plant is traumatized. When they do get in, they pass from cell to cell through pores called plasmodesmata. Bacteria also have strong walls but the viruses have evolved to have injection mechanisms that leave the capsid outside of the bacterium and just inject the nucleic acids. Those that have capsids still inside the infected cell will have degradation of the capsid to release the viral genome. •

Replication—this is multiplication of the genome via viral messenger RNA, viral protein synthesis, assembly of viral proteins, and viral genome replication. There are “early” genes that replicate the viral genome, and “late” genes that usually are responsible for the making of viral structural proteins.

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Assembly—there is the natural self-assembly of the virus particles as well as modification or “maturation” of the viral proteins. This maturation process usually happens after the virus has been released from the host cell.

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Release—the virus particles can be released by lysis or breakdown of the host cell. This happens in many bacterial and in certain animal viral infections. There is also the possibility of incorporation of the viral genome into the host genome. The viral genome is then referred to as a provirus or prophage (in bacterial host cells). These proviruses can become activated later on, which will kill the cell. In HIV disease, the virus is enveloped so the virus buds out of the infected cell.

THE REPLICATION OF THE VIRAL GENOME Unlike the replication of DNA that occurs in cellular, non-viral organisms, which is basically the same between organisms, the way viruses replicate their genome is different, depending on the virus type. There are notable differences between DNA viruses and RNA viruses. DNA virus genome replication happens in the nucleus of the host cell. The genome enters the host cell by several means. Remember, the virus has no metabolic abilities of its own; it needs the metabolism of the host cell. This includes the RNA processing machinery and the ability to make proteins. Large viral genomes may partially encode 38

for proteins that participate in the genome replication process. The DNA virus genome needs to get into the nucleus cells that have them. As you’ll see, bacteria do not have nuclei so this step is not necessary. RNA replication takes place in the host cell’s cytoplasm. The polarity of the RNA determines how it’s replicated. Positive-sense RNA gets translated into proteins immediately, while negative-sense RNA gets turned into a positive sense by using RNA replicase. In all cases requiring RNA replicase, the enzyme itself comes from the virus that makes the enzyme to create copies of their genome. Reverse transcribing viruses can be ssRNA (single-stranded RNA) or dsDNA (doublestranded DNA) viruses. Those with RNA genomes, particularly the retroviruses, use a DNA intermediate, while those with DNA genomes use an RNA intermediate. Both use what is called reverse transcriptase (also called RNA-dependent DNA polymerase) that converts RNA to DNA. It is called “reverse transcription” because normal transcription involves DNA going to make RNA. Retroviruses will make the DNA that has been made by reverse transcriptase and will incorporate it into the host DNA. These particular viruses are highly susceptible to drugs like lamivudine and zidovudine, which are reverse transcriptase inhibitors. Normal cells don’t have reverse transcriptase so it only affects the viruses. HIV Is a retrovirus.

VIRUSES AND DISEASE There are many common diseases that are directly related to viruses, including smallpox, chickenpox, influenza, and the common cold. Very serious diseases are also caused by viruses, such as HIV, Ebola, SARS, and the avian flu. There are potential virally-mediated diseases, such as chronic fatigue syndrome and multiple sclerosis. There are different things that a virus can do to the host; they can exist harmlessly with the host as is the case with the herpes simplex virus, which lies dormant for a long period of time. The chickenpox virus can also lie dormant, leading to herpes zoster or shingles later in life. Other viruses can be mildly protective to the host in order to prevent the presence of other diseases.

Other viruses can cause chronic and lifelong infections, in which the host is infective and has the virus replicating continually inside them. There are a number of individuals chronically infected with the hepatitis B and hepatitis C viruses, leading to a carrier status, in which the person does not get particularly ill but can pass the virus on. A high rate of carriers in a population will lead to an endemic viral infection. Most viruses get passed horizontally, through droplets, casual touch, blood, stool, contaminated food, contaminated water, and secretions. The degree of infection depends on how many susceptible individuals there are in the community, the means of transmission of the virus, and how virulent the virus is. Vaccines and improved sanitation will help reduce the means of infection as well as the number of susceptible individuals. People (and plants and animals) get quarantined when sick in order to prevent disease. Sometimes animals are destroyed to thin out the numbers of diseased organisms, such as happened to thousands of cows in Great Britain. Often with viral infections, there is an overlap between the incubation period and the symptomatic period, in which the individual is able to infect other people, called the communicative period. This is what makes it sometimes very difficult to prevent infections entirely. This will lead to epidemics, in which large numbers of people is infected, or pandemics, in which the entire world is affected by the presence of infection.

EPIDEMICS FROM VIRUSES There have been numerous epidemics and pandemics from viral infections throughout history. Smallpox, for example, killed about 70 percent of the Native American population because it was brought over from the Old World to the New World by Christopher Columbus’ crew. Another serious pandemic was the 1918 influenza pandemic caused by the influenza A virus, it killed about 5 percent of the population of the world. HIV has been a more recent pandemic, starting in sub-Saharan Africa, killing about 25 million people since it was first recognized as a viral infection in 1981. Very popularized viral epidemics have come from filoviruses, such as Ebola and Marburg viruses, leading to viral hemorrhagic fever.

VIRUSES AND CANCER Viruses can be significant in causing cancer. Cancer-causing viruses are called oncoviruses, which can be any type of viral particle. Viruses activate the immune system in some cases and can cause DNA mutations in the host. There are a number of cancercausing viruses in humans, such as hepatitis B and hepatitis C (which cause liver cancer), human papillomavirus (which causes cervical cancer, anal cancer, vaginal cancer, penile cancer, and vulvar cancer), Epstein-Barr virus (which caused Burkitt’s lymphoma, Hodgkin disease, and nasopharyngeal cancer), Kaposi sarcoma-associated herpesvirus, and even HIV (which leads to cancers by diminishing the immune system).

VACCINATIONS AND ANTIVIRAL DRUGS AGAINST VIRAL INFECTIONS Because viruses act inside cells, it is difficult to find drugs that act against them. The major exception to this is drugs that inhibit reverse transcriptase because this isn’t a normal part of the human host cell but is required for certain viral infections. This is why vaccinations are so helpful. Vaccinations are inexpensive ways to prevent infections. Vaccines have been used before viral infections were completely understood. There are vaccines against viral diseases such as smallpox, rubella, measles, mumps, and polio, although no one is getting smallpox vaccinations anymore because the disease has been eradicated throughout the world. There are vaccines for animal infections as well. There are four types of vaccines against viruses. There are live-attenuated vaccines (which are vaccines containing living but non-infective viruses), viral proteins, subunit vaccines, and killed whole viral particles. One of the downsides of live attenuated viruses is that it is possible for them to be mutated back to an infective virus again. They are not given to immunocompromised individuals because they can actually get the disease. Subunit vaccines are bioengineered to contain just capsids and not the nucleic acid portion. The antiviral drugs we’ve already talked about include the reverse transcriptase inhibitors. Other antiviral drugs include those that are nucleoside analogues. These are

drugs that mimic the building blocks of DNA so that the drugs are incorporated into the genome by mistake. This halts the viral life cycle. The backbone of DNA is broken, stopping the growth of viral DNA. An example of this type of antiviral drug is acyclovir, used for herpesvirus infections. For HIV, there are protease inhibitors that block the enzyme HIV-1 protease, necessary for the HIV replication cycle.

NON-HUMAN VIRAL INFECTIONS Viruses infect all types of cells in the world, including plants, other animals, archaea, and bacteria. Remember that viruses are relatively specific to a particular species and that some viruses, called satellite viruses, can only infect cells infected already by other viruses. Viruses can infect many different common animals, including livestock, horses, dogs, and cats—many of which are vaccinated as some are serious. Even insects can become infected with viruses, which have affected populations of bees. Plants are also highly susceptible to viruses. These are transported via vectors, which is also how many animal and human diseases get spread. Vectors are carrier organisms that carry the virus from organism to organism without getting sick themselves. Insects, some worms, single-celled organisms, and some fungal organisms have been found to be vectors. Efforts to decrease the numbers of vectors are ways to decrease plant virus infections. Plants can defend against viral diseases by making resistance genes or R genes. R genes trigger areas of cell death around the infection in order to limit the spread of virus particles in the plant. It causes dark spots on infected plants. There are natural antiviral disinfectants also produced by infected plants, such as salicylic acid, reactive oxygen species, and nitric oxide. The bacteriophage is a virus that only infects bacteria. There are 250 million bacteriophages per milliliter of seawater, making it the most abundant biological species in watery environments. These viruses bind to surface receptor molecules on the bacterium, injecting the viral genome into the bacterial cell. This triggers bacterial polymerase to translate viral messenger RNA into proteins that become new viral 42

particles or that help in the assembly of virus particles. There are viral enzymes that break down the bacterial cell membrane. This is a fast process, killing the bacterium within minutes, releasing new bacteriophages. Bacteria defend themselves from viral particles by making restriction endonucleases, which are enzymes that cut up the viral DNA because it is foreign to the cell. Bacteria also have the ability to have acquired immunity to the virus particles by retaining fragments of the viral genomes within the cell. The place in the ecosystem that has the most viral particles is seawater. Most are bacteriophages that infect the different bacterial species in the oceans. These viruses do not infect animals or plants and are necessary parts of the ocean ecosystem. They also kill off cyanobacteria and phytoplankton in the oceans, being an important part of the ocean food chain. They kill off bacteria that stimulate the growth of new organisms in the ocean, particularly phytoplankton. Viruses kill 20 percent of the ocean’s biomass every day with 10 times the viruses in the ocean as compared to archaea and bacteria.

KEY TAKEAWAYS •

Viruses have nucleic acids, protein-containing capsids, and lipid envelopes.

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Viruses have probably been around since the beginning of life and infect all cellular forms of life.

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Virus particles have several different types of shapes.

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The viral replication cycle involves the different stages of a viral infection of a cell.

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There are many human viral infections, some of which are cancer-causing.

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Immunizations decrease the number of susceptible individuals.

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Plants and bacteria have specialized methods of protecting themselves against viral infections.

QUIZ 1. What does the Baltimore classification relies on to make the differentiation between different types of viruses? a. The virus particle’s basic structure b. The type of nucleic acids in the genome c. The length of the viral particle’s genome d. The protein coat on the outside of the particle Answer: b. The Baltimore classification is based on the type of nucleic acids in the virus particle’s genome. 2. What is the protein coat around the individual virus called? a. Viral particle b. Virion c. Envelope d. Capsid Answer: d. The capsid, which is the protein coat that surrounds the viral nucleic acid molecule in order to protect it, is seen on all viruses. 3. What viral hypothesis on the origin of these entities indicates that viral particles developed and evolved billions of years ago at the origin of life itself? a. Vagrancy hypothesis b. Regression hypothesis c. Escape hypothesis d. Virus first hypothesis Answer: d. The virus first hypothesis indicates that viruses developed and evolved since the beginning of life on earth and didn’t require cellular structures to help develop the virus particles. The other theories depend on cells to make the virus particle develop in the first place.

4. What is the capsid on a viral particle made from? a. Lipid bilayers b. Capsomeres c. Pentons d. Hexons Answer: b. Capsids are protein coats made from different proteins, known as capsomeres or “subunits” of the capsid. 5. Why is it harder to infect a plant with a virus than it is an animal? a. Plants have thick cell walls that animals don’t have. b. Plant viruses have more ineffective machinery to allow for replication. c. Plants have better immune mechanisms than animal cells. d. Plant viruses are mainly RNA viruses that do not translate proteins well. Answer: a. Plant cells have thick walls that aren’t seen in animal cells so the plant often has to be traumatized in some way in order to have it infect the cell. 6. How do viruses attach to the cells they infect? a. There is random endocytosis of virus particles by the host cell. b. The protein on the virus attaches to a receptor on the host cell. c. There is a receptor on the virus that binds to a receptor on the host cell. d. There is lipid-to-lipid attachment of the virus and host cell. Answer: b. There is a protein on the virus that attaches to a receptor on the host cell to allow for attachment. 7. What replication step in DNA viruses isn’t necessary when infecting bacterial cells as opposed to animal cells? a. Getting through the cell wall of the bacterium. b. Synthesizing proteins for replication. c. Entering the nucleus of the cell. d. Injecting the genome into the cell.

Answer: c. Bacterial cells do not have nuclei so this particular step is not necessary for infecting bacterial cells and replicating the genome. 8. How do drugs like zidovudine work against the HIV virus? a. They prevent budding of the virus outside of the host cell. b. They are reverse transcriptase inhibitor drugs. c. They prevent the making of viral proteins. d. They prevent attachment of the viral particles to the cell. Answer: b. These are reverse transcriptase inhibitors, preventing the RNA from transcribing into DNA. This affects the virus but not the host cell. 9. Which type of vaccine is most likely to give disease to the vaccinated individual? a. Attenuated vaccines b. Subunit vaccines c. Viral protein vaccines d. Killed virus vaccines Answer: a. Attenuated vaccines contain live but weakened viral particles; they can mutate to a more virulent form or can infect those who are too immunocompromised to fight off the infection. 10. What is a virus particle called that can only infect a cell that has already been infected by another virus? a. Attenuated virus b. Weak virus c. Satellite virus d. Provirus Answer: c. A satellite virus is one that can only infect a cell that has already been infected by another viral particle.

CHAPTER 3: BACTERIA This chapter covers the topic of bacteria. Bacteria are single-celled organisms that, compared to viruses, are remarkably complex. These are prokaryotes as opposed to the typical animal and plant eukaryotic cells with the ability to divide and grow independently of other organisms. There are many types of bacteria, some of which are motile. The physiology of bacteria, particularly the way they can become motile, is discussed in this chapter.

PROKARYOTE VERSUS EUKARYOTE This chapter introduces prokaryotes, which is the broad classification that includes bacteria. A prokaryote is defined as a cellular structure (usually unicellular) that does not have a nucleus or membrane-bound organelles. Eukaryotes, the classification including plant, fungal, protist, and animal cells, have nuclei and membrane-bound organelles. These differences are believed to be the most important split between different types of cellular life. The most major difference is in the placing of genetic material. Prokaryotes have no membrane-bound organelles, which means the genetic material is not within an enveloped nucleus. Eukaryotes have mitochondria and chloroplasts which, incidentally, are believed to be prokaryotes that evolutionarily evolved from prokaryotes. The processes of chloroplasts and mitochondria in prokaryotes are done across the cell membrane rather than through organelles. Prokaryotes also have a cell wall made from peptidoglycans, which is not seen in eukaryotic cells. Prokaryotes are generally much smaller than eukaryotic cells. The DNA is not contained on chromosomes but are found in loops collected together in a nucleoid, which is not membrane-bound. Satellite DNA called plasmids are also found in prokaryotes. The DNA is tightly packed and lacks “introns” which are non-coding aspects of DNA. This is not the case with human DNA, which contains 95 percent introns. The genes are

expressed in groups rather than in separate genes. The groups are called “operons”. They are later divided into separate proteins. Prokaryotes also have a larger surface area to volume ratio. This means that they are more highly metabolically active when compared to eukaryotes. They divide faster and have a shorter generation time (which is the time from cell division to another cell division). Prokaryotes are “haploid”, meaning they have just one copy of the genes. On the contrary, eukaryotes are diploid, having two copies of a particular gene. They do not have histones, which are the proteins that condense the genetic material. They have their own condensing proteins and supercoil the circular piece of DNA in order to condense it. Transcription and translation into proteins happen at the same time in prokaryotes but not in eukaryotes.

PROKARYOTE STRUCTURE There are many different structures of bacteria. These are small cells—only about a tenth of the size of most eukaryotic cells, being less than 5 micrometers in length. The main shapes of bacteria include spherical, called “cocci” bacteria, rod-shaped, called bacilli, comma-shaped, called vibrio, and spiral-shaped, called spirochetes. There are very rarely other shapes, including star-shaped bacteria. The cell wall and the intracellular cytoskeleton determine what the shape of bacterial species is. The shape of the bacterial organism determines many things, including the mobility of the organism. While bacteria are essentially single-celled organisms, they often form multicellular shapes. Streptococcus bacteria form chains of varying lengths, while Neisseria species form pairs or diploid configurations. Staphylococcus species are rarely singular and come in bunches, looking like spherical bunches of grapes. Myxobacteria, Actinobacteria, and Streptomyces form aggregates, filaments, and hyphae, respectively. Figure 12 shows what different bacterial shapes look like:

Bacterial species can also form complex states, depending on the conditions they find themselves in. They communicate with each other through the act of what’s called “quorum sensing”, in which they migrate together in unfavorable circumstances. This happens with Myxobacteria, forming aggregates that have large fruiting bodies that have certain cells going into dormancy states, known as “myxospores”. These myxospores are resistant to adverse environmental conditions, such as situations of dryness, which normally doesn’t support bacterial growth. Another common bacterial phenomenon is the biofilm formation. This is the attachment of bacteria to surfaces, such as the lining of the bladder or GI tract in dense aggregations. There are larger aggregates that will form a microbial mat. These mats can be really thick, containing other types of microorganisms in the form of an ecosystem. There can be microcolonies, that have networks of channels that enable the enhanced diffusion of cellular nutrients. Bacteria in these biofilms and mats will be more difficult to kill when compared to individual bacterial organisms. Bacteria have a cell membrane that is made mainly of phospholipids. This membrane completely encloses the cell and defines the intracellular space. Inside this space is cytoplasm and a notable absence of membrane-bound structures seen in eukaryotic cells. There are, however, some protein-bound organelles that define different areas of

the bacterial metabolism. The carboxysomes, for example, are protein-bound structures that concentrate carbon dioxide inside the shell by using localized areas of carbonic anhydrase activity, which makes carbon dioxide from the bicarbonate that diffuses into the carboxysome. Bacteria also have a cytoskeleton that creates their structure. It also localizes the different proteins and nucleic acids within the cell. The cytoskeleton also manages the process of cellular division. It is not unlike the cytoskeleton of eukaryotes, that maintains certain compartments within the cell. Because there are no membranous structures inside the bacterial cell, those reactions that need a membrane must be done across the cell membrane. Electron transport, an important way of gaining cellular energy, happens between the cytoplasm inside the cell and the periplasm outside the cell. Figure 13 shows the basic structure of a bacterium:

A few bacteria engage in photosynthesis and will have highly folded plasma membrane structures, filling the cell with multiple layers of light-gathering membrane complexes. These will sometimes form lipid-enclosed structures known as chlorosomes. These are particularly seen in green sulfur bacterial species. The DNA or genetic material inside a bacterium is called a nucleoid rather than being membrane bound in a nucleus. The nucleoid generally consists of a circular piece of

DNA along with RNA and proteins necessary for protein synthesis. They do contain ribosomes, which are protein-creating structures; however, the structure of these ribosomes is somewhat different than is seen in eukaryotic cells. There are also nutrient storage granules within the bacterial cell. These may contain polyhydroxyalkanoates, sulfur, polyphosphate, and glycogen granules. There are also gas vacuoles inside Cyanobacteria, which help regulate the ability of these bacterial organisms to be buoyant in an aqueous environment. This allows them to move into layers of a body of water in order to regulate light exposure and the nutrient environment. Bacteria are surrounded by cell walls consisting of peptidoglycan. These are sugar chains (polysaccharide chains) that are crosslinked by small proteins or “peptides”. These are greatly different from the cell walls of plants (which are made from cellulose) and fungi (which are made from chitin). Archaea, smaller organisms we will discuss later, also have cell walls but these don’t consist of peptidoglycan. Cell walls are of two major categories, depending on whether they stain positively or negatively with the Gram staining technique, which is a popular way to see bacteria under a microscope. There are Gram-positive species and Gram-negative species. The Gram-positive bacteria have very thick cell walls containing both peptidoglycan and teichoic acids. They take up the Gram-stain and appear red under the microscope. The Gram-negative bacteria consist of thin cell walls that do not take up the stain and that are surrounded by a second lipid membrane consisting of lipoproteins and lipopolysaccharides. There are some bacterial species that aren’t of either classification, such as Mycobacteria species, which have a thick cell wall but also have a second layer of lipids. Many species of bacteria also have what’s called an S-layer, which is an array of protein molecules on the outside of the cell wall. These will both chemically and physically protect the cell surface, preventing the passage of macromolecules into the cell. There is no full understanding of the nature of this layer except that, in some cases, they confer virulence in certain bacterial species.

Flagella are a part of certain bacterial species. This are thin, rigid protein-containing structures that confer motility to the organism. They use ion transfer across the cell membrane electrochemical gradient to allow for mobility. Fimbriae, on the other hand, are also referred to as attachment pili. These are much thinner than flagellae and are distributed throughout the cell surface. These allow for attachment of the organism to surfaces. Pili are also appendages on a bacterial cell that allow for the transport of genetic material between two bacterial cells. These can be called conjugation pili or sex pili because of the exchange of genetic material. Many bacteria have a glycocalyx layer around the cell that can be similar to a capsule or even a slime layer that prevents complete engulfment by macrophages and other cells of the immune system in animals. They are also part of the recognition process of bacteria by the immune system and of the recognition of bacteria by each other—participating in the formation of bacterial biofilms. These types of structures are secreted from the bacteria themselves into the periplasm around the organism. These extra layers around bacteria will contribute to their virulence. Endospores are structures made by certain Gram-positive bacterial species (like Clostridium, Bacillus, Heliobacterium, and Anaerobacter species). These develop within the cytoplasm itself, with one endospore per cell. There is a DNA and ribosome core and a cortical layer that is rigid and made of peptidoglycans. They do not metabolize and resist extreme conditions of all types, viable for millions of years. Examples of sporeformers in human diseases include anthrax (from Bacillus anthracis) and tetanus, called by Clostridium tetani.

BACTERIAL PHYSIOLOGY For being such small organisms, one would think that they do not have much in the way of metabolism. And yet, there are many different metabolic types of bacteria. Bacteria can derive their energy from light in the process of photosynthesis (also called phototrophy) or using the breakdown of other chemical compounds, also called oxidation or chemotrophy. Chemotrophic organisms use terminal electron acceptors

(such as oxygen) in oxidation-reduction reactions or “redox” reactions, releasing energy that drives metabolic processes. Those chemotrophic organisms or “chemotrophs” will use inorganic compounds or organic compounds as electron sources. Those using inorganic compounds (such as ammonia, hydrogen, or carbon monoxide) are called lithotrophs, while those that use organic compounds as electron sources are called organotrophs. Organisms can be aerobic, using oxygen as a terminal electron receptor, or anaerobic, using carbon dioxide, sulfate, and nitrate as terminal electron receptors. There are also heterotrophs, which get carbon from other forms of organic carbon, autotrophs, which fix carbon dioxide in order to have carbon for cell structures, and methanotrophs, which uses methane gas as a source for electrons and to gain carbon for metabolic processes.

BACTERIAL GENETICS As mentioned, most bacteria have one circular chromosome, which can be very small (160,000 base pairs) or very large (12 million base pairs). There are a few bacterial types (such as Borrelia and Streptomyces) that have a single linear chromosome and even fewer that have more than one chromosome. Many bacteria have plasmids, which are extra-chromosomal DNA molecules that do things like confer antibiotic resistance, enhance metabolism, and create virulence factors for the bacterial species that contain them. The bacterial genome can code for just a few hundred proteins or a couple of thousand genes. These organisms will have introns (non-coding DNA stretches) but not nearly as many as are seen in eukaryotic organisms. The daughter cell inherits an exact copy of the parent cell because of the way these cells divide. Evolution, however, can occur because of mutations in the DNA during cell division or because of genetic recombination. As mentioned, there can be exchange of genetic material between cells. This can actually occur in three different ways: 1) Bacteria can take up DNA from the environment, particularly in environmentally stressful conditions. This is called transformation. 2) There can be an infection with bacteriophages in which foreign DNA

is introduced into the bacterium after an infection. This is called transduction. Bacteria will resist this by degrading foreign DNA and will use a system called CRISPR sequences, which means the retention of lengths of viral DNA in order to confer resistance to the infection in the future. 3) There can also be conjugation, which is the direct cell-to-cell transfer of the genome, usually among those bacteria in the same species. It can less commonly happen between species, often when conferring antibiotic resistance from one species to another. Each of these is referred to as horizontal gene transfer.

BACTERIAL COMMUNICATION There was once a belief that bacteria did not communicate with one another. This has been found to be untrue. In fact, bacteria that engage in bioluminescence or the giving off of light, will communicate and attract large animal species to their location. When bacteria engage in biofilm production, there are inter-cellular communication strategies that allow cells to act in unison toward the same goal. There can be cellular division of labor, doing things that can’t be done by one cell. Biofilms will increase bacterial resistance many-fold greater than single bacterial organisms. A particular molecular signal we’ve already talked about is quorum sensing. This helps determine how many organisms are in a local population so that, if there are enough organisms, the collective will behave in a particular manner that wouldn’t be done if the population of microorganisms was too low. Gene expression can be coordinated and specific pheromones (a type of hormone) can be released between the cells. Bacteria have the capability to form complicated relationships with other organisms. These include the ability to engage in parasitism, mutualism, and commensalism. Commensal bacteria are harmless to their host and just use the host as a means of growth but not harm to the organisms they reside with or in. There can be predatory bacteria that will kill other bacteria. There is, for example, Myxococcus xanthus, an organism that forms groups of cells that digest and kill other bacteria. Other predatory bacteria will have the ability to attach to and digest other

types of bacteria, and some will multiply inside the cytoplasm of other cells. These are different from pathogenic bacteria, which are dangerous to eukaryotic host organisms. Mutualists will grow on, in, or near other organisms for the mutual survival of the two organisms. For example, certain anaerobes require methanogenic Archaea (and vice versa) to survive. The Archaea species consumes hydrogen as part of their metabolic processes, while anaerobes require a low hydrogen environment in order to survive. Humans have numerous symbiotic or mutualistic bacteria that make vitamins and contribute to essential functions in the gut.

CLASSIFYING BACTERIA There is a wide diversity of bacteria, which can be classified on the basis of their metabolism, their cell structure, or on differences in certain cellular components. Modern ways of classifying bacteria involve looking at the genetics of the different species and is, in fact, how many different organisms are now classified. Historically, the term “bacteria” was applied to any single-celled prokaryote. Now, using genetics, there have been two domains identified: Bacteria and Archaea—two separate domains that have evolved from a common primordial ancestor. As it turns out, Archaea are closer to eukaryotes than they are to bacteria genetically. This has led to a three-domain system among cellular organisms, which are Bacteria, Archaea, and Eukarya. The Gram stain will characterize different bacteria into four main groups. This is just based on the characteristics of the cell wall. There are Gram-positive cocci, Grampositive bacilli, Gram-negative cocci and Gram-negative bacilli. Some organisms are not classified at all by this Gram-staining process and are considered “acid-fast” by virtue of other types of stains. Still other organisms are characterized by their ability to grow in certain media or through serological techniques. There are also the classifications of aerobic bacteria versus anaerobic bacteria. Using the standard in today’s modern medicine, which is to use the polymerase chain reaction in order to identify bacterial species and to classify them according to their genome, bacteria are now classified genomically rather than on the basis of their morphology, staining abilities, or metabolism. This has led to the identification of

nearly 10,000 different prokaryotic species, including both bacteria and archaea, but this number is expected to be considerably higher and not practically obtainable.

PROKARYOTE CELL DIVISION Bacteria undergo asexual reproduction through what’s called binary fission. They only grow to a fixed size before reproducing to create identical clone daughter cells at a rate of two at a time. There are some complex ways of sending off daughter cells, including the formation of fruiting bodies, the formation of hyphae, and the process of “budding”. Budding involves the cell developing a protrusion from its cell surface that ultimately breaks from the parent cell to form a daughter cell. Binary fission is the major way these bacterial cells divide. It is similar to mitosis in animal cells and plant cells but has a different purpose. When mitosis happens in eukaryotic cells, the goal is the growth of the overall organism or the replacement of old cells by newer cells. This is not the case with bacteria. They use the process of cell division in order to reproduce or to create new organisms in the population. In binary fission, the first step is copying the DNA of the organism. These are, as you remember, circular and not confined within a nucleus. There is an origin of replication— a spot on the chromosome—that is the first part that is duplicated. The two origin sites begin to move to opposite sides of the cell—a process that begins as soon as DNA replication starts. The cell will get longer over time in order to ultimately separate. Once the two chromosomes have separated, a septum forms in the middle of the elongated organism, ultimately pinching off into two identical daughter cells. As you’ll see when you study mitosis, this binary fission process is very similar to mitosis except that there is just one chromosome and there is no mitotic spindle in binary fission to act as the separation point. In addition, the separation and replication process in binary fission happens at the same time, which is not the case with mitosis. There are four phases of bacterial growth. The first phase is called the lag phase, in which the cells begin to adapt to a nutrient-rich environment. The actual period of growth is very slow in this phase. There are a lot of biomolecules being made but no real growth in the population. Next comes the logarithmic phase, also referred to as the 57

exponential phase. There is a significant rate of cell division and multiplication of cells. Nutrients are used up rapidly until at least one nutrient is depleted, which begins to limit the growth. The third phase of growth is called the stationary phase. This is directly caused by a lack of all of the necessary nutrients because they have been depleted. There is a reduction of metabolic activity and the consumption of all cellular proteins not deemed essential. Finally, there is a death phase, where there is a complete lack of necessary metabolic ingredients and the cells die off.

BACTERIAL MOTILITY As already mentioned, bacteria have ways of being motile. The most common way that bacteria move is through the action of flagella, which are long filaments that act as propellers to move the cell. The flagellum will rotate through the use of a reversible “motor” at its base, whereby it uses the electrochemical gradient across the membrane and the movement of ions across this membrane in order to generate power. Bacteria can have forward movement or tumbling movement. Tumbling helps the cell reorient themselves. There are four types of flagellated bacteria: monotrichous (one flagellum), amphitrichous (a flagellum at each end), lophotrichous (clusters of flagella at each end), and peritrichous (flagella all over the cell surface). There are stimuli in the environment that determine how and where the bacterial cell will move. There are phototaxis, chemotaxis, magnetotaxis, and energy taxis.

KEY TAKEAWAYS •

Bacteria are prokaryotic cells that lack a nucleus and defined, membrane-bound organelles.

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Bacteria can be of several different shapes and can be found in different organization types, even though they are technically single-celled organisms.

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Bacteria divide by binary fission, in which there is the production of identical daughter cells.

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Bacteria have different ways of fixing carbon to make structural components of the cells.

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The main way that bacteria move is through flagella, which are powered by an electrochemical gradient.

QUIZ 1. What is not a feature of a prokaryote? a. Nucleoid b. Mitochondria c. Circular DNA d. Peptidoglycan cell wall Answer: b. Each of these is a feature of a prokaryote, except that they do not have intracellular membrane-bound organelles, including mitochondria. 2. What is not a main difference between prokaryotic DNA and eukaryotic DNA? a. Prokaryotes are diploid and eukaryotes are haploid b. Prokaryotes have circular DNA c. Prokaryotes have few introns (noncoding segments) d. Transcription and translation occur simultaneously in prokaryotes Answer: a. Prokaryotes are haploid and eukaryotes are diploid, referring to the number of copies of the different genes. Haploid organisms have just one copy of a given gene. 3. What are the bacterial structures called in which there are channels made that allow for circulation of nutrients so they better reach the entire cluster of bacteria? a. Bacterial mats b. Bacterial spores c. Biofilms d. Microcolonies Answer: d. Microcolonies will form channels and a more complex structure that allows the better circulation and diffusion of nutrientcontaining liquids from the environment.

4. What is the main component of the bacterial cell membrane in bacterial organisms? a. Triglycerides b. Free fatty acids c. Phospholipids d. Cholesterol Answer: c. The membrane of bacterial cell consists of primarily phospholipids, which form a phospholipid bilayer, similar to other membranes, although the membrane structure of eukaryotic cells is somewhat different. 5. In bacterial organisms, where is the glycocalyx located? a. Around the nucleic acids in the cell b. Around the cell wall c. Surrounding nutrient granules d. Consisting of nutrient granules Answer: b. The glycocalyx is a layer surrounding the cell wall of the bacterial organism, forming a slime layer or sometimes a capsular layer. 6. What part of the bacterial anatomy is responsible for tetanus? a. Endospore b. Attachment pili c. Glycocalyx d. Slime layer Answer: a. Tetanus is caused by endospores created by Clostridium tetani, which creates the spores in order to survive in soil for many years until conditions are right for them to be infective.

7. What are bacterial plasmids made from? a. Protein b. Peptidoglycans c. Carbohydrates d. DNA Answer: d. Plasmids are extra-chromosomal DNA structures that confer certain properties on the bacterial species. 8. There are many ways that bacteria can get “new” DNA into the cell. What is it called when the bacteria take up foreign DNA into the cell walls from the environment? a. Transformation b. Transduction c. Conjugation d. Transference Answer: a. Transformation is when the cell takes up foreign DNA from the environment and uses the DNA as part of its own genome. 9. What is the major way that bacteria multiply? a. Budding b. Hyphae formation c. Binary fission d. Fruiting body formation Answer: c. Binary fission is the major way that bacterial cells divide and multiply, although it is certainly possible that specific organisms will multiply in any of the other ways as well.

10. What is the first step in binary fission? a. Elongation of the cell b. Separation of the chromosomes c. Duplication of the cytoplasm d. Replication at the origin of replication Answer: d. There is replication at the origin of replication, which is where the DNA starts to separate into two different chromosomes, which starts the binary fission process.

CHAPTER 4: ANIMAL CELL BIOLOGY This chapter explains animal cells and their biology. These are the cells and cell types people are more familiar with, with multiple organelles that unite to create basic animal cell physiology. The structure and function or “physiology” of the animal cell are presented in detail in this chapter along with the ways that genetic material divide. Both mitosis and meiosis, important in cellular and animal reproduction, are covered as part of this chapter.

ANIMAL CELL STRUCTURE Animal cells are different slightly from animal to animal but, as eukaryotes, they share most things in common. In this section, we will talk about different cell structures in all animal cells.

PLASMA MEMBRANE Any discussion of the anatomy of an animal cell involves that of the plasma membrane. This is a highly important structure that separates the inside of the cell from the outside of the cell. In animals, it is made from a phospholipid bilayer, cholesterol, and different types of proteins. It acts as a semipermeable membrane, meaning that it lets some things in and some things out of the membrane so that the inside of the cell is completely different from the outside of the cell. Figure 14 illustrates what the plasma membrane looks like:

We’ve talked about phospholipids, which make up the vast majority of the molecules of the plasma membrane. The hydrophilic part of the phospholipid is on the outer and inner layers of the membrane, while the phospholipids are sandwiched between two sheets of phospholipids. Cholesterol, also a lipid, makes up a portion of the cell membrane structure, which is described as a free-floating layer, in which structures are not completely rigidly confined but can fluidly “swim” around in the lipid bilayer. Also within the plasma membrane are proteins. There are proteins, called transmembrane proteins that are hydrophobic enough to be within the protein. Many of these proteins are channels that allow water, ions, and larger molecules to get through, often expending energy. An example is the sodium-potassium ion channel that pumps sodium out of the cell, while allowing potassium into the cell. There are also surface proteins associated with the plasma membrane. These will be on the surface of the cell membrane—on the inside and on the outside of the membrane. Some of these outside proteins have sugars attached to them, being called glycoproteins. These act as receptor sites and antigens on the cell surface. This means that they are used to “identify” the cell by the immune system and are used to bind molecules to the surface of the cell. Receptors are like the lock to a key. Molecules can be “keys” that

specifically bind to the “locks” that are membrane proteins, changing something about the cell to allow metabolic changes to occur within the cell. One interesting protein in the cell membrane is the membrane-associated G-proteincoupled protein, also referred to as G-protein-coupled receptors (GPCRs). These will attach to many things outside of the cell and, when attached to, they change the interior of the cell. It is a single globular protein imbedded into the cell membrane, having several segments. There is an alpha protein subunit that binds to GTP (guanine triphosphate) or GDP (guanine diphosphate), which are energy molecules like ATP. The active form of GPCRs binds to GTP and uses its energy to drive intracellular processes. There are about 1000 different GPCRs in animal cells that bind to things like drugs and other molecules, using the energy to allow signals in the cell to deeply enter the cell in order to affect a change within the cell. These are important receptors that drive many intracellular processes.

ORGANELLES The term, organelles, involves those structures within the cell that serve specific functions. Many are membrane-bound and act to help the cell perform its metabolic processes. Others house cell structures, creating an internal environment that allows for specific things being done in their interior. Organelles are not freely floating within the cell but are held in relative space by the cytoskeleton or “cell skeleton”. Figure 15 shows the internal structures of the cell:

CYTOSKELETON The cytoskeleton in eukaryotic cells consists of chains of proteins of three different types. These include microfilaments, intermediate filaments, and microtubules. •

Microfilaments—these are called actin filaments because they are mainly made from actin proteins. In fact, their major structure is that of two strands of actin protein wound in spiral formation. These are the thinnest of the fibers of the cytoskeleton. They act in the division of cytoplasm into two daughter cells, a process called “cytokinesis”. They aid in cell mobility of single-celled eukaryotic organisms so that cytoplasm can flow in one direction. They also act along with myosin to allow muscle cells to contract.

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Intermediate filaments—these are called “intermediate” because they are of a thickness between microfilaments and microtubules. They are made of multiple protein types, such as keratin, vimentin, lamin, and desmin. These (except for lamin) are found in the cytoplasm and function to maintain cell shape and

provide for structural support of the cell. In the nucleus, lamin and other proteins help support the shape of the nuclear envelope. •

Microtubules—these are the largest and thickest of the cytoskeleton fibers. They are hollow and are made from alpha and beta tubulin. They are responsible for making flagella and cilia in animal cells, which are the appendages that protrude out of the cell and move in relation to the cells. They are made in the centrosome, which organizes microtubules. Centrosomes have multiple microtubules emanating from them. The microtubules will pull the chromatids away from each other in the process of cell division called mitosis. Transport of organelles inside the cell takes place because of microtubules.

NUCLEUS The nucleus is probably the largest organelle in the cell. It is bound by a lipid bilayer membrane and contains the genetic information of the cell. While most animal cells will have only one nucleus, a few will have several nuclei and cells like red blood cells or RBCs have no nucleus (as it is extruded before the cells mature). Animal cells have DNA as their main source of genetic information. Within the nucleus in many cases is a nucleolus, which is contains protein, RNA, and DNA. It is responsible for making and modifying a type of RNA called ribosomal RNA or rRNA. This is RNA used to make ribosomes, which act to make proteins. Within the nucleus is DNA, the main genetic information within the cell. These are held in different strands of nucleic acid called chromosomes. The numbers of chromosomes within the cell depends on the animal. In humans, there are 23 pairs of chromosomes for a total of 46 chromosomes. While the majority of the DNA in animal cells is noncoding and have no known function, chromosomes contain genes—segments of DNA that code for proteins. The way they do this will be discussed later in this chapter. Normal DNA in the cells is folded and not visible until the time of cell division.

ENDOPLASMIC RETICULUM This is a membranous structure that consists of multiple stacks of membranes, usually near the nucleus. There are two types of endoplasmic reticulum or ER. There is rough endoplasmic reticulum or RER, which is studded with ribosomes. The ribosomes on RER are globular structures that are the main place that proteins get manufactured. The smooth endoplasmic reticulum or SER has no ribosomes on them. This SER is responsible for making cellular products like hormones and lipids, as well as the transport of messenger RNA from the nucleus to the protein-making part of the ER. Figure 16 illustrates the rough and smooth endoplasmic reticulum near a nucleus.

GOLGI APPARATUS These are also called Golgi complex, which is an organelle responsible for packaging proteins and lipids into vesicles, whereby they can be transported outside the cells or within the cells. They are the “post offices” of the cell because they organize molecules within their interior and package them for specific destinations.

MITOCHONDRIA There can be hundreds to thousands of mitochondria within a cell, depending on how metabolically-active the cell is. These are the mitochondrial powerhouses in the cells as they are responsible for the metabolism of the cell. It is a double-membrane cell structure that has a relatively smooth outer membrane and a highly invaginated inner membrane, forming cristae (which means folded or creased). As you’ll see, metabolism necessary to make cellular energy happens mainly in the mitochondria, which are especially numerous in liver cells, kidney cells, and muscle cells because of their high metabolic demands. Figure 17 is an illustration of the anatomy of a mitochondrion:

RIBOSOMES As mentioned, ribosomes are mainly found on rough endoplasmic reticulum; however, they can be freely floating in the cytoplasm. Their function is strictly for protein synthesis. There is a large subunit and a small subunit to these structures. The small subunit acts to attach the messenger RNA strand to hold it in place during the translation process, while the larger subunit manufactures the growing protein chain. There are three parts to the larger subunit: •

Aminoacyl binding site (A site)—this part binds a transfer RNA molecule that has been charged with an amino acid and attaches this RNA molecule to the messenger RNA message.

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Peptidyl binding site (P site)—this part transfers the bound peptide on the tRNA to the polypeptide chain, holding the growing chain in proper position.

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Exit site (E site)—this is the terminal binding site for transfer RNA, where uncharged transfer RNA molecules are released from the protein translation complex.

LYSOSOME These are small membrane-bound organelles within the cell that contain acid hydrolases, which are digestive enzymes. They break down old parts of the cell, microorganisms, and large macromolecules that have come to them from the Golgi apparatus and have been labeled for digestion. They are referred to as “phagolysosomes” when used in white blood cells and other immune cells responsible for killing off microbes (like bacteria).

VACUOLES These are storage places within the cells. They have a lipid bilayer and will store just about anything within the cells. In animal cells, they will participate in endocytosis, or the taking in of nutrients from the outside, and exocytosis, or the exit of substances out

of the cell. In another chapter, you will find out that they serve bigger functions in plant cells than they do in animal cells.

PEROXISOMES These are small structures within the cell. They make hydrogen peroxide, which is a byproduct of various metabolic processes the peroxisome participates in. They have a peroxidase enzyme that breaks down this hydrogen peroxide in order to make a safer byproduct, which is water and oxygen.

ANIMAL CELL PHYSIOLOGY In this section, we’ll talk more about the cellular processes that make up cell physiology in the animal cell. Some of these processes are the same in all cells; however, for the purposes of this section, we will be referring to the physiology of animal cells.

CELL MEMBRANE PHYSIOLOGY The main purpose of the cell membrane is to allow certain substances to pass into the cell, while allowing others to leave, and still others not to have access across it at all. Some substances passively cross the cell membrane, while others actively cross the membrane. The difference between these is that passive transport requires no energy, while active processes require cellular energy in order to take place. Passive activities include osmosis and diffusion, while active processes include phagocytosis, pinocytosis, exocytosis, and active transport. Diffusion involves the transport of molecules from an area of high concentration to an area of low concentration. When this happens across a membrane, the goal is to have equal concentrations on both sides at equilibrium. This involves oxygen, water, carbon dioxide, and ammonia (mainly gaseous substances and water). Some ions and glucose will diffuse through channels made from proteins. It is referred to as facilitated diffusion. Diffusion is what happens across a cell when oxygen exchanges for carbon dioxide in the animal body. Nutrients and waste products can exchange across the cell membrane via facilitated diffusion.

Osmosis is the diffusion of water across a semi-permeable membrane. Water goes from an area of less water molecules (a more concentrated solution) to an area of more water molecules (a less concentrated solution). It requires no energy and allows for the cells to have their “plump” features. In a hypertonic solution, however, which is one where there is a high concentration of other substances, the water content is less and the cells will become dehydrated in order to equalize the concentration of substances (called solutes) on both sides. This is called equalization of the osmotic pressure. The reverse would happen in a hypotonic solution, such as water; the cell would burst. This is why intravenous fluids are not water but contain 0.9 percent salt. This is called normal saline and has an osmotic pressure that is roughly equal to that of plasma and that of the intracellular structures in plasma, such as red blood cells. Like diffusion, osmosis is a completely passive process. Active transport involves the movement of substances, particularly ions, from an area of low concentration to an area of high concentration. This involves cellular energy and is why there is a higher concentration of potassium in the cell and a higher concentration of sodium outside of the cell. In this case, the sodium-potassium pump makes use of cellular energy to make sure that the concentration of these two ions is kept at a steady state, despite diffusion. Molecules like amino acids and glucose also are transported via an active transport process. Phagocytosis involves the active process of eating substances by the cell from the outside. There will be evaginations from the cell that surround whatever is needed to be eaten and will completely engulf the substance, taking it inside the cell. These often then combine with the contents of lysosomes in order to break the substance down. This is how cells take up microbial organisms like bacteria and destroy them with lysosomal enzymes. Pinocytosis is the act of taking in fluids from the outside in larger quantities than can be taken in across the membrane itself. It is referred to as cell drinking. Exocytosis is the passage of substances outside of the cell in what is the opposite process of phagocytosis or “endocytosis”. Exocytosis is important in nerve cells, which use this process to send

out neurotransmitters (chemical nerve messengers), and in digestive cells that send out digestive enzymes.

MITOCHONDRIAL PHYSIOLOGY Mitochondria have important physiological importance within the cell. These are responsible for the making of ATP molecules, which are the energy producing cells of the animal cell. ATP or “adenine triphosphate” is an adenine molecule with three phosphate side chains. There is energy stored in these phosphate molecules, particularly the third one. It takes energy to make an ATP molecule and, when it goes to make ADP plus phosphate, it releases energy that is used to drive many cellular processes. So, how is ATP made? There is a group of biochemical reactions done in and around the mitochondria that together make many ATP molecules. There are three basic processes in place to break down glucose, which is the main molecule metabolized in animal cells. In fact, all other substances (like amino acids, fatty acids, and others), are broken down into molecules that are a part of glucose in order to participate in metabolism. The first process actually takes place in the cytoplasm near the mitochondria. It is called glycolysis and breaks glucose down into pyruvate through several metabolic steps in order to make a few ATP molecules. These ATP molecules are, for the most part, used up in the participation of other metabolic reactions but this spending of energy later becomes necessary. Glycolysis is an anaerobic metabolism process because it doesn’t involve oxygen. The second process is called aerobic respiration because it involves oxygen. It takes the pyruvate made through glycolysis, brings it across the mitochondrial membrane, and involves the Krebs cycle or citric acid cycle. This makes more molecules of ATP and recycles many metabolites in order to do this. This happens inside the mitochondrion. The third process is called electron transport. It takes place across the membrane of the mitochondrion and makes the most ATP of any cellular process. Electrons are passed from one molecule to another and finally to oxygen, which accepts the electrons in order to make CO2 and water. The entirety of these three processes is called cellular

respiration (which is different from the respiration that happens in multicellular organisms with a respiratory system).

NUCLEUS PHYSIOLOGY The nucleus is the largest organelle in the cell and can easily be visualized using a light microscope. It contains the genetic material, DNA, within the cell structure. The DNA is in the form of multiple chromosomes that control which proteins get made by the cell. You should know that every cell of a multicellular organism contains the same DNA but, because of differentiation and the regulation of gene expression, each cell creates its own unique set of proteins. While DNA does not contain genes that make lipids, nucleic acids, and carbohydrates directly, they do make the enzymes that collectively make these other structures. The main metabolic process that occurs in the nucleus is transcription. Transcription involves the taking of genetic material (the DNA) and separating portions of it (certain genes) to have messenger RNA made. This involves multiple enzymes and participating proteins. There are enzymes that isolate the DNA to be transcribed, enzymes that separate the DNA strands, and an enzyme called RNA polymerase that makes the RNA molecule. Messenger RNA goes on to leave the nucleus through pores in the nuclear envelope in order to participate in translation. The DNA and RNA molecules are read via three-nucleic acid groups called codons. Each codon in the DNA molecule codes for a different matching codon on the RNA molecule, which goes on to match to a specific amino acid. There are statistically more codons made from the four different nucleotide bases than are necessary so some amino acids have two codons that code for the same amino acid and there are both start and stop codons that tell the RNA molecule when to start making the nucleic acid and when the gene is technically finished the transcription process.

RIBOSOMES Ribosomes take the mRNA and turn the message into protein molecules. There are transfer RNA molecules (tRNA) that are charged with individual amino acids. They link

up in the translation process in the ribosomes of the cell. In the translational process, the three nucleic-acid-containing codons match to a specific charged tRNA molecule so that a specific protein is made out of the messenger RNA molecule and the transfer RNA molecule. These proteins aren’t finished after translation but go through what’s called post-translational modification in order to be the finished protein necessary to engage in cellular processes.

THE CELL CYCLE The cell cycle is also referred to as the cell division cycle. It is the events that take place in the animal cell leading to DNA replication (the doubling of DNA) to ultimately produce two identical daughter cells. In cells that have a nucleus, there are three major phases of the cell cycle: interphase, mitotic phase, and cytokinesis. The cell grows and develops in interphase, building up the nutrients necessary for mitosis to occur. In mitosis, the chromosomes double in number and divide to opposite sides of the cell. During cytokinesis, the rest of the cell separates into the two daughter cells. Sometimes, the cell cycle is divided into four separate phases, known as the G1 phase or Gap 0 phase, S phase (synthesis phase), G2 phase, and M phase. The first three phases are called “interphase” and the M phase is divided into karyokinesis (which is the division of chromosomes) and cytokinesis (which is the division of the entire cell into daughter cells. Cells that do not divide and are in quiescence are said to be in the G0 phase. Interphase is the combination of the Gap 1 phase, S phase, and Gap 2 phase. The Gap 1 phase involves an increase in cell size and ends at the G1 checkpoint (which ensures that the cell is ready for DNA synthesis). In the S phase, there is DNA replication. In the Gap 2 phase, which is a gap between DNA synthesis and mitosis, the cell will continue to grow. There is a G2 checkpoint that ensures that everything is in place for mitosis. Mitosis involves the use of cellular energy to make two daughter cells. There is a metaphase checkpoint that makes sure the cell is ready to complete the cell division process.

G0 involves a cell that is quiescent and senescent. Some cells are always in the G0 phase after being formed, such as neurons, which do not divide. Fully differentiated cells also often are in the G0 phase because they no longer divide. Certain cells do not ever get into the G0 stage, such as epithelial cells, which always divide and replace themselves throughout the organism’s lifetime. Interphase is when the cell prepares for cell division. It is also referred to as the preparatory stage or intermitosis. More than 90 percent of the cell cycle happens in this phase. The three phases in this stage (G1, S, and G2) are involved in the preparation for mitosis. Growth and biosynthesis happen during this phase; it slows down considerably in the M (mitotic) phase. The S phase starts with DNA synthesis to make two sister chromatids. There is little protein synthesis and RNA transcription happening while this division of chromosomes happen. The G2 phase involves the beginning of microtubule organization in order to from a mitotic spindle.

MITOSIS Mitosis is relatively brief and consists of nuclear division or karyokinesis. It is broken down into five tightly regulated steps. In this phase, the five steps include prophase, prometaphase, metaphase, anaphase, and telophase. This is followed by cytokinesis, which separates the cells. The sister chromatids are placed together in the nucleus and lines up along a mitotic plate. The chromosomes separate and are pulled to opposite sides of the cell. The nuclear envelope breaks down in the cell so that the chromosomes are actually pulled to opposite poles of the cell. Figure 18 shows what mitosis looks like:

Mitosis is immediately followed by cytokinesis, the division of the cell organelles and cytoplasm into two daughter cells. Some cells have cytokinesis happening at the same time as mitosis, while others have a separation of the two processes—something that’s called “endoreplication”, which means there are multiple nuclei within the cells, at least for a period.

MEIOSIS Meiosis is a type of cell division that divides the cell but reduces the number of chromosomes in half, creating four haploid cells called gametes from a single totipotent stem cell. Meiosis happens in all sexually-reproducing single-celled and multicellular organisms (including animals, fungi, and plants). When the cell has errors in meiosis, there is aneuploidy, which is the lack of complete separation between chromosomes in the meiotic process so that some of the haploid cells do not have a complete set of chromosomes, while others have too many. Figure 19 shows what meiosis is like:

During meiosis, DNA replication is followed by two rounds of cell division without replication, so that four haploid cells are created. The two main aspects of meiosis are referred to as meiosis I and meiosis II. Before meiosis can begin, the DNA is replicated in the S phase so that there are two identical sister chromatids. After this happens, there is a prolonged G2-like phase called meiotic prophase. During this time, there is genetic recombination, in which there is cutting and splicing of the NA so that genetic information is exchanged during crossovers. This ensures that the haploid cells are unique and contain different combinations of genes. In female animals, there is elimination of three of the four haploid gametes so that just one gamete survives to produce the single ovum. This is not the case with male animals. Meiosis I involves the segregation of chromosomes in order to produce two haploid cells; the process is also called reductional division because the number of chromosomes is divided in half. Meiosis II, on the other hand is referred to as equational division, 79

which is similar to mitosis in that the sister chromatids are separated. This ultimately involves the creation of 4 haploid daughter cells. Recombination occurs in prophase I of meiosis I. This creates the genetic variation seen in the cell. Meiosis II is most similar to mitosis and has prophase II, metaphase II, anaphase II, and telophase II.

KEY TAKEAWAYS •

The animal cell is surrounded by a semipermeable membrane that is mostly made of a phospholipid bilayer.

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The cell structures are held in place by a cytoskeleton, made from three different types of filaments.

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There are multiple organelles in the cell that perform the different functions within the cell.

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Cellular energy is created mainly in the mitochondria of the cell.

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The cell cycle involves a resting, quiescent phase, preparatory phases, and mitotic phases.

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Meiosis results in haploid cells that act as gametes in the process of reproduction.

QUIZ 1. What is the major component of cell membranes when it comes to numbers of molecules? a. Intramembranous proteins b. Phospholipids c. Cholesterol d. Glycoproteins Answer: b. Phospholipids make up the majority of the molecules making up the cell membrane. Interestingly, because proteins are heavier, they make up more of the actual mass of the cell than lipids. 2. What do membrane-associated G-protein-coupled proteins do? a. They exchange sodium and potassium ions b. They block the transport of glucose inside the cell c. They affect intracellular changes within the cell d. They help make ATP for membrane processes Answer: c. G-protein-coupled proteins will bind to molecules outside of the cell and affect intracellular changes within the cell itself. They cause signaling molecules to become activated, sending a signal deep within the cell. 3. Where are ribosomes mainly located on an animal cell? a. On rough endoplasmic reticulum b. Within the nucleus c. Membrane-bound within the cytoplasm d. Inside lysosomes Answer: a. The ribosomes are studded along the surface of rough endoplasmic reticulum or RER, which accounts for the “roughness” or rough appearance of the endoplasmic reticulum.

4. What is the main function of the mitochondria inside an animal cell? a. To package lipids for transport b. To make proteins c. To send signals to other parts of the cell d. To create cellular energy Answer: d. Mitochondria are the metabolic powerhouses of the cell that create cellular energy through metabolic processes. 5. What molecule requires protein channels to cross across the cell membrane in what’s called facilitated diffusion? a. Carbon dioxide b. Glucose c. Ammonia d. Oxygen Answer: b. Glucose requires a special protein channel in order to cross the cell membrane—a process called facilitated diffusion. 6. If an animal cell were placed in water, what would happen to the cell? a. Water would passively enter the cell and would burst the cell. b. Water would passively leave the cell and the cell would dehydrate. c. Solutes would leave the cell, shrinking the cell. d. Water would be pumped out of the cell, equalizing the osmotic pressure. Answer: a. The water would go from a high concentration of water outside of the cell to an area of low concentration inside the cell passively; this would ultimately burst the cell. 7. What cell process makes the most ATP energy in the animal cell? a. Anaerobic respiration b. Glycolysis c. Electron transport d. Krebs cycle

Answer: c. The vast majority of ATP molecules are created as part of the complex electron transport process in the cell. The other processes also make ATP but to a lesser extent. 8. Which type of molecule is coded for by the DNA in the animal cell? a. Carbohydrate b. Lipid c. Nucleic acid d. Protein Answer: d. DNA only condes for proteins; it does not code for any other type of molecule but for the proteins that participate in making these other molecules. 9. Which type of cell in a complex animal organism is most likely to be in the Gap 0 or G0 stage of the cell cycle? a. Liver cell b. Epithelial cell c. Skin cell d. Neuron Answer: d. Neurons do not divide and instead are always quiescent and are in the G0 stage of the cell cycle. The other cells are always dividing or can go on to divide after periods of quiescence. 10. Which is the last phase in the process of mitosis? a. Prophase b. Telophase c. Metaphase d. Anaphase Answer: b. Telophase is the last phase in the process of mitosis, which goes through five different phases in a specific order.

CHAPTER 5: CELLULAR METABOLISM This chapter describes the inner workings of cellular metabolism. Animal cell metabolism involves primarily cellular respiration and the use of oxygen to break down nutrients for use as fuel or energy, usually resulting in the making of ATP, the universal energy currency of the cell. There are processes in place for anaerobic respiration and fermentation, which will be covered in this chapter. Plants use their cellular machinery to participate in photosynthesis, which yields oxygen and utilizes carbon dioxide. This process is also discussed as part of this chapter.

CELLULAR RESPIRATION We’ve talked briefly about cellular respiration in the previous chapter but it bears a closer look as this is the means by which all animal cells get the energy it takes to drive all cellular processes. The purpose of cellular respiration is to take the nutrients taken up by the cell and to covert them to adenosine triphosphate (ATP), which is the chemical energy currency in the cell. These are strictly “catabolic reactions”—called so because they are involved in the breakdown of larger molecules into smaller ones, using the energy derived from this process to create another high energy molecule. As you will see, these are also redox reactions, which are oxidation, reduction reactions involving the adding and subtraction of hydrogen ions and electrons. These reactions, aside from creating high energy bonds, are called exothermic reactions, meaning that they release energy. This is where the heat comes from in warm-blooded animals as the reactions are not completely efficient in exchanging energy from one covalent bond in a molecule to another covalent bond. These reactions are not the “opposite” of photosynthesis but represent the process of using light as an energy source in a series of anabolic reactions that build molecules. The main reactant for aerobic respiration is glucose, although all carbohydrates, fats, and proteins can get “fed” into the cycle. Because it is “aerobic”, it must involve oxygen 85

which, in the case of these biochemical reactions, becomes the final electron receptor in order to make CO2 and water. Basically, the reaction involved in aerobic respiration is this: C6H12O6 + 6 O2 goes to 6 CO2 + 6 H2O + heat (this reaction is spontaneous and does not innately require energy). There are also two important molecules made in these biochemical reactions: NADH and FADH2, which are used for the electron transport chain, which will be discussed. Flavin adenine dinucleotide, or FADH2, is a cofactor made during the Krebs cycle and contains hydrogen atoms, that give off electrons in the electron transport chain. Nicotinamide adenine dinucleotide, or NADH, is a related compound used in the electron transport chain as well. These are energy molecules like ATP, but are used in different reactions than ATP. So, how much ATP is made in aerobic respiration after a molecule of glucose is used up? We’ll break it down soon but, if the system worked perfectly, 38 molecules of ATP are made from a molecule of glucose (2 from glycolysis, 2 from the Krebs cycle, and 34 from the electron transport chain) but because these reactions rely on membranes and because membranes are inherently leaky, the reactions are inefficient so that only about 28 to 30 molecules are actually created in these reactions. This means that aerobic metabolism is up to 15 times more efficient than anaerobic metabolism. On the other hand, some anaerobic organisms, like those that use methane (methanogens), will use other organic molecules as their final electron receptor, yielding more ATP molecules than can be gotten from the typical anaerobic reactions that are seen in other animal organisms.

GLYCOLYSIS This is the part of the ATP-producing process that takes place in the cytoplasm of the cell. It takes glucose (a single molecule per reaction) and turns it into 2 pyruvate molecules. This reaction uses up two ATP molecules but yields 4 ATP molecules so that the net gain is 2 ATP molecules. Figure 20 shows what the reactions in glycolysis look like: 86

Let’s look at how this process works from a biochemical standpoint: •

Step 1: This involves hexokinase, an enzyme that takes a “hexose” sugar (namely glucose) and phosphorylates it (adds a phosphate group) gotten from ATP. This is one of the reactions that uses ATP to drive the reaction. This leads to a molecule called glucose-6- phosphate or G6P. Remember that every molecule ending in ase, is an enzyme. A kinase is any enzyme that adds a phosphate molecule to another molecule. Atomic magnesium (Mg) is also involved to help shield the negative charges from the phosphate groups on the ATP molecule.

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Step 2: This starts with glucose-6-phosphate and uses phosphoglucose isomerase to make fructose-6-phosphate (F6P). Basically, it switches a few carbon atoms around so that the sugar is fructose instead of glucose. The six-

membered ring becomes a five-membered ring. One carbon is taken out of the ring but is not lost completely by the molecule. •

Step 3: This step takes fructose-6-phosphate and the enzyme phosphofructokinase to add another phosphate molecule, using another ATP molecule to create fructose-1,6-bisphosphate. This also uses atomic magnesium in order to shield the reaction from negative charges of the phosphate groups.

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Step 4: This is a cleavage reaction involving aldolase, which takes fructose-1,6bisphosphate and turns it into two molecules that have three carbon atoms in it: The first is glyceraldehyde-3-phosphate (GAP) and the second is dihydroxyacetone phosphate (DHAP). The DHAP molecules need to be further acted on by triphosphate isomerase to turn it into a GAP (glyceraldehyde-3phosphate) molecule. These two steps lead to two molecules of GAP—not quite the pyruvate molecule we need to complete this reaction but it’s getting closer to that endpoint.

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Step 5: The basic thing that happens in this reaction is that the GAP molecules get acted upon by glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which adds phosphate to the molecule to make 1,3-bisphosphoglycerate. This involves an NAD molecule as a cofactor as well as a phosphate molecule (which is where the second phosphate comes from). The NAD takes on a hydrogen atom to yield NADH plus an extra hydrogen atom.

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Step 6: This takes 1,3-bisphosphoglycerate and ADP to make 3phosphoglycerate and ATP. It uses phosphoglycerate kinase, which takes the second phosphate molecule from 1,3-bisphosphoglycerate to make ATP from ADP. Magnesium is a cofactor. Because there are two of these molecules, two ATPs are made, making the net gain of ATP now zero.

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Step 7: This step rearranges the 3-phosphoglycerate using phosphoglycerate mutase to make 2-phosphoglycerate. It uses a mutase enzyme, which is an enzyme that takes a group from one position on a molecule to another. This is necessary to get the molecule in the pathway closer to its endpoint, which is pyruvate. 88

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Step 8: This step takes enolase, an enzyme, and removes a water from 2phosphoglycerate to phosphoenolpyruvate (PEP), resulting in PEP plus water. Enolase is a “dehydrating” enzyme because of the removal of water.

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Step 9: This is the final step in the glycolysis pathway. It takes PEP (phosphoenolpyruvate) and removes the phosphate molecule. It takes the extra hydrogen molecule made earlier, ADP, and PEP to make pyruvate (which has no phosphate molecules on it) and gives it to ADP to make ATP. Because there are two of these per glucose molecule, it adds two more ATPs to the glycolysis pathway to make a net total of 2 ATP molecules in the pathway.

The final result is one glucose molecule leading to 2 pyruvate molecules and 2 ATP molecules. If this is all humans, for example, had, there would be a lot of pyruvate left over and only 2 ATP molecules made. This pyruvate molecule needs to go on in the process of carbon molecule breakdown so that CO2 can be made from the glucose molecule. Organisms that do not use oxygen will still use the pyruvate in the process of fermentation, which will soon be discussed. Remember, too, that there are two NAD molecules leading into this process, which get reduced to make 2 NADH molecules. The addition of a hydrogen ion to the NAD molecule is called reduction, which is one-half of the “redox” reactions that go on in this process. Heat is given off in the process, making this an exothermic pathway. These NADH molecules go on later to make ATP in the oxidative phosphorylation pathway. Now, pyruvate isn’t completely ready to enter the Krebs cycle or citric acid cycle just yet. There is a “connecting” reaction called oxidative decarboxylation. In it, pyruvate needs to be oxidized to make acetyl CoA, which actually enters the cycle. This gives off one molecule of CO2 and a molecule of NADH in the process. This requires pyruvate dehydrogenase complex (PDC)—located in the mitochondria of eukaryotic cells but in the cytoplasm of prokaryotes.

KREBS CYCLE OR CITRIC ACID CYCLE So far, oxygen has not been required; this is how some organisms operate when no oxygen is available and what happens in multicellular animals when there is a relative lack of oxygen. When oxygen Is available, the acetyl-CoA enters the Krebs cycle. When there is no oxygen, fermentation happens. The Krebs cycle (also called the tricarboxylic acid cycle or citric acid cycle), takes place in the mitochondria matrix of the cell. Figure 21 shows the reactions that take place in the Krebs cycle:

There are eight steps to the citric acid cycle, which is a closed loop. This breaks down glucose further into CO2 and generates some important energy-producing molecules. It starts with acetyl CoA and oxaloacetate and forms citric acid or citrate (and thus the name). This is a six-carbon molecule. Through a series of reactions, 2 molecules of NAD become three NADH molecules and one FAD becomes an FADH2 molecule. There is a series of reactions inside the mitochondrial matrix that take the oxaloacetate and acetyl-CoA, removes two carbon dioxide molecules to turn the entire thing back into oxaloacetate, which is recycled for the next loop. Another energy molecule (GTP or ATP, depending on the organism) gets made in this cycle. Because there are two acetyl CoA molecules per glucose molecule made, the net end is that there are six NADH molecules, 2 FADH2 molecules, and 2 ATP molecules (or GTP molecules) made. Because GTP can be used to make ADP without difficulty, most sources consider that ATP is essentially made in this cycle, at least in higher animals.

OXIDATIVE PHOSPHORYLATION This is a highly important part of cellular respiration, taking place in the mitochondrial cristae. Remember that there are all of these high-energy molecules that aren’t ATP, which can be used to make ATP in the process. It involves a “proton gradient” or a positively-charged gradient (also referred to as a chemiosmotic potential) across the inner membrane of the mitochondria. ATP synthase is heavily involved in this process as many ATP molecules are made using this gradient to drive the biochemical process. So far, there has been a lot of “reduction” or reductive chemical reactions going on. This is a time for oxidation to take place. This is why it’s called oxidative phosphorylation. It takes oxidative processes to “phosphorylate” the ADP molecule to make ATP. This is where oxygen is necessary because something has to be the final electron acceptor in this chain of electrons being transferred from one molecule to the next. Oxygen is a perfect electron acceptor because it can bind with hydrogen atoms to make water. Figure 22 describes what oxidative phosphorylation looks like:

This process occurs in the inner mitochondrial membrane—in the cristae. There is a pH gradient across the membrane with electrons being passed back and forth across the membrane until the final donation process takes place. ATP synthase is a rotary mechanical motor enzyme that needs to be rotated in order to do its job. The flow of hydrogen atoms across the pH gradient drives the rotation process so that ATP can be made from ADP. This ATP synthase is the whole purpose of this electron transport chain in that the chain is used to drive this enzyme. It should be noted that, in prokaryotes, such as bacteria and archaea, this process can happen but there are different electron receptors, different enzymes, and no mitochondria involved. The process instead happens across the cell membrane itself and uses different chemical substrates. Bacteria and other prokaryotes must grow under a variety of environmental conditions with electron donors being things like lactate, hydrogen, or formate, and electron acceptors being DMSO, oxygen, or nitrate. Because these are oxidative reactions, they can lead to the formation of reactive oxygen species, such as hydrogen peroxide and superoxide, which ultimately lead to free radical formation and cell damage. This is a natural part of the metabolic process and is why the body has antioxidants to take care of these normal metabolic end-products.

In the case of eukaryotes, the electron donors in the process are the high energy products that were made in glycolysis and in the Krebs cycle—namely, the NADH and FADH2 molecules that seemingly didn’t make sense before. Just to summarize this entire process, these are the ATP production quotas from a single molecule of glucose: •

Glycolysis—this uses up 2 ATP molecules but gives off 4 later for a net of 2 ATP molecules made. It also makes 2 NADH molecules that go to the oxidative phosphorylation process to make 1.5 net molecules of ATP (because it takes ATP energy to transport it across the mitochondrial membrane.

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Oxidative decarboxylation—this is the intermediary step between glycolysis and the Krebs cycle. It makes 2 NADH molecules that go on to make 5 ATP molecules in oxidative phosphorylation.

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Krebs cycle—this is the largest source of ATP molecules. Two are made as part of the Krebs cycle itself, while 15 are made from the 6 NADH molecules created by the cycle and used in oxidative phosphorylation. Three ATP molecules come from 2 FADH2 molecules created by the cycle and used in oxidative phosphorylation.

The total yield is 30 to 32 ATP molecules, most, as you can see by the tally, coming from high energy molecules in oxidative phosphorylation. Theoretically 38 ATP molecules are made; however, it takes energy to move ADP, phosphate, and pyruvate across the membranes, resulting in losses that offset the otherwise high yield. The result is the complete oxidation (or breakdown) of glucose into CO2 and water. The breakdown for ATP production is 2.5 ATP molecules per molecule of NADH and 1.5 ATP molecules per molecule of FADH2. Interestingly, cellular respiration can, in some situations and in some cells, purposely be inefficient for the express purposes of generating heat. Newborn humans have brown fat, which contains an uncoupling protein called thermogenin that purposely short circuits the electron transport chain, generating heat energy instead of ATP. This protein is also expressed in hibernating animals that allows them to stay warm during the cold weather.

FERMENTATION Some organisms undergo the process of fermentation in order to generate ATP in the absence of oxygen, using other substrates to generate this type of energy. In fact, the scientific definition of fermentation is a metabolic or enzymatic process that creates energy out of an organic molecule in the absence of oxygen or an electron transport system. In such cases, the final electron receptor is an organic molecule rather than oxygen. Fermentation is believed to be the oldest metabolic pathway—something that prokaryotes and eukaryotes have in common. From an evolutionary standpoint, this was the pathway that developed before there was sufficient oxygen on earth. What it means is that, even though higher order animals get the vast majority of their ATP through aerobic mechanisms, the capacity to undergo fermentation still exists as part of an older evolutionary pathway. In fact, mammals undergo fermentation in muscle cells when intense exercise is done and there is insufficient oxygen. The end result is the creation of lactic acid, a common metabolite in muscle during exercise. Invertebrates have fermentation capabilities, producing things like alanine and succinate. Bacteria undergo fermentation in low oxygen environments, creating acetate and formate. These bacteria interact with methanogens, which are Archaea species; these convert the acetate to methane gas. Figure 23 describes lactate fermentation in mammals:

Glycolysis is also an evolutionarily old pathway; its end product, pyruvate, gets bypassed out of going into the Krebs cycle, going on to fermentation instead. The main end products of fermentation include lactic acid, ethanol, carbon dioxide, and hydrogen gas, although a few organisms can produce acetone and butyric acid. They are not fully oxidized and become waste products as they cannot be metabolized any further. Fermentation generally takes place in an anaerobic environment (which means without oxygen). Because more ATP is made with oxidative phosphorylation, this is the preferred method by most species. Certain yeast species, like Saccharomyces cerevisiaex , actually prefer fermentation when sugar is abundant. Other species do not tolerate oxygen at all and are considered obligate anaerobes. Some yeast products make ethanol in the fermentation process. Glucose goes to 2 pyruvate molecules in glycolysis and then gets diverted into acetaldehyde and then

ethanol. Carbon dioxide is given off in the process, which is how dough rises when yeast is added. This is, of course, the same process that happens when sugar and yeast mixes together to make alcoholic beverages. Ethanol can be generated in large quantities using corn, sugar beets, and sugarcane—ultimately added to gasoline and used for fuel. Figure 24 illustrates ethanol fermentation:

The ethanol pathway takes glucose and makes 2 pyruvate molecules as in glycolysis. This is an exothermic reaction that gives off heat. It binds phosphate to ADP to make ATP and converts NAD into NADH. There is then a reaction that causes the pyruvate to break into acetaldehyde and carbon dioxide. The hydrogen ion from NADH and the energy of the previous reactions goes on to reduce acetaldehyde into ethanol, regenerating NAD again so that it can be reused. The two enzymes necessary for these last two reactions are pyruvate decarboxylase and alcohol dehydrogenase.

The most basic form of fermentation is called homolactic fermentation, in which the only end product is lactic acid. It starts with glycolysis and its end product, pyruvate, but goes to make lactic acid in a single redox reaction. This is one of the only respiratory pathways that doesn’t produce a gaseous byproduct. It happens in mammalian muscle cells and in lactobacilli and some fungi. The sour taste of yogurt comes from the lactic acid made by lactobacilli. There is also heterolactic fermentation, in which lactic acid isn’t the only end product. Some goes on to make carbon dioxide and ethanol (using phosphoketolase). Some also goes on to make acetate or other waste products. The reasoning behind the need to do this at all is because lactic acid is too acidic to drive certain biological processes. This is why food is fermented in the first place—it drives out other bacteria and keeps them from taking hold, extending the shelf life of food. Another reason to have heterolactic fermentation is because, if things like ethanol and CO2 are produced as end products, they are volatile, leaving the situation so that the rate of forward reactions is kept up. Too high a concentration of an end product like lactic acid will drive the concentration backward, slowing the growth of the organism itself. Things like propionic acid and butyric acid become better end products because they aren’t as acidic and won’t interfere with cellular growth. Several organisms will produce hydrogen gas as part of the fermentation process, including those that make butanol, butyric acid, caproate, and glyoxylate. The hydrogen gas will help to regenerate NAD from NADH. Remember that this is how NAD is recycled in many fermentation processes. The hydrogen gas is used by methanogens and organisms that are sulfate reducers as well and, in high concentrations, can be given off as a gaseous substance.

PHOTOSYNTHESIS Photosynthesis is the process by which light energy becomes chemical energy— something common to plants, most algae, and cyanobacteria. The chemical energy is stored in carbohydrate molecules (sugars) that are essentially made by CO2 and water. In the majority of cases, the waste product of this reaction process is O2 gas. It is these

organisms that ultimately lead to the oxygen present in on earth as well as the organic molecules present on earth. There is no single photosynthetic pathway for the different species that participate in it. It does, however, start out always with light being absorbed by proteins known as reaction centers. These reaction centers contain chlorophyll pigments located inside chloroplasts—organelles unique to higher order photosynthetic organisms. It can also be done in bacteria that have no chloroplasts but have pigmentation in their plasma membranes. Figure 25 shows the process of photosynthesis:

The light energy goes into the splitting of water, freeing hydrogen atoms and leaving oxygen behind as a waste product. These hydrogen atoms create two energy molecules: 1) ATP and 2) nicotinamide adenine dinucleotide phosphate (NADPH). These are shortterm energy storage molecules used to make long-term storage in the form of sugars. Some plants use the Calvin cycle, which takes the energy gotten from the initial light-

dependent reactions (NADPH and ATP) to make sugar molecules out of CO2. There are other organisms (especially bacteria) that use a type of “reverse Krebs cycle” to do the same thing. In the Calvin cycle, the organic compound called ribulose bisphosphate is acted on along with CO2 and energy to make higher order organic molecules. Ultimately, the process goes on to make glucose and other six-carbon sugars. Photoautotrophs are organisms that can take CO2 alone to make organic molecules. Photoheterotrophs use other organic molecules besides CO2. Most organisms (algae, cyanobacteria, and plants) undergo oxygenic photosynthesis; that is, they make oxygen. Certain bacterial species undergo anoxygenic photosynthesis. They use light energy but do not give off oxygen. In a vague sense, photosynthesis is the opposite of cellular respiration, although different enzymes are involved. This process, known as carbon fixation, is endothermic and involves the reduction of carbon dioxide. Reduction, as a rule, means to add hydrogen atoms to something. Rather than giving off energy, these endothermic reactions store energy in the form of carbohydrate molecules—an energy stored in the chemical bonds of the carbohydrate molecule. The process necessarily must involve the consumption of water in order to provide the hydrogen atoms necessary for reduction. In oxygenic photosynthesis, the reaction proceeds as such: CO2 plus 2 H20 molecules plus a photon of light energy goes to carbohydrate plus oxygen plus one water molecule. Note that, in actuality, water is both a reactant (starting molecule) and end-product of photosynthesis; it’s just that it takes more water to put in the reaction than is given out at the end of the reaction. In anoxygenic photosynthesis, carbon dioxide mixes with arsenite instead of water. This leads to arsenate and carbon monoxide instead of oxygen. There are two phases of photosynthesis. The first involves light-dependent reactions. Light is captured to make ATP and NADPH, which as mentioned are temporary storage molecules. The second in involves light-independent reactions, which uses the energy molecules made in the first phase to fix carbon.

CHLOROPLASTS In those organisms that have chloroplasts, this is where the energy gathering occurs. The structure of a chloroplast is shown in figure 26:

One of the main structures inside chloroplasts are called thylakoids. These are folded cylindrical sheets of membranes that have a very large surface area so as to gather the most light possible. Bacteria that have no chloroplasts either use the cell membrane itself or bunched up pieces of cell membrane that are also called thylakoids. In algae and plants, there are ten to a hundred chloroplasts per cell. These are membranous structures that have an internal stroma that is filled with stacks of thylakoids, where photosynthesis takes place. Each thylakoid is membranous and has its own lumen, called the thylakoid space. Within the membrane, similar to the idea that inside mitochondrial cristae there are membrane-bound enzymes, there are membranebound protein complexes in these thylakoids that participate in the process of photosynthesis. There is a variety of pigments used in absorbing light as part of photosynthesis. By far the most important and abundant is chlorophyll. Other pigments used in photosynthesis are xanthophylls, carotenes, fucoxanthin, phycoerythrin, and 100

phycocyanin . These will be the pigments seen in brown algae, green-blue algae, and red algae. The pigments are imbedded in complexes known as light-harvesting complexes. Light-dependent reactions happen in the chloroplast membrane (in the thylakoids). The chlorophyll pigment absorbs a photon of light, losing an electron in the process. This electron flows from one molecule to another in a complex that leads to the production of NADPH from NADP. There is a proton gradient produced by this process—the same proton gradient in mitochondria that is necessary to make ATP using ATP synthase. The chlorophyll molecule gets its electron back by splitting water to make oxygen gas (O2) as a byproduct. Not all wavelengths of light work for photosynthesis. This is completely dependent on the pigment used in the organism. The part of the light spectrum that is not absorbed is “given off” in a sense as the visible color of the organism. In plants, the light not absorbed is mostly green so that the color of the organism is green. In red algae and other non-green organisms that participate in photosynthesis, different spectrums of light are absorbed and not absorbed than is seen in plants. There are cyclic and non-cyclic forms of light-dependent reactions in the thylakoid membranes of the chloroplast. The non-cyclic forms involve the capture of light by chlorophyll that frees up an electron from the pigment, shuttling the electron down an electron transport chain called a Z-scheme. This generates a chemiosmotic gradient across the thylakoid membrane that charges the ATP synthase molecule to make ATP. The final electron acceptor in this case is NADP, which takes it to make NADPH. The cyclic photosynthetic reaction is similar to the non-cyclic form but makes only one ATP molecule and does not create an NADPH molecule. The electron that is passed down the electron chain and is ultimately returned to the system to start over again. This is, of course, why it is called cyclic. When chlorophyll loses its electron (when light is absorbed by it) it is oxidized and needs an electron back again. In most plants and in cyanobacteria, the electron donor in this case is water. Two water molecules are split as part of photosynthesis to yield O2 and four hydrogen ions that have electrons to share. These are shared through a series

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of reactions to reduce chlorophyll again. They also are used in part to create the chemiosmotic membrane potential that drives ATP synthase. The Calvin cycle is a light-independent or dark reaction series in plants. There is an important enzyme called RuBisCO that takes the CO2 from the atmosphere and fixes it to make three-carbon sugars that are later combined to make things like sucrose and starch. It relies on both ATP and NADPH to drive these reactions. Fortunately, these molecules are in abundant supply because of the light-dependent reactions. The end product made from the Calvin cycle is called triose phosphate, a 3-carbon sugar. Ribulose-1,5-bisphosphate is the five-carbon sugar in the cycle that takes on CO2 and splits to make glyceraldehyde-3-phosphate, also referred to as triose phosphate. Most of these will go on to regenerate the cycle again, similar to what goes on with oxaloacetate in the Krebs cycle; however, some will not do this and will join to make a six-carbon sugar outside of the cycle. Other molecules are subsequently built from these six-carbon sugars with the storage molecule in plants being starch (chains of glucose molecules).

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KEY TAKEAWAYS •

Glycolysis is an evolutionary older metabolic pathway that takes glucose and turns it into pyruvate and energy.

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The point of the Krebs cycle and glycolysis is to make energy-storing molecules that go on to drive the process that makes ATP energy.

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A fully-oxidized or metabolized glucose molecule goes on to make CO2, water, and energy.

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Fermentation involves making energy without the use of oxygen.

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Photosynthesis takes light energy and turns it into temporary energy-storing molecules that are used to drive light-independent pathways in the plant cell.

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Light-independent pathways in plants will fix carbon from carbon dioxide to make sugars.

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QUIZ 1. Which word does not describe the process of cellular respiration reactions? a. Redox reactions b. Exothermic reactions c. Catabolic reactions d. Anabolic reactions Answer: d. These reactions are all exothermic (giving off heat), catabolic (breakdown), redox reactions (involving the exchange of electrons and hydrogen ions). They are not anabolic. 2. Which aspect of aerobic biochemical reactions leads to the most ATP molecules? a. Fermentation b. Glycolysis c. Electron transport d. Krebs cycle Answer: c. Electron transport yields many more ATP molecules (about 34 theoretically) when compared to the other aspects of aerobic respiration. 3. Where in the cell does glycolysis take place? a. Nucleus b. Rough endoplasmic reticulum c. Cytoplasm d. Mitochondria Answer: c. Glycolysis specifically happens in the cytoplasm without the aid of any membranes. It delivers the pyruvate molecules to the mitochondria for the rest of the pathway leading to aerobic respiration.

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4. Which molecule essentially starts and finishes the closed loop that is the Krebs cycle? a. Oxaloacetate b. Citrate c. Acetyl CoA d. Pyruvate Answer: a. Oxaloacetate gets recycled over and over again in the Krebs cycle in order to further break down the glucose that started the entire process of cellular respiration. 5. Where in the cell does oxidative phosphorylation take place in eukaryotes? a. Mitochondrial matrix b. Cell membrane c. Mitochondrial cristae d. Outer mitochondrial membrane Answer: c. This must take place across a membrane in order to generate a pH or electrochemical gradient, which drives the reactions that make ATP from ADP. The mitochondrial cristae represent the inner membrane of the mitochondria. 6. Where do most of the ATP molecules come from in cellular respiration? a. NADH b. FADH2 c. GTP d. Pyruvate decarboxylation Answer: a. Most of the ATP comes from NADH. The yield is 2.5 ATP molecules per molecule of NADH and only 1.5 ATP molecules per molecule of FADH2. There are many more NADH molecules than FADH2 molecules made prior to oxidative phosphorylation, making these the greatest source of ATP in cellular respiration.

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7. What is the beginning substrate in the fermentation process? a. Glucose b. Acetate c. Carbon dioxide d. Oxaloacetate Answer: a. All fermentation ultimately starts with glucose, leading into the glycolysis pathway and then leading to a variety of fermentation pathways. 8. What is the major downside of having lactic acid as an end product of fermentation? a. It is not completely oxidized. b. It is acidic and blocks the growth of the organism. c. It is too volatile for the organism. d. It gives off CO2 gas. Answer: b. The major downside of homolactic fermentation, in which only lactic acid is made, is that it is too acidic, adversely affecting the growth of the organism making the acid. 9. What is the most abundant photosynthetic pigment on earth? a. Xanthophylls b. Phycoerythrin c. Fucoxanthin d. Chlorophyll Answer: d. The most abundant photosynthetic pigment is chlorophyll, found in most photosynthetic plants. The others are pigments that are seen in some plants and algae but are less abundant.

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10. What is the main waste product in the act of photosynthesis? a. Water b. CO2 c. O2 d. Acetate Answer: c. In photosynthesis, the actual waste product is O2 gas, which is given off after H2O is split to give an electron back to chlorophyll in the chloroplast.

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CHAPTER 6: GENETICS Genetics is the topic of discussion in this chapter. It is the study of how traits are passed from one generation to the next, which involves the building blocks of genetics, DNA and RNA. These are divided into chromosomes and genes that together write the code that determines the offspring’s genotype (or genetic code) and phenotype (or physical appearance). Genes are tightly regulated so that some genes are expressed, while others are suppressed. This process of gene regulation is also covered in this chapter.

MENDELIAN GENETICS Mendelian genetics comes from the work of Gregor Mendel in the 1960s. He was an Austrian monk who worked on pea plants and discovered some of the basic tenets of genetics without the knowledge of genes, chromosomes, and DNA. Rather than believing that inheritance was simply a matter of blending of parental essences, he believed that there were discrete units of inheritance, we now know to be genes, and that genes were inherited independently. In the modern understanding of Mendelian genetics, it is known that every person gets a copy of genes and that each gene inherited is called an allele. For each trait, there are two alleles or two copies of the gene—one inherited from each parent. If the two alleles received from each parent are identical, the individual is said to be homozygous for the trait. If, on the other hand, the two alleles are different, the individual is said to be heterozygous for the trait. We now know that most traits are polygenic and not based on single genes. As mentioned, Mendel studied pea plants. He cross-bred these plants that had selected traits, such as smooth peas and wrinkled peas, tall plants and short plants, and purple flowers and white flowers. Figure 27 shows what the cross-breeding of genes looks like:

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He crossed homozygous dominant traits with homozygous recessive traits, leading to an F1 or first filial generation. Each of the organisms in the F1 generation are heterozygous but will look as though they have the dominant trait. This organism appearance is referred to as the phenotype, which is what it looks like regardless of its genotype (or collection of genes). If this F1 generation is cross-bred together, the end result is a 3:1 ratio of dominant phenotypes to recessive phenotypes. Mendel when on to say that traits come in hereditary units called factors. Factors TT (written as capital 2 capital t’s) involve being homozygous for the dominant trait; factors Tt (written as capital T, lower case t) involve being heterozygous for the dominant trait; factors Tt (written capital T, lower case t) involve being homozygous for the recessive trait. The only phenotype that is of the recessive trait is tt (written as 2 lower case t’s) because, having the T allele that carries dominance over the trait. Figure 28 shows the Punnett square for the purple flowered trait: 109

A Punnett square is a way to predict whether offspring of parents with certain traits will have the trait or not. The example in figure 28 showed the Punnett square for the purple flower trait, with B being representative of a dominant purple allele and b being representative of a recessive purple allele. With the 3:1 ratio of dominant phenotypes, you need to see that the genotype ratio of these traits is 1:2:1, or 1 BB: 2 Bb: 1 bb. Its phenotype is going to be dominant in three of these genotypes and recessive in 1 of these genotypes. Mendel had a Law of Dominance, indicating that each organism has the phenotype of one parent only. If the dominant gene is present, the dominant trait will result. If the recessive gene is present, the trait must be homozygous to shine through. What you should know is that since then there has been the discovery of things like “incomplete penetrance” in which the dominant trait isn’t completely expressed.

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Mendel’s Law of Segregation indicates that, for each trait, the alleles are separated so that one allele gets passed onto the offspring, with the specific pair getting passed on being completely random. This means that there is a 50:50 chance of passing on each gene to the offspring. Law of Independent Assortment means that for different pairs of alleles, such as trait TT and trait BB, the alleles get separated from one another independently so that the inheritance of genes at one allele doesn’t affect the inheritance of genes at another location. We now know that sometimes genes that are close together on a chromosome get inherited together with their closeness on the genome influencing their coinheritance. A trait or allele can be autosomal or x-linked in animals. This applies to traits on the autosomal chromosomes or the X chromosomes. In humans, there are 23 pairs of chromosomes, of which 22 are actually paired in males and females. These are number one through twenty-two. The twenty-third pair is the XX or XY pair. Females only have X chromosomes and an XX pair indicates a female. Males have both an X chromosome and a Y chromosome. Their gametes (which are haploid as you’ll remember from the section on meiosis) have either an X chromosome or a Y chromosome. This means that the male of the species determines the genetic phenotype (male or female) of the species. If a trait is x-linked, it means that it is only passed from the female to a male offspring because the “matching” chromosome—another X chromosome—does not exist in the male as they have an XY genotype. The trait can be recessive or dominant but there are only rare x-linked dominant traits. Most are recessive, with the female of the species carrying the trait but not having the disease. We’ll talk more about this later. Pedigrees are ways that individual families can be studied as to what is being inherited in the family tree. In fact, a pedigree is a lot like a family tree but shows which members have the disease and which do not have the disease. It easily can tell what type of inheritance is going on—if a number of family members exist in order to make predictions on what type of inheritance the trait has (autosomal dominant, autosomal

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recessive, or x-linked recessive). Remember that x-linked dominant traits are very rare. Figure 29 shows a pedigree chart for breast cancer in a family:

DOMINANT INHERITANCE When a trait is said to be dominant, it takes just one allele to be inherited for the trait to be expressed in the phenotype of the individual. Any recessive allele will be masked by the dominant one so that the phenotype for the TT genotype is the same as the phenotype for the Tt genotype. Only the tt genotype will show the recessive trait. An example of an autosomal dominant disease is Huntington disease. The affected individual is usually of the Hh genotype and will ultimately get the disease. They will pass the disease onto half of their offspring. Because this is a rare disease, it would be uncommon to have two parents having the disease; however, if both parents were heterozygous for the disease, they would pass the disease onto ¾ of their children. In an autosomal dominant pedigree, both males and females will be affected and there will be no skipping of generations. There will be about a 50:50 chance of expressing the gene in the offspring of an affected person (provided that the other parent does not have the gene). Both homozygous and heterozygous individuals will have the same phenotype and, in the case of a homozygous dominant parent, all of the children will be affected.

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RECESSIVE INHERITANCE Recessive traits require an individual to have both copies of the allele in order to have the trait. Any dominant trait along with it will mask the recessive nature of the gene. It is represented with a lower-case letter, such as tt. There must be a copy of the gene from both of the parents in order to get the gene and the alleles must both be the same. In a Tt versus Tt situation, only 25 percent of offspring on average will get the trait. If a TT (homozygous dominant) parent mates with a tt (homozygous recessive) parent, none of the offspring will get the trait but all will be carriers. The pedigree for an autosomal recessive trait will often skip generations and, if it is rare, it may appear to be sporadic in nature. This is because there are few carrier individuals around to mate with another carrier or with someone who has the disease state. An example of a recessive disease in humans is cystic fibrosis. If there are two carriers, a fourth of their children will have the disease. This will often come as a surprise to parents who do not realize they are carriers. Males and females will be equally affected.

X-LINKED RECESSIVE INHERITANCE As mentioned, there are few x-linked dominant diseases and more x-linked recessive traits. Those affected are largely male because they do not have two X chromosomes to have the recessive allele masked by another allele. Females are largely carriers as most of these diseases are rare so the chances of a carrier female mating with an affected male, leading to females with the disease is very uncommon. A pedigree will show that males are almost exclusively affected and that males cannot transmit the disease to their sons. All female offspring of an affected male will automatically be carriers because the male parent only has the abnormal gene to pass to his daughters. Each son of a carrier female will have a fifty percent chance of getting the disease. Both hemophilia and Duchenne muscular dystrophy are considered X-linked recessive diseases.

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DNA AND GENETICS DNA is the basic carrier of genetic information in almost all forms of life and in all cellular life. In humans and higher order animals, each cell (except red blood cells) will have the complete DNA message, even though not all genes are expressed in every cell. There is nuclear DNA and mitochondrial DNA. Because no mitochondria enter the ovum from the sperm cell at the time of conception, all mitochondrial DNA comes from the mother. As mentioned, there are four bases in DNA. These include adenine (A), thymine (T), cytosine (C), and guanine (G). The order of the bases in the DNA molecule is known as the “DNA sequence”. The double helix of the DNA consists of two sequences that match with each other. The base pairs are connected by means of weak hydrogen bonds, with certain bases only matches of A with T and G with C. This means that the complementary base is found on the opposite DNA strand. Figure 30 shows what the DNA strand looks like:

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The DNA sequence is made up of nucleotides. A nucleotide is a pentose sugar molecule (deoxyribose sugar) that has a three-prime (hydroxyl side) and a five-prime (phosphate side) segment. The covalent bonds (strong bonds) connect the three-prime side on one sugar molecule to the five-prime side on another sugar molecule. Attached to the sugar molecule is a nitrogenous base (the A, T, G, C bases just mentioned). Figure 31 shows a guanine nucleotide with the pentose sugar and its base:

When nucleotides link together, they are called polynucleotides or, in the case of a long polynucleotide of deoxyribose nucleotides, DNA. There is a phosphodiester bond that connects the sugars, forming what’s called the backbone of the DNA molecule. The DNA molecule is stabilized as a double strand, with nitrogenous bases connecting to one another via hydrogen bonding. This is a weaker bond than the covalent bond seen in most molecules, which means it doesn’t take as much energy to split the two strands as it does to split each strand apart by itself. These strands, when connected, are considered anti-parallel. One strand runs from the five-prime to the three-prime end, while the opposite strand runs from the three-prime end to the five-prime end.

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As mentioned, all of the DNA necessary for the organism is contained within a single cell but not all genes are expressed. If the human DNA were arranged in a single piece and stretched out, it would be about 2 meters long per cell. This results in creative DNA packaging within the cell. The long pieces are separated into chromosomes and are wound, looped, coiled, and folded so that they fit within the nucleus. Histone proteins facilitate this folding and coiling so that DNA can be condensed into what’s called chromatin. Chromatin is DNA plus histone proteins. DNA can also be supercoiled, which is the case in prokaryotes, which do not have histone proteins. Supercoiling uses other proteins to tightly compact the DNA in what is usually a single circular chromosome. Eukaryotes have linear chromosomes in most cases, with different organisms having different numbers of chromosomes. The appearance of DNA when not actively in mitosis or meiosis is that of a bunch of string in a pile.

CHROMOSOMES AND GENES Chromosomes themselves are the totality of the DNA message, which involves thousands of different genes. A gene is considered any sequence of DNA (or RNA in some organisms) that codes for a protein that is functional in the cell. In most organisms, the DNA is first copied into RNA, which acts as an intermediary template molecule coding for a protein. The totality of the genes in an organism’s chromosomes is called a genotype, which interacts with both developmental and environmental factors in order to determine what the phenotype of the organism will be. We’ve talked about genes as though they have the power to do major things to the phenotype of the organism when in fact it is usually a combination of many different genes that impact the phenotype. These genes interact with the environment in order to determine the actual phenotype seen. The different variables in a specific gene cause the different alleles seen in a given population. So, when speaking of having a specific “gene” it basically means that the term refers to a specific allele of the gene and not the gene itself.

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The idea of genes was first suggested by Gregor Mendel, whose genetic theories have already been discussed. He did not understand genes themselves but proved the existence of distinct inheritable units in his study of pea plants. He was also the first to describe independent assortment of genes and to recognize that there were dominant and recessive genes. He also understood the concepts of heterozygosity and homozygosity. The actual term “gene” wasn’t developed until 1905, when Wilhelm Johannsen first introduced it. Gene sequencing was first accomplished in 1972 and became more efficient in 1977 by Frederick Sanger. This was further automated, which lead to the Human Genome Project, which successfully sequenced the entire human genome by 2003. As mentioned, DNA runs from the five-prime end to the three-prime end on one strand and from the three-prime end to the five-prime end on the other strand. When a gene is transcribed from DNA to RNA (and when DNA is replicated, these are done from the five-prime end to the three-prime end. The exposed hydroxyl end at the three-prime end is called a nucleophile because it attaches a nucleotide to this end. When a gene is transcribed, it takes the message and creates an RNA molecule. This is similar to DNA but has uracil instead of thymine and is a less-stable molecule because it does not form a double helix; it is a single-stranded molecule. The reading sequence involves codons that are three base pairs in length. The base sequence ATT, for example will code for something different than the base sequence TAA. As a gene is being transcribed, mutational errors can occur such that the reading sequence is off by a base pair so that the entirety of the rest of the sequence is completely misread. There can also be single base mutations, which means that a single amino acid is wrong; however, this may or may not affect the structure of the protein. The total complement of genes is referred to as the organism’s genome. Thousands of genes are located on a single chromosome. The locus is the region on the chromosome where the gene is located. The portion of the gene that is tightly locked into histone proteins is usually not expressed. Those that are unraveled are accessible for the reading of the gene. As mentioned, prokaryotes have genes that are arranged one after the other

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without introns (noncoded sections of DNA); however, there are many introns in eukaryotic DNA, interspersed between exons, which are the coded segments of DNA. A gene may consist of exons and introns with the introns ultimately spliced out of the RNA molecule or are not translated by the ribosomes. Genes contain a regulatory sequence that is necessary for their expression. There must be a promoter region on a gene that signals it is ready to be transcribed. There are transcription factors that attach to the promotor sequence along with RNA polymerase. There can be more than one promotor region per gene. There can be regulatory regions in the different genes. These alter the expression of the gene and will bind to transcription factors to cause the DNA to form a loop so that the transcribed region will be closer to the RNA polymerase binding site. There are things like enhancers that bind to activator proteins that make RNA polymerase more available and silencers that bind to repressor proteins to make DNA less available to RNA polymerase. What gets transcribed is called pre-RNA. There are many untranslated regions, such as those that contain ribosomal binding sites, terminator ends, and both start and stop codons. There are, particularly in eukaryotes, sequences of exons and introns that get spliced so that only the mature RNA will code for the protein. Prokaryotes are slightly different. Their genes are organized into operons, which code for multiple proteins at a time. They get transcribed as a continuous messenger RNA, called polycistronic mRNA. This is the scientific term for polygenic mRNA. While there are separate proteins made, they often are related to one another when it comes to the different functions they have in the cell, so they need to be regulated together.

GENE MUTATIONS Gene mutations can occur when genes are transcribed. The error rate in eukaryotic cells is very low; it is higher in RNA viruses. What this means is that, per generation in humans, about 1 to 2 new mutations occur.

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There are different types of mutations. A point mutation is the mildest and changes just one base pair. This may or may not effectively change the structure of the protein. There can be a frameshift mutation, in which a single base is inserted or deleted. These are more serious because they can change the entire reading of the codons, causing a nonsense protein or a premature stop codon to be read that leads to a shortened, nonsensical protein. There can be large duplications, deletions, rearrangements, or inversions of big parts of the chromosome. Errors can occur when DNA is being repaired. There can be multiple different alleles for the same trait in the population of a species. These are referred to as polymorphic genes because they can change the phenotype of the individual. The most common allele in the population is referred to as the “wild type”, while the other alleles are mutations of this allele. There is the presence of the different alleles in various frequencies because of natural selection and because of genetic drift. The wild type may not be the fittest allele and it may not be the oldest allele; it is simply the most common allele. Some mutations do not affect anything because there are sometimes multiple codons that code for the same amino acid. These are referred to as synonymous mutations. Others will be conservative mutations because they change the amino acid but not the specific function of the protein. Mutations that are lethal or deleterious will be selectively removed from the population (through natural selection). Some genetic diseases can be specifically due to mutations that occur in an individual or can be inherited from the individual’s parents—provided that the parents have a reasonable chance of procreating despite their mutation. A few mutations are considered beneficial to the organism, in which case it may affect the ability of the organism to thrive in the environment.

GENOME The genome is the total amount of genetic material in an organism—including coding and non-coding segments. The size of the genome differs greatly from organism to organism. The smallest genomes are in viruses, while the largest genomes are in plants.

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According to the Human Genome Project, the total number of protein-coding genes is about 20,000 with about 13 genes encoded in the mitochondrial genome. Only about 12 percent of the entire genome consists of protein-coding genes, with the rest being introns, noncoding RNAs, and things called retrotransposons. Essential genes are believed to be critical for the survival of the organism. This number is small in bacteria and represents only about 250-400 genes—less than 10 percent of existing genes. Most are involved in protein synthesis. Humans are believed to have 2000 essential genes. A synthetic organism has been created that has a minimal genome, consisting of about 473 essential genes in the organism. Essential genes are used for basic cell functions and for the life cycle of the organism. Most proteins come from transcribed messenger RNA. Some genes are called RNA genes because the genes’ end products are the actual RNA molecules. These include transfer RNA and ribosomal RNA. Some RNA molecules are referred to as ribozymes, which are actually capable of enzymatic functionality, while microRNA is made to serve as regulatory molecules. The genes that make these products are called non-coding RNA genes.

REGULATION OF GENE EXPRESSION Gene regulation is the process of controlling which genes get expressed at different times. Not all genes can be expressed in the different cells of the organism, even though all cells have the same copy of DNA. The different set of genes that get expressed determines what properties the cell has. There are many different regulatory steps in gene regulation—most of them affiliated with the transcription of genes. The cell will regulate its gene expression depending on what it perceives are the external environmental factors. These include the temperature, environmental stresses, and available nutrients. Internal signals, such as whether or not the cell is infected and metabolic needs, will also determine gene expression. Gene expression can happen in transcription (most common), in RNA processing, in translation, and in posttranslational modification.

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Gene regulation determines what the cell does and what it looks like. Cells that need a certain protein or enzyme will have the gene for that enzyme turned on at some point. Cells that will never need a protein turned on will have that segment of DNA blocked from transcribing. There can be growth factors that bind to cell receptors after being created because of internal factors or because a receptor turns on their production. The growth factor triggers a set of transcription factors to get made that will activate a promotor region in the DNA molecule so that the gene gets turned on. In reality, genes can be regulated at multiple levels so that the numbers and quality of proteins made by the cell can change according to need. As mentioned, transcription is the most common way that genes get regulated. The different ways that genes can be regulated include the following: •

Chromatin accessibility—the chromatin can be tightly wound or can be more relaxed in order to make the genes more available for transcription.

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Transcription—the most common regulatory mechanism, in which transcriptional factors bind to DNA sequences that will promote or repress the DNA’s transcription.

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RNA processing—this is the processing that happens to RNA causing it to be allowed or not allowed to leave the nucleus for translation. The same pre-mRNA can result in a different messenger RNA molecule, depending on how it’s spliced.

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mRNA stability—messenger RNA can be broken down quickly or stay stable for long periods of time, depending on factors inside the cytosol. MicroRNA can bind to mRNA, causing it to be chopped up rather than used.

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Translation—there may be more or less of the ability to translate into a polypeptide.

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Protein processing—there can be changes in post-translational modification so that the protein can be used (or not used) in a specific way.

Interestingly, DNA can be regulated between species. While humans share 98.8 percent of DNA within chimpanzees, there are great differences in phenotype. Besides these similarities and differences, genes that are identical between primates and humans can 121

cause species’ differences because they regulate the numbers and types of genes that get expressed between the different species.

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KEY TAKEAWAYS •

Mendelian genetics looks at how genes get independently sorted and at the difference between dominant and recessive genes.

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The most common genes are either autosomal recessive, autosomal dominant, or x-linked dominant.

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The basis of genetics in most organisms is DNA and the genes contained within the DNA.

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Genes are regulated at multiple levels but particularly at the level of transcription.

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QUIZ 1. In the Punnett square analysis of two parents that each have a dominant (T) allele and recessive (t) allele: what is the ratio of dominant to recessive phenotypes of offspring having the trait? a. 1:2 b. 3:1 c. 1:3 d. 1:2 Answer: b. The ratio of dominant to recessive traits is 3:1 when using the Punnett square with three times as many dominant traits as recessive traits seen in the offspring. 2. In the Punnett square analysis of two parents that have a dominant T allele and a recessive t allele, what is the ratio of homozygous dominant to homozygous recessive genotypes in the offspring? a. 1:1 b. 3:1 c. 1:3 d. 1:2 Answer: a. The ratio of homozygous dominant and homozygous recessive traits is 1:1 with the entire ratio of all genotypes being 1:2:1, with the ratio representing homozygous dominant: 2 heterozygous: homozygous recessive. 3. What is it called when a trait is equally expressed in the offspring of the male and female animal? a. Autosomal dominant b. Codominance c. X-linked recessive d. Autosomal recessive

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Answer: b. Codominance involves the equal expression in the offspring of alleles because an allele for the trait is neither dominant nor recessive but is considered codominant. 4. The parent who is homozygous for a dominant trait will pass the trait onto what percentage of their children on average? a. 25 percent b. 50 percent c. 75 percent d. 100 percent Answer: d. A total of 100 percent of the children of a parent with a homozygous dominant trait will get the trait. This is because they have no other allele to pass on to their offspring other than a dominant trait. 5. What type of chemical bond connects the sugar backbone in the DNA molecule? a. Hydrogen bond b. Phosphodiester bond c. Hydroxyl bond d. Ester bond Answer: b. There is a phosphodiester bond that links the sugars forming a sugar-phosphate-sugar bond between the 5-prime and the 3prime end of the adjoining deoxyribose sugars. 6. What aspect of chromatin most allows for the tight packaging of DNA into their tightly-wound structures? a. Hydrogen bonding b. Double helix c. Histone proteins d. Chromosomes Answer: c. While chromatin uses each of these features to shrink the size of the DNA molecule so it fits inside the cell nucleus, it is the

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histone proteins that most allow for the folding and coiling of the DNA into the structure called chromatin. 7. Where in the cell does RNA polymerase function? a. Ribosome b. Cytoplasm c. Endoplasmic reticulum d. Nucleus Answer: d. RNA polymerase creates new RNA molecules from a DNA template gene. It operates in the nucleus where the DNA is located. 8. In prokaryotes, the genes are often located in operons. What is an operon? a. A piece of DNA that codes for several proteins b. Areas of noncoding DNA c. Areas of regulatory genes along with introns d. Areas of DNA that code for pre-messenger RNA Answer: a. An operon is a piece of DNA in prokaryotes that codes for several, often related, proteins. 9. About how many protein-coding genes are there in the human genome? a. 2000 b. 6000 c. 20,000 d. 200,000 Answer: c. There are about 20,000 coding genes in the human genome, which represents about 1-2 percent of the total genome.

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10. Where does most gene expression happen? a. Post-translational modification b. Regulation of messenger RNA substance c. Translational stage of protein synthesis d. Transcription of DNA Answer: d. Most gene expression happens at the transcriptional level, changing which genes get transcribed to RNA and which genes do not get transcribed.

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CHAPTER 7: EVOLUTION The focus of this chapter is the evolutionary process, whereby individual species and populations gradually change over time because of the natural selection of the species that have inherited advantages over other species. Much of this involves Darwinian evolutionary principles, which is covered in this chapter. The history of evolution on earth and the origin of species has been largely uncovered and these are important topics of discussion in this chapter.

DARWINIAN EVOLUTION In this section, we will talk about Darwinism or Darwinian evolution, even though there were evolutionary theories before and after Charles Darwin, the naturalist who developed the theories. This is because, for many years, this was the theory that was followed by scientists for more than a century and because the theories have validity in the study of evolution. His theories first came to light in a book he wrote after studying birds and other animals called “On the Origin of Species”. The theories predated the work of Gregor Mendel so they do not include more modern theories of heredity and, of course, they do not include the vast amount of information that has come to light since then, such as the presence of genetic drift, which is the variation in the relative frequency of different genotypes in small populations, because of the chance disappearance of particular genes as organisms die or do not reproduce. The four basic ideas of evolution created by Charles Darwin include these: •

There are more individuals produced in a population each generation than can survive.

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There is phenotypic variation among individuals in a population, which is heritable.

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Those individuals with traits that are better suited to the environment will survive.

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•

In reproduction isolation, there will be the emergence of new species.

The basis for Darwin’s evolution was that all organisms can trace their descent to a common ancestor and that, because of natural selection, there becomes a diversity of species. Natural selection proposes that the heritable traits developed by a generation will vary and that some of the traits confer a natural advantage that allows some variations to have a reproductive advantage, perpetuating those particular variations in later descendants, leading to changes in the population. Many of Darwin’s theories came from the study of finches on the Galapagos Islands. He noted specific variations in the bird species, so that those that had certain types of beaks ate seeds and those that had other types of beaks ate insects. He argued that, through natural selection, changes in beak types were self-selected so that there was a reproductive advantage to certain birds in situations of limited resources. Divergences happened, he said, so that more resources (seeds and insects both) could be utilized by the different variations in the species. The Galapagos Island is an isolated island off of Ecuador, containing species similar to those in the mainland but isolated enough that they needed to adapt to local conditions over long periods of time and over multiple generations. The process of the development of new species led to the formation of more than one distinct species of animals, including birds. Darwin proposed that there can be changes of species over time, that new species can originate from pre-existing species, and that there must be a common ancestor to all species. He believed that the diversity of species is because of the inheritance over time of traits that diverged from the ancestor species. He referred to the change in heritable traits over many generations as “descent with modification”. This is now what we call evolution.

NATURAL SELECTION One of the key aspects of Darwin’s theories was that of “natural selection”. It explains how populations evolve over time in certain ways that allow the population to be better suited to their environment over the generations. It is based on the idea that traits are 129

heritable and are passed from parent to child. It is also based on the theory that more offspring are created than can survive and that can be supported by the environment. This leads to competition for limited resources in the environment. In addition, the offspring will have differences in their heritable traits (and will appear different). Some individuals in a population will have inherited traits that help them live and reproduce to a better degree than those with other traits. These better-adapted organisms will have more offspring than those that are less adapted to the environment. In other words, the trait must confer a reproductive advantage. This leads to an increase in the numbers of individuals who are better adapted to the environment. The concept of natural selection isn’t random. The traits that get inherited are not in some way inherently superior to other traits. Instead, these traits are beneficial in relation to the environment. In other words, in rat species, for example, black rats stick out more than tan rats if the rocks they live on are tan. This means that more black rats get eaten by hawks so that tan rats survive better to reproduce. The reverse would be true if the rocks were black. The traits need to be something that is heritable in the genes of the organism rather than something that develops over the lifetime of the organism. If a bird species gets smarter at collecting food over time and survive to reproduce, this may not be inherited by the next generation—unless bird intelligence itself is inherited and gets passed on as a heritable trait. Finally, the origin of these gene variations is that of mutations that are basically random and that are passed onto offspring through sexual recombination. We all know that there are random variations in the act of meiosis that assure that the offspring are different from their parents. There will be mutations that lead to more different offspring than would typically be seen by meiosis and recombination alone. Natural selection is the cornerstone of biology today. It is different from artificial selection (which involves the selection of desired characteristics by breeders) in that it is random and depends almost entirely on the environment that the selection occurs in. There is genetic drift, which is completely random; however, most genotype and

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phenotype changes are not random and occur because the change confers an advantage in the environment the organism lives in. Interestingly, there have been natural selection theories predating Darwin. In fact, classical philosophers had expressed these ideas in limited form. Islamic theorists also proposed natural selection as the struggle for existence. Darwin’s grandfather (Erasmus Darwin) reintroduced these classical arguments in the 18th century. Jean-Baptiste Lamarck suggested that there were inherited characteristics that acted as a mechanism for evolutionary change. Eventually the inherited changes caused the development of new species. Darwin studied natural selection during his trip on the second voyage of the HMS Beagle between 1831 and 1836 but didn’t actually realize what he had discovered until he worked with an ornithologist who studied examples of the birds retrieved from the Galapagos Islands. In 1859, he came out with his book On the Origin of Species, which laid out the theories of natural selection. Darwin was inspired by the work of Thomas Malthus, who wrote an essay indicating that the food supply grows at a slower rate than the population that eats the food, leading to an inevitable shortage in the supply of food and the need to have adaptations that make some organisms more adaptable to the short food supply. As mentioned, there must be a reproductive advantage to the organism in order for natural selection to take place. It doesn’t have to be a large advantage but it has to be heritable so that the advantage can increase over successive populations. There is no intentional choice as there is in artificial selection, just an evolutionary advantage of one trait over another. The idea of fitness is important to natural selection. Organisms that are fitter have a better chance of survival, leading to the phrase “survival of the fittest”. Fitness is not just how long an organism lives but is more about how successful it is at reproducing. In other words, an organism can live a shorter period of time but, if it produces twice as many offspring that survive to reproduce themselves, it will be the fitter organism. It doesn’t necessarily mean there is an improvement in fitness but that it allows for the removal of those organisms that are less fit in the population.

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With competition, the fitness of one organism is lowered by the presence of another organism. This is because both organisms must share territory, water, food, or other resources. Competition may occur between organisms of the same species or between other species. Competition plays a significant role in natural selection because, without competition, there would be no need for natural selection in a species as all species would survive equally. There are three types of natural selection. The first is directional selection, in which a single “extreme” phenotype is favored over other species. The second is stabilizing selection, in which an intermediate species is favored over the extremes. The third is disruptive selection, there is more than one extreme favored over the intermediate organisms. Natural selection can act on any heritable phenotype with selective pressure produced by any aspect of the environment—including sexual selection and competition between those in the same or other species. Disruptive selection can be a precursor to the development of different species. Selection can be classified by the life cycle it acts on. There is viability or survival selection, which increases the organism’s probability of survival, as well as fecundity or fertility selection, which increases the rate of reproduction of the organism. Within fecundity selection, there can be factors that act on the survival of the gametes themselves and factors that act on the ability or inability to create a viable zygote. Other ways to classify natural selection include those at the level of the individual versus those at the level of the group. Selection, in other words, can mean that certain traits act on individual organisms that have or don’t have the advantage. The selection can also act on the group of organisms to change the entire group’s ability to survive. The later classification of group selection is probably less of a factor than individual selection. Natural selection has played a role in the development of antibiotic resistance among microorganisms. Since the discovery of antibiotics, bacteria have developed ways to become resistant to the antibiotics. This is borne out in the development of methicillinresistant Staphylococcus aureus (MRSA), which developed the ability to be resistant to antibiotics that typically they used to be susceptible to. Those that were susceptible to penicillin/methicillin died out, leaving behind mutated organisms that survived and

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multiplied. There are even MRSA strains that have become resistant to the antibiotics used to kill them as well—leading to even more resistant “superbugs” in the environment. This is also seen in insect populations that have become resistant to pesticides. Natural selection can only result in evolutionary changes if the new traits and new species coming out of it have differences in fitness that allow them to survive. Things like genetic recombination, changes in karyotype number, and changes in the size and arrangement in chromosomes may have an advantage or a disadvantage to the organism. Some genetic changes have no effect because there is synonymous substitution of a DNA base pair or because the change occurred in non-coding DNA. Most changes in regulatory genes in the DNA will be lethal to the embryo or will have a mutation that doesn’t affect survival.

MODERN SYNTHESIS IN EVOLUTION Evolutionary theory did not end with Darwin. Remember, he knew nothing of genetics and of the theories of Gregor Mendel and others that have come to understand the way genetics and evolution work. Darwin was successful in convincing most biologists since then that evolution actually occurred but wasn’t as successful in convincing scientists that natural selection was how evolution occurred. There were other theories, such as Lamarckism (inheritance of acquired characteristics), orthogenesis (the presence of progressive evolution), saltationism (evolution by jumps in speciation), and mutationism (evolution driven by mutations). Remember that Darwin believed in blending inheritance rather than gene-related inheritance. With blending inheritance, any new generation of changes in an organism would be diluted out by half with each successive generation. This negated the idea that blending actually took place. The other theory of Darwin, that of pangenesis, was wrong. This was the theory that gemmules were flowing from all parts of the reproductive body in order to create the gamete. Weismann argued the theory of germ plasm. He said that there were two aspects of an organism: germ plasm and the soma (or the rest of the body). Only the germ plasm

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determined what was inherited. This turned out, of course to be true. Germ plasm or reproductive cells influence the offspring. He proved his theory by cutting the tails off of mice and proving that the baby mice grew normal tails. In this way, the body or soma did not influence the offspring. Individuals who believed in Mendelian theory rejected the ideas of natural selection—a problem that was solved by researchers who studied and developed the ideas of population genetics. Evolutionary genetics applied genetics to natural populations. Over time, there have been many other additions to theories of evolution that add to the natural selection theories. The modern synthesis theory of evolution indicates that populations contain genetic variation that is random and is from random mutation and from recombination. Natural selection, gene flow, and random genetic drift produces population variances over time. Diversification into different species comes when there is reproductive isolation among populations that give rise to differences that ultimately become different species. The main differences between Darwinism and modern synthesis in evolution include these three things: •

In modern synthesis, there are several mechanisms in evolution besides natural selection, such as genetic drift.

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There are heritable units called genes (which did not exist in Darwin’s theories) with variations in a population occurring because of the numbers of different alleles in the population.

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Speciation usually happens due to the gradual accumulation of small genetic changes with macroevolution being microevolution over a long period of time.

The thing most controversial is the idea that gradual changes in genetic makeup cause speciation. This is because fossil records do not show gradual changes in organisms but a more rapid speciation occurring. This is called “punctuated equilibrium”, which is believed to be a fact that may or may not directly oppose the microevolution-tomacroevolution theory. In other words, both things may be in play at the same time.

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HISTORY OF EVOLUTION ON EARTH AND ORIGIN OF SPECIES There are many ways that the history of evolution on earth can be reconstructed. Much of it includes fossil evidence and carbon dating to indicate when things were present on earth. In addition, modern genetics can be used to estimate when a split occurred between different species. Earlier dates, however, remain mainly speculative as there is little genetic or fossil evidence as to when certain things occurred. What remains is a geological timescale of when things were likely to have occurred on earth as part of the history of evolution and origin of species. •

3.8 Billion years ago—this is the best guess available for the beginning of life on earth. It is believed that life first began with RNA species rather than DNA species. There was a common ancestor that gave rise to two main groups in life: bacteria and archaea as the first major split in living organisms.

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3.5 Billion years ago—this is when the oldest fossil records of single-celled organisms first derive from. Shortly after that (about 3.46 billion years ago) the first methanogens (methanogenic archaea organisms) began feeding on methane in the absence of oxygen at this time.

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3 Billion years ago—this is the first record of viruses, although some scientists believe they were first on earth from the time life first began.

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2.4 Billion years ago—this is when the waste product of photosynthetic cyanobacteria, oxygen, began to build up in what’s called the “great oxidation event”. This has been challenged with the idea that other bacteria were responsible for this oxidation event. There was a decline in methane-producing bacteria so that oxygen was allowed to build up about this time.

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2.3 Billion years ago—earth freezes over completely and later melts, leading to more oxygen being released into the atmosphere, further oxygenating the earth.

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2.15 Billion years ago—there is fossil evidence of photosynthesis from cyanobacteria, believed to be the first photosynthetic organisms. Some believe that this in fact happened earlier than this, during the great oxidation event.

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2 Billion years ago—this is believed to be when the first eukaryotic organisms developed. It is believed that it happened when a single cell engulfed a smaller cell in an example of endosymbiosis. Engulfed bacteria became mitochondria, providing energy to the cell. Later on, eukaryotic cells engulfed photosynthetic bacteria, which evolved to become chloroplasts in plant cells. This happened on at least three different occasions, resulting in organisms that became green algae and green plants.

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1.5 Billion years ago—this is roughly when the common ancestors that make up plants, fungi, and animals split into separate cell lines. No one knows which of these three separated themselves out first. Bacteria and archaea had already separated out and were on earth before the first eukaryotes occurred.

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900 Million years ago—this is believed to be when the first multicellular organisms appeared. It is believed the process was similar to the modern Choanoflagellates , which form colonies as part of their life cycle. It is otherwise unknown why there was a shift from unicellular to multicellular organisms.

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800 Million years ago—This is when the early multicellular animals split off from one another. The oldest animals to split off were the sponges. They split off from Eumetazoa (the oldest animal ancestor of all other animals besides sponges). A small group called placozoa broke off about 20 million years after that, which still survive as the oldest type of animal besides sponges.

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770 Million years ago—there was another ice age, and the earth was covered in frozen water.

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730 Million years ago—The comb jellies or ctenophores split off from other multicellular organisms. They relied on water flowing through body cavities to acquire nutrients and oxygen.

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680 Million years ago—the first ancestor of cnidarians (jellyfish and related animals) break away from the other animals.

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630 Million years ago—this is the first situation of bilateral symmetry with a caudal and cranial (head and tail) end. The closest surviving organism that has

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this feature is called Acoela. The earliest fossil record of a bilateral animal organism dates from this era and was a type of worm. •

590 Million years ago—the organisms called Bilateria, which are animals with bilateral symmetry, split into deuterostomes and protostomes. Deuterostomes split off to become all the vertebrate animals (plus Ambulacraria, an outlier group); protostomes split off to become all of the arthropods (crabs, shrimp, spiders, insects, etc.), certain worms, and rotifers (microscopic invertebrates). These are differentiated in many ways but, most specifically, by the way their embryos first develop, which is different between the two types.

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580 Million years ago—this is when the earliest fossils of cnidarians (sea anemones, jellyfish, and coral) have come from.

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575 Million years ago—the Ediacarans appear but disappear about 33 million years later. These were macroscopic soft-bodied organisms that had fern-like fronds. The period of time they existed in was called the Ediacaran period.

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570 Million years ago—this is when the Ambulacraria break off from deuterostomes, leading to starfish and their relatives as well as a couple of wormlike families (that aren’t actually worms as worms are not deuterostomes). The sea lily is thought to be the “missing link” between vertebrates and invertebrates and split off at this time. This means that vertebrates, like humans, are closer to starfish than they are to crabs and shellfish.

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565 Million years ago—this is when the first animal trail fossils were discovered to have come from and when animals are first believed to be moving under their own power.

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540 Million years ago—the first chordates (animals with a backbone) break off as well as the sea squirts, which have larvae that look like tadpoles that ultimately become bottom-dwelling filter feeders.

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535 Million years ago—this was when the Cambrian explosion was, with many different new types of fossilized bodies being seen. Some say that this is an

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artificial “explosion” because there just weren’t many fossils found prior to that era in evolution. •

530 Million years ago—this is when the first true vertebrate appears. A vertebrate is an animal with a backbone. It looked much like a hagfish or lamprey and evolved from a jawless fish. Trilobites were first seen at this time and lasted about 200 million years. Figure 32 shows what a trilobite looked like:

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520 Million years ago—this is when another possible “first vertebrate” appeared, called the Conodonts. These looked much like eels.

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500 Million years ago—this was when the first land animals existed. The first to do this were called euthycarcinoids, which are the missing link between insects and crustaceans. The oldest known ancestor of cephalopods existed at this time— the precursor of the squid.

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489 Million years ago—this was a great period of diversity called the Great Ordovician Biodiversification Event. Many new varieties of plants and animals started to appear at this time.

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465 Million years ago—this was when plants first began to occur on land.

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460 Million years ago—this was the major split between cartilaginous fish and bony fish. Cartilaginous fish include the sharks, skates, and rays, and are different from the bony fish, like tuna and other fish.

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440 Million years ago—this is a split that occurred between two types of bony fish into the lobe-finned fish and the ray-finned fish. Lobe-finned fish became reptiles, birds, amphibians, and mammals, while the ray-finned fish became the fish we know today.

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425 Million years ago—this is when the coelacanth splits off from lobe-finned fish and is what the modern-day coelacanth looks like today. These species haven’t changed for millions of years.

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417 Million years ago—this is when the lungfish split off from the other lobefinned fish, which are fish but have air-sacs that act as sophisticated lungs along with their gills. They can breathe in or out of water.

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400 Million years ago—this is when the first woody stems develop as well as the oldest known insect.

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397 Million years ago—Tetrapods develop at this time, which are the first four-legged animals. These give rise to all land and air animals.

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385 Million years ago—this is when the oldest fossilized tree first came from, although there had been plants on land for a period of time.

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375 Million years ago—this is when there was the Tiktaalik, which was an intermediary species between fish and four-legged animals. Fins of this animal develops into limbs.

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340 Million years ago—the first real tetrapod split occurred with amphibians branching off from the Tetrapods.

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310 Million years ago—The sauropsids and the synapsids break off from the tetrapods to make the dinosaurs, birds, and reptiles (among the sauropsids) and the synapsids (which become reptiles that had jaws, branching off to make mammals).

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320 to 250 Million years ago—this is when the Dimetrodons (a type of synapsid) were dominant on land. While these synapsids look much like dinosaurs, they are not of the same classification and are not dinosaurs.

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275 to 100 Million years ago—this is when the therapsids evolve alongside the pelycosaurs, with some of them, called cynodonts, having dog-like teeth becoming eventually the first mammals.

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250 Million years ago—this was the end of the Permian period and was a time of mass extinction, when trilobites were killed off. The sauropsids become dominant over the synapsids in the age of the dinosaurs. Mammals still existed but they were small and relatively nocturnal. The modern-day octopus developed at this time as well as the large marine reptiles in the oceans of the world.

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210 Million years ago—this is when the first bird footprints came from, suggesting that some early dinosaurs were developing into birds during this time.

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200 Million years ago—this is the end of the Triassic period, when there is another mass extinction. Dinosaurs dominate the earth after this time. The first warm-blooded animals evolved by this time.

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180 Million years ago—there is the first split in the mammal population to have a group of mammals that lay eggs instead of bearing young. These monotremes gave rise to the duck-billed platypus (which lays eggs as a monotreme).

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168 Million years ago—there is fossil evidence of a flightless, half-feathered dinosaur in China, which may be the first step toward the dinosaur evolution into birds. At 150 million years ago, the Archaeopteryx lived in Europe as the first known bird there.

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140 Million years ago—there was a split between placental mammals and marsupials like kangaroos. They did not originate in Australia but came from South-East Asia to North America, South America, and finally Antarctica and Australia.

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130 Million years ago—the first flowering plants came to be on earth. 140

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105 to 85 Million years ago—there was a major split among placental animals into four different groups: 1) Laurasiatherians (hoofed mammals, whales, bats, and dogs), 2) Euarchontoglirians (primates, rodents), 3) Xenarthra (anteaters and armadillos), and 4) Afrotheres (Elephants and aardvarks).

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100 Million years ago—this is when dinosaurs reached their largest size on earth, including the giant sauropod, the Argentinosaurus.

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93 Million years ago—there is a starvation of oxygen within the oceans during this time, possibly because of a volcanic eruption, wiping out more than a fourth of all marine invertebrates.

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75 Million years ago—this is when the ancestors of modern primates split off from rodents and rabbits. Rodents ultimately go on to represent 40 percent of modern mammal species.

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70 Million years ago—this is when the first grasses evolve but they do not become prominent for several million years.

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65 Million years ago—this is when the infamous Cretaceous-Tertiary (K/T) extinction occurred, wiping out the dinosaurs and related reptiles. This goes on to pave the way for mammals to dominate the earth.

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63 Million years ago—this is when primates split into dry-nosed primates and wet-nosed primates. The wet-nosed primates evolved to become lemurs, while the dry-nosed primates became monkeys, apes, and humans.

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58 Million years ago—the tarsier splits from the rest of the dry-nosed primates. It had very large eyes in order to see better at night.

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55 million years ago—there is a sudden rise in greenhouse gases that raise the temperature of the earth, wiping out many species in the deeper oceans; this was called the Paleocene/Eocene extinction.

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50 Million years ago—this is when the Artiodactyls, a cross between a wolf and a tapir, begin evolving into whales.

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47 Million years ago—this is when early whales called protocetids live in shallow seas and go to land in order to give birth.

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40 Million years ago—This is when higher primates diverge from the rest of the primates to colonize South America.

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25 Million years ago—this is when apes split off from Old World monkeys. Around 18 million years ago, gibbons split off; around 14 million years, orangutans split off from other great apes to live in Asia; about 7 million years ago, gorillas split off from the other great apes.

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6 Million years ago—the first humans diverge from their closest relatives: the chimpanzees and the bonobos. It is shortly after this that man becomes a twolegged walker.

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KEY TAKEAWAYS •

Darwin studied finches in the early 1800s and published his findings in the 1859 work entitled: On the Origin of Species.

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Darwin did not know about genes and heredity at the time but believed that natural selection is what created the different species.

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It is now believed that multiple things lead to evolution, including genetic drift, mutations, and natural selection.

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The first forms of life on earth started around 3.8 billion years ago.

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The first split in evolution came when bacteria and archaea evolved from a common ancestor.

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About 1.8 billion years ago, the first animals, plants, and fungi split off from a common ancestor.

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Humans came on the scene about 6 million years ago.

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QUIZ 1. What did Darwin mainly study in developing his theories of evolution? a. Turtles b. Apes c. Fish d. Birds Answer: d. Darwin studied differences in finch populations that conferred reproductive advantages to different types of finches by virtue of differences in the shapes of their beaks, allowing those that could eat certain things to survive and reproduce. 2. What is the greatest fact that must take place before a trait can be increased in a population of animals, allowing for evolutionary changes in a population? a. The trait must change during the individual’s lifetime. b. The trait must offer a reproductive advantage to the animal. c. The trait must be heritable. d. The trait must change the feeding characteristics of the animal. Answer: b. Regardless of the trait, it must offer some type of reproductive advantage so that the species is able to reproduce more readily than organisms that do not have the trait. This is the only way that the trait can grow and perpetuate over time and over subsequent generations. 3. What antibiotic has become much less useful over the years because of resistant microorganisms like MRSA? a. Penicillin b. Tetracycline c. Vancomycin d. Mupirocin

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Answer: a. MRSA has led to marked resistances of organisms to penicillin, so that it has become much less effective in the treatment of many bacterial infections. 4. What is true of most large mutations in DNA that occur in an organism’s offspring? a. They offer a neutral advantage to the offspring. b. They offer a slight disadvantage to the offspring. c. They decrease the reproductive rate of the offspring. d. They are lethal to the offspring. Answer: d. Most large mutations in DNA are lethal to the offspring; some will be neutral; and very few will be either advantageous or disadvantageous to the offspring. 5. After the first common ancestor began on earth, what organisms involved the first split that occurred in species on earth? a. Archaea and bacteria b. Bacteria and viruses c. Bacteria and fungi d. Archaea and viruses Answer: a. The first major split occurred between archaea and bacteria about 3.8 billion years ago, shortly after life first began on earth. These represent two of the major domains on earth. 6. About when did the great oxidation event occur in order to allow oxygen to build up in earth’s atmosphere as a waste product of photosynthetic bacterial metabolism? a. 3.8 billion years ago b. 3.1 billion years ago c. 2.4 billion years ago d. 1.4 billion years ago

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Answer: c. At about 2.4 billion years ago, there were bacteria (possibly cyanobacteria) that started giving off enough oxygen as a waste product in order to have oxygenation of the earth and oxidation of iron. 7. How did the first multicellular animals first get oxygen and nutrients? a. Diffusion b. Hollow bodies c. Primitive circulatory systems d. Photosynthetic parasites Answer: b. The first multicellular organisms first get oxygen and nutrients by having hollow bodies through which water and nutrients flow to provide these things to the rest of the organism. 8. What type of animal was the first bilateral animal on earth as part of evolution? a. Insect b. Fish c. Jellyfish d. Worm Answer: d. The first bilateral organism among animals was a type of worm, of which at least one related species survives to this day. 9. Which organism are mammals least related to evolutionarily-speaking? a. Reptiles b. Amphibians c. Birds d. Fish Answer: d. Mammals belong to the “lobe-finned fish category” versus the “ray-finned fish category”, which are what the modern-day fish come from.

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10. Which animal came along first from an evolutionary standpoint? a. Lungfish b. Tiktaalik c. Amphibians d. Birds Answer: a. Lungfish came first and have the ability to thrive on land during drought periods or in water. They were first seen around 417 million years ago.

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CHAPTER 8: BIOLOGICAL DIVERSITY This chapter covers the main divisions in nature and living things, outlining the six major kingdoms and their subdivisions. The way that biological species are defined is discussed in this chapter. The major features of each kingdom and how kingdoms and their subdivisions are determined are important topics of this chapter. Because archaea and Protista haven’t yet been covered, they are also discussed in separate sections.

THE THREE DOMAINS Historically, there was just two domains (bacteria and eukaryotes) and five kingdoms. As there has been more research, however, there are now three domains: Archaea, Bacteria, and Eukarya. This has been developed out of research studies on ribosomal DNA, which is different for the three domains. As you will see, there are now six kingdoms under this classification. Figure 33 shows the hierarchy of taxonomy in identifying organisms:

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The system of taxonomy, as you can see, goes from domain to kingdom to phylum to subphylum to class to order to family to genus to species. When we talk about Homo sapiens (humans) or Escherichia coli (a type of bacterium, we are using just the genus and species to define the organism.

ARCHAEA DOMAIN This is the latest domain to be identified. They are all single-celled organisms and look similar to bacteria, having genes that relate both to eukaryotes and bacteria. These are similar to bacteria in other ways, such as the fact that they are prokaryotes like bacteria, lacking any organelles. They have a circular chromosome and flagella, reproducing by binary fission. Their cell wall is different from bacteria; they have different cell membranes; and they have unique ribosomal RNA types. These features are different enough to warrant a new domain. Archaea are considered extreme organisms, living under extreme environmental conditions. There are three established phyla in this domain (although several others have been proposed): •

Crenarchaeota—these are the hyperthermophiles and thermoacidophiles, living in hot or hot and acidic environments.

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Euryarchaeota—these are the methanogens that produce methane as a byproduct of metabolism in an oxygen-free environment.

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Korarchaeota—this is the least-known species of archaea, with organisms found in hydrothermal vents, obsidian pools, and hot springs.

As mentioned, there are several other proposed phyla, including Nanoarchaeota and Micrarchaeota.

BACTERIA DOMAIN Bacteria have been studied in an earlier chapter. These are prokaryotic organisms that have their own peptidoglycan cell wall and ribosomal RNA type. There are five main categories or phyla of bacteria, including the following: 149

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Proteobacteria—this is the largest group, accounting for those bacteria like Salmonella, Vibrio species, Helicobacter pylori, Escherichia coli, and other bacteria.

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Cyanobacteria—these are photosynthetic bacteria, known for their blue-green color.

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Firmicutes—these are gram-positive bacteria including Bacillus species, Clostridium species, and mycoplasma.

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Chlamydiae—these are parasitic bacteria that reproduce inside their host’s cells and include Chlamydia trachomatis and Chlamydophila pneumoniae, both of which are pathogens in humans.

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Spirochetes—these are corkscrew-shaped bacteria that will twist when moving. Examples of these include Borrelia burgdorferi and Treponema pallidum, both of which are pathogens in humans.

EUKARYA DOMAIN These include organisms that have nuclei and organelles. They are divided into four kingdoms: Protista, Plantae, Fungi, and Animalia. The ribosomal RNA is different from the other domains. Plant and fungi contain cell walls that are different from that of archaea and bacteria. Most plants and animals that one thinks of and multicellular organisms come from this domain.

THE SIX KINGDOMS Just beneath domains in the taxonomy classifications of life are the kingdoms. The six kingdoms have been divided according to the type of cell (prokaryote and eukaryote), cell wall characteristics, ribosomal RNA, reproduction, and nutrient acquisition. When it comes to nutrient acquisition, there can be ingestion, absorption or photosynthesis. Types of reproduction include sexual reproduction and asexual reproduction. Let’s take a look at the six kingdoms:

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Archaebacteria—this is the kingdom of the prokaryotic archaea. Their ribosomal RNA type is unique to them and they tend to live in extreme conditions. The ones closest to humans include the methanogenic species seen in the GI tracts of animals, including humans. Other organisms (some of whom we’ve talked about) include methanogens, thermophiles, halophiles, and psychrophiles. These are prokaryotes that need a variety of things for metabolism, including possibly oxygen, carbon dioxide, sulfide, and hydrogen. They take up nutrients via chemosynthesis, absorption, and non-photosynthetic photophosphorylation. They divide by budding, fragmentation, or asexual reproduction.

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Eubacteria—these are the true bacteria under the Bacteria domain. Most, surprisingly, do not cause disease, which means they are nonpathogenic. They reproduce by binary fission, meaning their growth can be exponential in situations of plenty of nutrients. As you know, they have a variety of shapes, including rod-shaped, round, comma-shaped, and spiral. These include actinobacteria, cyanobacteria (also called blue-green algae), and true bacteria. They are prokaryotic and may or may not require oxygen for metabolism. They can gain nutrients through chemosynthesis, photosynthesis, or simple absorption.

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Protista—these include many different organisms, including those that have characteristics of fungi, plants, and animals. These are eukaryotic, meaning they have a nucleus and enclosed organelles. Some have chloroplasts, while others have mitochondria. Some are pathogenic and parasitic, while others are mutualistic or commensal to a host. Organisms that are in this category include green algae, amoeba, diatoms, slime molds, brown algae, and euglena. They require oxygen necessary for metabolism. Nutrients can be acquired through ingestion, photosynthesis, and absorption. They can reproduce via meiosis but most undergo asexual reproduction.

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Fungi—this kingdom includes unicellular and multicellular organisms. These do not undergo photosynthesis but tend to “recycle” nutrients back into the

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environment by decomposing organic matter. Some of these are toxic to humans but are responsible for making many kinds of antibiotics. These are eukaryotic cells and include yeasts, mushrooms, and molds. Oxygen is necessary for metabolism. They get nutrients via absorption and will undergo sexual or asexual reproduction through spore formation. •

Plantae—these are the part of the life cycle that undergoes photosynthesis and include many different species, including seed-bearing plants and non-seedbearing plants, flowering and nonflowering plants, and vascular and nonvascular plants. We will talk more about plants in a subsequent chapter.

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Animalia—this is the animal kingdom. They are eukaryotic and, while most are aquatic, there are many land animals. They depend on plants and other animals for nutrition. Most will reproduce via sexual reproduction, which involves male and female gametes that are fertilized. Fish, insects, mammals, amphibians, sponges, and worms belong to this category. All require oxygen for metabolism. They acquire nutrients via ingestion. A few will undergo asexual reproduction as part of their life cycle.

ARCHAEA In this section, we’ll talk about archaea as a domain because it hasn’t been discussed before. These are prokaryotic microbes that have no cell nucleus. Previously considered bacteria, they will have different ribosomal RNA and other different features that make them unique among species. There is just one kingdom, called the Archaebacteria and multiple phyla. As you will see, they share genes similar to eukaryotes as well, particularly those involved in the enzymatic control of transcription and translation. While considered extreme organisms, they are also found in more traditional environments, such as marshlands, soil, oceans, and in the human mouth, on the human skin, and in the gut. There are many archaea species in the oceans, where they play a role in the nitrogen cycle and the carbon cycle. They can be commensals or mutualists but tend not to be pathogenic. There are several phyla that have been proposed as already mentioned. The Euryarchaeota and Crenarchaeota are well-known

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and understood, while several others (such as Korarchaeota, Parvarchaeota, and Micrarchaeota) have been proposed and are less understood. There is a lot of horizontal gene transfer between organisms, making the classification of species difficult. In addition, some argue there aren’t many practical reasons to separate out many of these species, with the subcategory of phyla being more practical. As mentioned in the last chapter, life began on earth about 3.8 billion years ago with the identification of biogenic rocks that date from about 3.7 billion years ago. It is possible that a thermophile that was neither an archaea organism or a bacterial organism was the common ancestor to bacteria and archaea species. Archaea have ether-linked lipids, which differ from the ester-linked lipids in bacteria and eukaryotes. Their cell membranes are made of pseudopeptidoglycan rather than peptidoglycan (in bacterial species). Their chromosomes are circular like bacteria but have transcription and translation enzymes like the eukaryotes. There are no membrane-bound organelles. They have various metabolisms, with methanogenesis being unique to the domain. They reproduce both asexually and through horizontal gene transfer, similar to bacteria. While Archaea as a domain appear more similar to Bacteria, they are actually closer biochemically to Eukarya because of shared translation and transcription protein systems and because of other biochemical similarities. Recent research suggests that Bacteria probably came first and then Archaea, followed later by Eukarya. As mentioned, their cell membranes are unique, having ether linkages in the cell membranes, making them more stable than that of Bacteria and Eukarya. This is probably why they survive better in extreme environments when other organisms do not survive. Archaea can be less than 0.1 micrometers in diameter or over 15 micrometers in diameter, with different shapes, such as spherical, rod-shaped, spiral, or plate-shaped. Even needle-shaped and irregular lobe-shaped archaea can be seen, as well as rectangular rod-shaped organisms. Their cytoskeleton and cell walls help to acquire these unique shapes. Some will aggregate or will form filaments, seen also in biofilms. There is a Thermococcus species that fuses together to form single “giant” cells. Another

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genus called Pyrodictium form long, hollow tubes, known as cannulae, forming a bushshaped group of organisms. Almost all of these archaea species will have a cell wall. The cell walls do not consist of peptidoglycan like bacteria but consist of pseudopeptidoglycan, which has its own chemical structure but looks somewhat like bacterial cell walls. These organisms will often have flagellae that act similar to bacteria with their action powered by a proton gradient, just like in bacteria. The composition of the flagella is different than is seen in bacteria. Rather than having a hollow flagellum seen in bacteria, the flagellum is made by adding protein subunits to the base. As mentioned, the cell membranes of archaea are unique. Remember that phospholipids have a hydrophobic and a hydrophilic end. In most organisms, these are seen as a lipid bilayer, with two lipid sheets connected to one another by the fact that the hydrophobic cores are not separable. The four main ways that the lipid membranes of archaea are unique include the following: •

Ether lipid bonds at the hydrophilic, glycerol end. This makes the bond more stable than in bacteria and eukaryotes.

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The glycerol end is the mirror image of that seen in other organisms. This means they have different enzymes making their cell membrane.

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The lipid tails are different than other organisms with multiple side-branches not seen in other organisms, making them less leaky during high temperatures.

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In some archaea, this membrane is not a lipid bilayer but a lipid monolayer with two polar ends and a hydrophobic interior.

The metabolism of archaea as a domain is somewhat unique to these organisms. Some will be chemotrophs, getting energy from sulfur and ammonia compounds. These include anaerobic methane oxidizing organisms, methanogens, and nitrification organisms. The energy released from these compounds will make ATP energy via the process of chemiosmosis—very similar to that seen in the mitochondria of eukaryotic cells.

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There are also phototrophs that use the sun’s light for fixation of carbon, which is not true photosynthesis because they do not make oxygen. These include the Halobacterium species. There are lithotrophs (that gain energy from inorganic compounds) and organotrophs (that gain energy from organic compounds). As mentioned, there are methanogens that make methane gas, which is believed to be one of the earliest forms of metabolism. Acetotrophs are archaea that take acetic acid and break it down into methane gas and carbon dioxide. Others will use CO2 from the atmosphere to fix carbon, using a type of Calvin cycle or reverse Krebs cycle. As for genetics, they have a circular chromosome like bacteria as well as plasmids, which are of course, independent from the main chromosome. Plasmids can be passed from one organism to another in a process like bacterial conjugation. They have the ability to become infected by dsDNA viruses that have specific and unusual shapes. Up to 15 percent of the proteins on the archaea genome are unique to this domain, such as those that participate in methanogenesis. While the RNA polymerase molecule is unique to the domain, the way that transcription and translation happens is very close to what happens in eukaryotes. Archaea can reproduce via binary fission, multiple fission, fragmentation, or budding. They do not participate in mitosis or meiosis. The cell cycle is related to both bacterial and eukaryotic cell cycles. Unlike bacteria, however, they have multiple origins of replication using DNA polymerases that are very similar to that seen in eukaryotes. While eukaryotes and bacteria will make spores, this is not true of the archaea. Certain of the Haloarchaea species will switch cell shapes in order to survive in low salt concentrations, these do not represent reproductive structures like spores are. About 20 percent of the microbes in the ocean are archaea. While the first ones known to man were extremophiles, living in very high temperatures, very low temperatures, and in different chemical environments, they are also “mesophiles”, meaning they live in moderate conditions, such as marshland, oceans, intestinal tracts, soils, and sewage. The four main extremophiles are thermophiles, acidophiles, alkaliphiles, and halophiles. Some species of archaea belong to more than one group and the organisms of the same phylum do not necessarily share the same extreme environments. There are also

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hyperthermophiles that live in extremely hot environments above 176 degrees Fahrenheit. There is even a strain that can reproduce above the boiling temperature of water. There is a strain called Picrophilus torridus that can grow at the remarkable pH of 0. There is speculation that, in extreme outer space environments, these microbes might be the only form of life that is possible. They reside in high enough concentrations in the ocean to affect the ecology of the ocean; however, as many of these are just being discovered, it is no known how they play a role. They may partly play a role in the nitrogen cycle of the ocean by virtue of being able to undergo nitrification.

PROTISTA Protista is a kingdom among the eukaryotes that has not yet been discussed in this course. This is a heterogeneous group that consists mostly of unicellular or simple multicellular forms. There are many different types of organisms in this kingdom, including algae, protozoa, molds, and slime. They will have both sexual and asexual reproduction and can be sessile (nonmotile) or can move via cilia, pseudopodia, or flagella. The different subdivisions include diatoms, brown algae, green algae, slime molds, amoebas, flagellates, ciliates, foraminiferans, radiolarians, heliozoans, and apicomplexans (sporozoans). Many ingest food rather than synthesize food as is seen in plants. The major classifications depend on their methods of locomotion. Figure 34 shows some of the different types of Protista:

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Amoebas have pseudopodia as their major means of transportation. These are used for both feeding and for locomotion, giving them their characteristic irregular shape (although there are shelled forms of these organisms). They reproduce solely asexually but do not have regular mitosis like other eukaryotes. The pseudopodia move via the coordinated action of microfilaments that push out the cell membrane; they do not have cell walls. There may be many pseudopodia at once, depending on the circumstances. Amoebas have a two-part cytoplasm. There is an inner endoplasm, which is granular, and an outer ectoplasm, which is clear. The nucleus contains most of the cell’s DNA and there are contractile vacuoles that excrete water in order to maintain a proper osmotic equilibrium within the cell. They use phagocytosis to get food, by sending out pseudopodia to engulf the food. They also participate in pinocytosis or cell-drinking. The foraminiferans are related to the amoeba but form a calcareous shell around themselves. These are marine animals that do not engage in motility and live on the ocean bottom. They die off, leaving behind a shell that forms an ooze that will become sedimentary rocks. Foraminifera are members of a phylum that includes amoeba. Figure 35 shows the different shapes of these organisms:

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The tests consist of different shapes and materials of shells. There are chitin tests and tests consisting of calcium carbonate. Most of these organisms reside in the ocean, although a few are found in soil or other aquatic environments. Most are microscopic, although there are very large species that are as large as 20 centimeters in diameter. There are 10,000 living species of foraminifera and four times that many existing in fossil form. The radiolarians or Radiolaria or Radiozoa are radially symmetrical organisms that secrete spherical skeletons made from silicates. They are unicellular organisms that reside in aquatic environments. Figure 36 shows a picture of the radiolarian species:

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These radiolarians are small protozoa that have a central capsule that divides the cell into its inner and outer endoplasm and ectoplasm. They are part of the zooplankton seen in the ocean, their skeletons forming an ooze on the bottom of the ocean floor that ultimately forms rock. They have multiple thin pseudopods supported by microtubular bundles that help the organism be buoyant. Many have engulfed symbiotic algae that provide the energy for the organism. Aside from the shell, they are related to the amoeba and Foraminifera. Within their group, there are many organisms that have different structural features. Flagellates (the singular of which is flagellate) are unicellular organisms that have at least one flagellum. The flagella are made from a characteristic “nine plus two” arrangement, which is nine fused pairs of microtubules surrounded by two central singlets of microtubules. They arise from a basal body at the edge of the organism. Some will have a cytostome, which is another term for mouth, in which food is taken in. The structure of the flagella will determine the classification of the organism. The Euglena is a type of flagellate that uses the flagella for locomotion. There is one facing forward and one that faces backward. Figure 37 shows what a euglena looks like:

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It is believed that flagellates are a primitive classification of organisms believed to have evolutionarily given rise to all other protozoans, fungi, higher plants, and even animals. Most are commensal organisms that live within the body structures of other organisms. They can have sexual or asexual reproductive capabilities. The trypanosomes, for the most part, live commensally within a host organism and are known for a complex life cycle. The genus of these organisms is called Trypanosoma, which is a type of parasitic flagellated protozoan. They often require more than one obligate host to complete their life cycle, many having some type of vector to transmit disease to higher animals and humans. In humans, they are responsible for African sleeping sickness and Chagas disease—both tropical diseases. Figure 38 shows the life cycle of the organism that causes Chagas disease:

Ciliates are the type of Protista that includes the paramecium. This is an oblong organism with numerous cilia covering the organism. They range in size from 50 to 330 micrometers in length and are oblong in shape. There is an elastic membrane called a pellicle and multiple cilia around the organism that act in movement of the organism in a single direction. There is an area that is called the oral groove that is responsible for “eating” and an area called the cytoproct that is an “anal pore”, where excretion occurs.

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Paramecium feeds on bacteria and on many small organisms, with some types having chlorella that are responsible for creating some nutrients. Like other similar organisms, they have contractile vacuoles that contain water that release the water into the cell to combat osmotic changes in the environment. These organisms have an avoidance reaction, in which the cilia beat backward in order to avoid a barrier before restarting in a different direction to move out of the way of the barrier.

THE DIFFERENT ANIMAL PHYLA This section is a brief review of the different animal phyla. The Kingdom Animalia is large with organisms of many different unrelated animal organisms. Most of the phyla are included in this discussion: •

Nematoda—these are the roundworms, of which there are more than 80,000 species—15,000 of these are parasitic.

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Nematomorpha—this is a small group of parasitic nematodes that live partially inside the body cavity of arthropods. There are only about 350 species.

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Priapula—this is a very small phylum consisting of 18 species, the largest of which are carnivores.

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Kinorhyncha —this is a small phylum with just about 150 species, related to the nematodes.

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Loricifera—this is a newer phylum of microscopic organisms that have an exoskeleton called a lorica and a part called an introvert that extends and retracts the mouth.

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Onychophora—this is a small phylum that consists of the velvet worms. They are loosely connected to arthropods.

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Arthropoda—this is the largest animal phylum with about 3.7 million species of arthropods. They are defined as having chitin exoskeletons and include the arachnids (spiders), scorpions, centipedes, millipedes, insects, and crustaceans. The insects are the largest classification with 30 separate orders.

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Tardigrada—a minor phylum of microscopic animals that live in damp or aquatic habitats. Each has a head, four segments, each having two legs.

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Sipuncula—this is a minor phylum with just about 150 species of tube-like marine animals that have tentacles.

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Mollusca—this is a large phylum of mostly aquatic animals. They have a mantle and a muscular foot with a radial teeth band and a shell. There are 50,000 to 150,000 species in this phylum.

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Annelida—these are the terrestrial segmented worms with at least 15,000 different species.

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Ectoprocta—this is an aquatic phylum that consists of 5000 different species.

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Phoronida—this is a very small phylum with just 12 species that build tubes made of chitin.

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Nemertea—these are aquatic unsegmented ribbon worms, living mostly in aquatic regions.

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Platyhelminthes—these are the flatworms, also a large phylum. It includes the tapeworms and parasitic flukes.

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Rotifera—these are the rotifers that live in fresh and seawater.

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Brachiopoda—these are the lamp-shells that have only 350 living species. They are bivalves that have different interiors than the typical bivalves seen in Mollusca.

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Entoprocta—this is a small phylum of sessile marine animals.

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Gastrotricha—these represent just 700 species of aquatic animals.

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Cnidaria—this is a large phylum of sea anemones, corals, jellyfish, and hydroids.

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Ctenophora—these are the comb jellies of which there are just 80 living species.

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Xenacoelomorpha—this is a new phylum consisting of minor deuterostomes.

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Echinodermata—this is a large phylum including organisms with radial symmetry, such as the sea urchins, starfi sh, sand dollars, and sea cucumbers.

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Hemichordata—these involve the acorn worms and other marine organisms.

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Chordata—this is the phylum that contains the vertebrates. This is considered by some to be a superphylum, containing the tunicates, the lancelates, and the “Craniata” or Vertebrata, the vertebrates.

Under the subphylum Vertebrata, there are these classes: •

Agnatha—the jawless fishes

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Chondrichthyes—the cartilaginous fishes

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Osteichthyes—the bony fishes

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Amphibia—the amphibians

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Reptilia—the reptiles

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Aves—the birds

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Mammalia—the mammals

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KEY TAKEAWAYS •

There are three main domains in living things, including Bacteria, Archaea, and Eukarya.

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Among the kingdoms, there are six different kingdoms, most of them belonging to Eukarya, although there are many more bacteria and archaea species on earth when compared to eukaryotes.

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Archaea is one of the domains, with Archaebacteria being the kingdom. These are prokaryotes and have their own characteristics different from bacteria and eukaryotes.

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Protista is a kingdom among Eukarya that consists mainly of unicellular organisms.

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There are many major and minor animal phyla that include Arthropoda, which is the largest phylum among the Animalia kingdom.

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QUIZ 1. Which classification of organisms in life is considered the most allencompassing? a. Kingdom b. Domain c. Phylum d. Class Answer: b. The broadest classification of life involves the domain, of which there are three. The system goes from domain to kingdom to phylum to subphylum to class to order to family to genus to species. 2. Which classification of organisms in life is the most specific, resulting in the smallest number of organisms included in the classification? a. Class b. Family c. Subphylum d. Genus Answer: d. Genus is the most specific of those listed, although species is the most specific of the classification systems. 3. Which kingdom includes archaea species? a. Eubacteria b. Archaebacteria c. Protista d. Plantae Answer: b. There is just one kingdom in the archaea species, which is the archaebacteria kingdom, making up a diverse group of extreme organisms, called so because of the often-extreme environments they live in.

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4. Which organism is considered prokaryotic rather than eukaryotic? a. Blue-green algae b. Diatoms c. Amoeba d. Green algae Answer: a. Blue-green algae are actually cyanobacteria rather than algae so these are prokaryotes. The others are Protista, which are eukaryotic cells. 5. What do the archaea cells have as part of their cell walls that make them unique in their own domain? a. Pseudopeptidoglycan b. Peptidoglycan c. Cellulose d. Chitin Answer: a. Pseudopeptidoglycan is the main component of the cell wall of archaea, which makes it unique to these organisms. 6. What aspect of archaea cell membranes is not unique to their membrane? a. They have a lipid monolayer b. They have a mirror-imaged glycerol molecule c. They have an ester linkage d. They have multiple, branched side-chains Answer: c. Each of these is a unique feature of the lipid membrane of archaea except that they have an ether linkage in their cell membrane, which adds to their stability in high temperatures and in high salt environments.

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7. What type of classification is the Protista classification? a. Phylum b. Domain c. Kingdom d. Family Answer: c. The Protista classification is a kingdom and is one of the six different kingdoms that life exists as. 8. What is used as the major difference between the types of Protista? a. Means of locomotion b. Cell membrane types c. Metabolic features d. Cell wall types Answer: a. These organisms are differentiated by their different means of locomotion. 9. What is the shell made of in the radiolarians as a whole? a. Calcium carbonate b. Chitin c. Cellulose d. Silicates Answer: d. The radiolarians secrete a silicate shell, which is unique to these species. The foraminifera will secrete chitin or calcium carbonate shells or tests.

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10. What organism type is responsible for African sleeping sickness and Chagas disease? a. Trypanosoma b. Amoeba c. Paramecium d. Flagellates Answer: a. The genus Trypanosoma is responsible for the tropical diseases known as African sleeping sickness and Chagas disease.

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CHAPTER 9: PLANT FORM AND FUNCTION This chapter in the course involves an extensive discussion of the cellular structures, basic anatomy, and reproductive functions of plants. Plants use much different nutrients when compared to animals and use these nutrients to participate in photosynthesis and in making nutritional substances used by many animal species. Plants are the subject of a great deal of discussion when it comes to biotechnology and genetic modification. This hot topic is covered in this chapter.

PLANT CELL STRUCTURE We’ve already covered the basic structure of the animal cell and, in truth, plants and animals share many of the same organelles. These are eukaryotic cells, meaning that they have a nucleus, a cell membrane, and multiple organelles. The main differences between animal and plant cells are the presence of a cell wall in plant cells, the presence of chloroplasts in plant cells, and the presence of central vacuoles in the plant cell. Plant cells do not have chloroplasts in the place of mitochondria. They also make ATP through cellular respiration in mitochondria. Before getting into the structure of the plant cell, lets understand the different types of plant cells in any given plant: •

Parenchymal cells—these make up the majority of cells in a plant. These carry out photosynthesis and are mainly seen in the leaves of the plant. They also undergo cellular respiration and store proteins and starches in the plant.

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Collenchyma cells—these are elongated cells with thick cell walls that provide the support to the growing plant. They have the ability to change their shape as a plant grows.

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Sclerenchyma cells—these are found in parts of the plant that have stopped growing. They provide the main supporting structures for the plant and have

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extremely thick cell walls. Technically, these cells are dead and incapable of growth. •

Xylem cells—these are the cells that transport water (and some nutrients) through the plant, starting with the root and going up to the stems and leaves of the plant.

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Phloem cells—these are the transport cells that take nutrients made during photosynthesis and send them to all parts of the plant. It is the phloem cells that transport the sap of the tree, which is high in sugars for the plant’s support.

There are the basic cell structures in plant cells that are the same as are seen in animal cells, with the addition of some special features that make them uniquely plant cells. Figure 39 shows what a plant cell looks like:

Chloroplasts are found only in algae and plant cells. They function strictly in photosynthesis, turning water, light energy, and carbon dioxide into cell nutrients. They are oval in shape like mitochondria and, similar to mitochondria, they have two membranes. Between the inner and outer membrane is an intermembrane space. Inside the chloroplast itself is the stroma.

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There are many stacked discs in the chloroplast called thylakoids, containing a high concentration of mainly chlorophyll but other pigments as well, such as carotenoids. The pigment is what captures light energy. The stacks of thylakoids together are called grana. Figure 40 shows what a chloroplast looks like:

Plant cells also contain a large central vacuole that isn’t seen in animal cells. It is so large that it often takes up 30 to 80 percent of the cell itself. It contains different things, including water, ions, and small molecules. The main purpose of the central vacuole is to help maintain the turgor pressure of the plant cell. The plant cell prefers to have a high turgor pressure so that it stays “plump”. A plant cell without a high turgor pressure will wilt the plant. Plants in general do better when they live in hypotonic conditions with water rushing into the cell through osmosis, plumping out the cell and resulting in a high turgor pressure. This is different than animal cells, which require isotonic environments. Plants have a cell wall made of several things, depending on the cell. Most cell walls are made of cellulose, although there can be pectin, lignins, and hemicellulose as part of the cell wall. As you can imagine, the cell wall protects the cell from bursting in situations of high turgidity. Plant cells, in fact, have more than one cell wall. There is a flexible

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primary cell wall layer that is formed outside of the growing plant cell. There is also a secondary cell wall that is formed inside of the primary cell wall when the cell has matured.

PLANT MORPHOLOGY Plant morphology is basically the same thing as plant anatomy from a macroscopic viewpoint. We will learn more about the structure and function of plants later in this chapter but in this part, we will look at the most obvious parts of the plant structure. In this section, we will look at the morphology of vascular plants, which is the typical plant one thinks of with regard to plants. Figure 41 shows the basics of plant morphology:

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The roots of the vascular plant usually are not seen as they grow underground. They are responsible for the absorption of nutrients and water for the plant. There are two different types of roots: taproots and fibrous roots. The taproot is a single thick root extending beneath the plant with a network of roots that extend out from it. Fibrous roots are roots that have no taproot. There is just a dense collection of thinner roots without a major taproot. Both types of roots are covered in root hairs. The hairs increase the surface area of the root so that more water and nutrients can be absorbed. The stems of the plant are the parts above the plant that hold the reproductive structures and the leaves. There are three types of stem tissues: 1) ground tissue (this is parenchymal tissue that makes up the bulk of the stem, 2) dermal tissue (this is the “outer skin” layer of the plant that protects the interior of the stem), and 3) vascular tissue (this involves the xylem and phloem of the stem or the vasculature of the plant). The xylem is a tubular structure that moves water in one direction up the plant. The phloem is a tubular structure that moves water and nutrients up and down the plant. Water is moved up from the roots in the xylem, while energy and nutrients move through the plant from the leaves to the rest of the plant. The leaves of a plant are the major area of photosynthesis. Most leaves are flat and green but, in other plants, the “leaves” can be needles as in conifer trees or thicker structures as in aloe plants. Leaves have dermal tissue, vascular tissue, and ground tissue, attached to the stem through a structure called a petiole. Leaves will have stomata, which are pores through which the water can pass in the process of evaporation. This contributes to the transpiration process, in which water moves throughout the plant. There is an outer cuticle and epidermis in plant leaves with mesophyll in between. Figure 42 shows the structure of the leaf:

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The flower of a plant is referred to as an inflorescence. There are many types of flowers, all of which are the main reproductive structures of flowering plants. Flowers will carry both the male and female aspects of reproduction of a plant. These will be covered further when we talk about the reproduction of plants. Fruit on a plant comes from the flowers and forms many different shapes and sizes. Fruits will hold the seeds of the plant and contain the plant’s ovary. Exceptions to this are fruits like strawberries, which are accessory fruits. This type of fruit comes from the head of the flower. On the accessory fruit are the seeds, which are mature plant ovaries that contain the seeds of the plant inside them.

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REPRODUCTION OF PLANTS Plants, like animals, undergo meiosis and fertilization. There is halving of the number of chromosomes in the sex cells, leading to gametes. The male and female gametes will fuse in fertilization in order to create a diploid cell with the full number of chromosomes. Of course, this is not the exact process happening in plants as happens in animals. There are two separate generations of organism. The first is the gametophyte generation that begins with a spore that is haploid. The spore will divide by mitosis to make many identical haploid spores. Ultimately, sexual reproduction takes place, leading to a sporophyte generation, starting with a zygote. These develop and then some of the cells form spores again, restarting the gametophyte generation again. The main difference is that haploid cells will undergo mitosis as well as diploid cells. Figure 43 shows the life cycle of the plant:

While plants do some things different among the different types of plants, we’ll take a look at the life cycle of the angiosperm plant, which are the flowering plants. Most of these are land plants and none will have locomotion. The gametes are delicate single cells with the need for a mechanism for two gametes to reach each other in a safe manner. There must also be a way for the dissemination of offspring so that there isn’t competition between the different organisms for light, soil, and water.

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FLOWERS Flowers start as buds, which are modified leaves that develop to have the male and/or female reproductive organisms. These inflorescences (clusters of flowers) ultimately turn into the fruit of the plant. There are four different structures attached to the floral stalk. These are the sepals, the petals, the stamens, and the carpels. These can be grouped in multiples of threes, fours and fives. Figure 44 shows the structure of a flower:

The sepals are the green part that encloses the flower bud. All of the sepals together are called the calyx. Inside this are the brightly colored petals, collectively called the corolla. The calyx and corolla together are referred to as the perianth. These are not directly involved in reproduction but protect the flower and attract the pollinators. Inside the corolla are the stamens, which are the spore-producing structures, collectively called the androecium. These are the male parts of the flower in which the microsporangia form. The stamens will have a filament or stalk that has the anther and

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pollen sacs, which is where the pollen is formed. There are nectaries or a single nectary at the base of the stamens that secrete the food reward for the pollinators. In the middle of the flower are the carpels, collectively called the gynoecium. These are the female parts of the flower in which the megasporangia form. They enclose the ovules that have an egg inside. The ovule, after fertilization, will mature into a seed with the carpel maturing into a fruit. These carpels and fruit are unique to the angiosperm type of plant. A perfect bisexual flower will have both stamens and carpels, while a unisexual or imperfect flower will have no stamens (called carpellate) or no carpels (called staminate). Some plants will have staminate and carpellate flowers on the same plant and are monoecious. Species that have separate plants with staminate and carpellate flowers are called dioecious. The receptacle is the stem to which the flower or inflorescence is attached with the peduncle being the stalk of a flower. The calyx or cluster of sepals most resemble the leaves because they are green. Sepals can be separate (polysepalous) or fused (synsepalous), forming a tube rather than separate sepals. The corolla (or petals) of the flower will attract insects and birds for pollination).

POLLINATION Pollination involves the transfer of pollen from the anthers to the stigma of the same plant species so that there can be germination and growth of the pollen tube to the ovule. There can be self-pollination in some species or cross-pollination. Pollen transfer happens by water, wind, insects, birds, and other animals. Most of the animal crosspollination happens because of bees. They feed on the nectar and pollen so they can pollinate one or more species of plant. Plants that have adapted to this will have a flower that has a landing platform for the bees. These flowers are often yellow or blue in color in order to attract the bees. The first phase of pollination involves the landing of a pollen grain on a stigma of a receptive plant. It has glandular tissue that nourishes the pollen tube as it elongates and grows down the style of the flower. Flowers have a chemical mechanism that prevents 177

self-fertilization. It makes it impossible to have a flower pollinate itself in most cases. The pollen tube enters the ovule in the carpel and penetrates one of the sterile cells on either side of the egg, called synergids. These will degenerate and lead to fertilization of the egg. Figure 45 shows the important structures in fertilization:

When a pollen grain reaches the tip of the carpel, called the stigma, it germinates into a pollen tube. It forms two sperm cells that travel down the pollen tube into the style, the micropyle, and into the ovule chamber. The pollen tube ruptures, and the sperm cell fertilizes the egg, while the other sperm cell fuses into the polar nuclei, forming what’s called the endosperm nucleus. The fertilization of the egg inside the carpel by a pollen grain leads to seed formation in the carpel. The formation of fruit without the egg being fertilized is known as parthenocarpy. A fruit is nothing more than a ripened ovary, which differentiates it from a vegetable, because a vegetable does not have reproductive organs. This is what makes squash, eggplant, and tomatoes fruit versus carrots and turnips, which are modified roots. Potatoes, ginger, and onions are modified stems. Figs and pineapple are the combined gynoecia of more than one flower (or a whole inflorescence).

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After double fertilization, each ovule develops into a seed, consisting of a plumule (which involves the embryonic leaves of the seedling) and a terminal bud. The terminal bud is where the growth of the stem takes place. There will be one to two cotyledons that store food used by the germinating seedling. Those angiosperms that produce two cotyledons (which include beans and squashes) are called dicots Those that produce just one cotyledon (which include grasses and corn) are called monocots. The seed also contains the hypocotyl and radicle, which form the stem and primary root, respectively. There are seed coats that come from the walls of the ovule that protect the seeds. The food from the cotyledons comes from the endosperm which gets the food from the parent sporophyte. Seeds are basically a dormant embryo with stored food and protective coats. They allow dispersal of the species to new locations and survival of the species during unfavorable climate situations, such as wintertime. Germination happens when there is a new generation of plants that develop in good climate situations.

FRUITS There are three main types of fleshy fruits of plants. These are the berries, drupes, and pomes. Berries have many seeds made from one carpel (a syncarpous ovary). Tomatoes are berries that have a thin exocarp (surrounding the berry), while oranges have a thick and leathery exocarp. Pumpkins have a hard exocarp. The fruit wall, or pericarp, is divided into three regions: the inner layer, or endocarp; the middle layer, or mesocarp; and the outer layer, or exocarp. Drupes are stone fruits with just one seed per carpel. They have a woody endocarp, which is adherent to the seed. The drupes include the cherry, plums, and peaches. Raspberries and blackberries are drupe fruit that have multiple druplets that aggregate together. Pomes are fleshy fruits such as pears and apples. Dry fruits can be dehiscent or indehiscent. Dehiscent fruits open up at maturity to release the seeds. Indehiscent fruits have the pericarp intact when the fruit is shed from the plant. Seeds get transported by several mechanisms. These include wind, water, hitchhiking (cockleburs that stick to passing animals and human clothing), edible fruits (which have

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seeds pass through the animal GI tract or that get buried), and mechanical disbursement (by expelling the seed).

SOIL UTILIZATION AND PLANT NUTRITION Most plants get their mineral nutrition via the roots in soil. The main minerals, like calcium and potassium, are dissolved in water. Interestingly, less than 1 percent of the water that reaches the leaves participates in photosynthesis and plant growth. Most of it is lost in the transpiration process (to be discussed later). This process forces water up through the stems and cools the leaves. The water from the soil enters the epidermis of the root. It travels through the cytoplasm of root cells, called the symplast, passing from cell to cell through the plasmodesmata that connect the cells. The apoplast is the nonliving spaces between the cells; water transports in the root through this part as well. Apoplastic water needs to enter the cytoplasm of the cells inside the epidermis, called the endodermis. It then passes through the stele and finally into the xylem, which is the “vessel” of the cell. The xylem is part of the apoplast because it isn’t inside the cell itself. Water can pass out of the xylem at any point to nourish the stems and other tissues of the plant. At the leaves, the xylem passes through the petiole of the leaves and into the veins of the leaves. The finest veins of the leaves are where the water exits into the spongy and palisade layers of the leaf. Most of the water is lost through transpiration, with one percent used in metabolism. Minerals enter the root via the active transport into the symplast of epidermal cells. They enter the xylem and tracheids to travel up the roots and stems of the plant. Tracheids are elongated cells in the xylem of vascular plants that serve in the transport of water and mineral salts. So how does water go up the plant against gravity? Because the tracheids and xylem vessels are lifeless, the transport of water is completely a phenomenon of physics. As It turns out, roots are not absolutely necessary; however, leaves are a necessary part of the process. Water is pulled upward by evaporation (transpiration) that causes negative pressure above the plant, drawing water up the plant. Water is cohesive, which means it clings to itself when confined to tubes of small bore. This is the extra pull necessary to

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get water to the top of very tall plants, like sequoia trees. This is called the cohesion theory. Food, messenger RNA, plant hormones, and certain organic substances made by the plant cells are transported in the phloem of the plant. The main sugar made in plants is sucrose. This, along with amino acids and small organic molecules enter the cells and pass through plasmodesmata that connect cells to adjacent cells. Once in the phloem, the molecules can be transported to any part of the cell. The process of girdling a tree (removing a band of bark around the tree) removes the phloem. The tree will live for a period of time but will ultimately die because the roots are starved. Transfer of food content through the phloem is dependent on the metabolism of the phloem cells, which is completely different from the xylem. Sugar will leave the sieve tubes near the leaves and stems (pumped out through active transport), with water following by osmosis. This increases the turgor (or pressure) in these areas, which causes the food and water to be pushed through the phloem under this high pressure. The sugar is used by the plant for nutrition and any that is left over becomes starch. Starch is insoluble in water and doesn’t affect the concentration of sugar in the phloem.

TRANSPIRATION This is the evaporation of water from primarily the leaves. Leaves have stomata that are open for CO2 and O2 to pass as part of photosynthesis. The surrounding air doesn’t have a hundred percent humidity, making it drying for the leaves and resulting in substantial evaluation. This transpired water needs to be replaced by the transport of water from the roots to the leaves through the xylem. This provides the engine for pulling water up from the roots, bringing minerals along with it. The process also cools the leaves, similar to the way that the evaporation of water from human skin will cool the body. There are several factors that impact the amount of transpiration that goes on, including the following: •

The amount of light—there is greater transpiration during light hours. This is because light will warm the leaf and will stimulate the opening of the stomata. 181

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Temperature—water will evaporate more rapidly at high temperatures so transpiration will happen at a higher rate.

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Humidity—transfusion happens during drier periods of time versus when the environment is more humid.

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Wind—increased wind will increase transpiration.

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Soil—during times of dry soil, the turgor of the plant decreases and this results in closing of the stomata and decreased transpiration.

In order to participate in photosynthesis, green plants need carbon dioxide and a way to get rid of the waste product, which is oxygen. On the other hand, plants need to carry on cellular respiration, which requires oxygen and gives off carbon dioxide. Both of these must take place in a plant. Unlike animals, there is no gas transport system in plants. The roots, leaves, and stems of the plant respire at lower rates than is seen in animals. Because plants have most of their cells close to the surface, gases can diffuse across cells. Remember, the interior of most cells is dead and structural; the outer surface can participate in gas exchange through diffusion. The leaves have stomata that engage in the transpiration process and in gas exchange. Stomata will open when light strikes on them, which changes the turgor of guard cells that line the stomata walls. Increased turgor in the guard cells will cause the stomata to open, while decreased turgor will close the stomata. Light is absorbed by phototropin in the guard cell, causing a pump to turn on in the cell membrane, increasing the potassium concentration in the guard cell. This raises the osmotic pressure in the cells, opening the stomata. Open stomata are crucial for gas exchange in photosynthesis, which is why they open during the light hours. They also increase water loss through transpiration. There is a hormone called ABA or abscisic acid that triggers closing of stomata when the soil cannot keep up with transpiration. ABA will bind to guard cells, resulting in a rise in guard cell cytosol pH. This causes the loss of potassium in the guard cells, closing the stomata. ABA will also close the stomata when bacteria are present so as to avoid bacterial invasion.

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Higher CO2 concentrations in the environment will decrease the number of stomata on a plant leaf. Specimens from before industrial times have greater densities of stomata than modern-day specimens, reflecting the increase in CO2 from environmental factors, such as the industrial revolution. Fossils have shown that high CO2 levels in the past (and warmer temperatures) decrease the numbers of stomata, while low levels of CO2 and ice ages have increased the numbers of stomata.

PLANT BIOTECHNOLOGY Plant biotechnology for the most part involves altering the genes of plants to create GMO (genetically modified organism) plant. These are also called biotech crops and are often used in agriculture. The goal of GM crops is to create a crop that has a trait that doesn’t occur in nature. Genes can be altered in order to increase the plants’ resistance to diseases, certain pests, spoilage, chemical herbicides, and certain environmental conditions. This affects about 12 percent of the crops in the world.

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KEY TAKEAWAYS •

Plants have parenchymal cells that will participate in photosynthesis.

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The xylem and phloem will engage in water and food transport in most plants.

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The driving force for water transferring from the roots to the leaves is transpiration, which creates a negative pressure situation for water.

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The reproductive organs for angiosperms are located in the flowers of the plant.

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The fruits of the plant house the seeds, which allow for germination during adequate conditions of warmth, good soil, and light.

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Plant biotechnology mainly involves creating genetically-modified plants that have advantages over plants that are not genetically modified.

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QUIZ 1. What part of the plant cell makes ATP energy through cellular respiration? a. Chloroplasts b. Mitochondria c. Cell membrane d. Ribosomes Answer: b. Plant cells undergo cellular respiration in the same way as happens in animal cells. They have mitochondria that undergo cellular respiration and make ATP energy. 2. Which is the most abundant cell type in a plant? a. Parenchymal cells b. Xylem cells c. Collenchyma cells d. Phloem cells Answer: a. The parenchymal cells are the most abundant cell type, being the major cells to undergo photosynthesis in the leaves of the plant. 3. What is the major component of the cell wall in plant cells? a. Lignins b. Cellulose c. Pectin d. Chitin Answer: b. The main component of the cell wall in plant cells is cellulose, although lignins, hemicellulose, and pectin can also be components of these cell walls.

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4. Which type of plant does not generally have a tap root? a. Carrot plant b. Rutabaga plant c. Beet plant d. Pea plant Answer: d. The main taproot in the first three plants (carrot, rutabaga, and beet) is the vegetable itself. The pea plant has a regular root and stem system without a taproot. 5. What do the ovules in the flower ultimately grow into after fertilization? a. Carpel b. Seed c. Fruit d. Stamen Answer: b. The ovules, which are part of the carpels will develop into the seed after fertilization. Then the carpel itself matures into the fruit of the plant, which houses the seed. 6. A plant that has a male flower and a female flower on the same plant is called what? a. Carpellate b. Staminate c. Monoecious d. Dioecious Answer: c. A monoecious flower is one that has a male flower (staminate) and a female flower (carpellate) on the same plant, while a dioecious plant has these male and female flowers on different plants.

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7. In a seed, what are the cotyledons? a. The structures that nourish the seedling. b. The protection of the seedling. c. The part of the seed that forms the root. d. The structure of the seed that forms the stem. Answer: a. The cotyledons (of which there are one or two) are the structures that nourish the seedling as it grows and develops. Dicots form two cotyledons, while monocots have just one cotyledon. 8. What is the fluid within the root cell called in a plant? a. Apoplast b. Plasmodesmata c. Symplast d. Epidermis Answer: c. The symplast is the cytoplasm or interior of the cells inside the root cells, through which some of the water gets absorbed and sent from cell to cell via the plasmodesmata that connect the root cells to one another. 9. Which factor does not increase the rate of transpiration in a plant? a. Wind will increase transpiration b. High soil water will increase transpiration c. High humidity will increase transpiration d. Light will increase transpiration Answer: c. In fact, conditions of low humidity will increase transpiration as it increases the evaporative process.

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10. Which are the cells in the leaf that are responsible for opening and closing the stomata in the leaves? a. Guard cells b. Epidermal cells c. Palisade cells d. Endodermal cells Answer: a. The guard cells will increase in osmotic pressure and will become more turgid when light strikes them, opening the stomata in the light hours.

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CHAPTER 10: FUNGI FORM AND FUNCTION This chapter discusses fungi, their anatomy and physiology. Fungi are a broad category of organisms, ranging from microscopic organisms to the commonly-known fungi, such as mushrooms. What they have in common and how they differ from one another are covered in this chapter. Fungi have their own unique way of reproducing themselves, which will be explained as part of this chapter.

FUNGAL DIVERSITY As you have seen, the different kingdoms are extremely diverse and the kingdom of fungi is no exception. They arose from some type of protist ancestor to break off from existing protists to create their own kingdom. These organisms generally have a “body” called a mycelium, which is made from filaments that spread out in order to absorb nutrients. The individual filaments are referred to as “hyphae” that have cell walls made from chitin. They have a unique mechanism of growth referred to as cytoplasmic streaming. Fungi in general will reproduce through sexual and asexual means. They are known to form spores. In fact, spore forming is something nearly all fungal organisms can do and there are a few species that only use spores in order to reproduce. Spores can be formed through sexual and asexual means with fruiting bodies responsible for storing and dispersing spores. The single-celled fungi (called yeasts) can reproduce through an asexual process called “budding”. As you’ll see, fungi are important to the nutrient cycles in living things. They rely on decomposition of organic matter for nutrients in many cases, although a few are parasitic or predatory in nature. There are some mutualistic and commensal relationships between fungi and plants. They also have affiliations with cyanobacteria and algae, with whom they create lichens. One species has a mutualistic relationship with leaf-cutter ants.

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There are four different phyla in this kingdom. They are based on characteristics of their spores. These include the following: •

Chytridiomycota or Chytrids—these are the oldest and earliest group, with one species adversely affecting the amphibian populations throughout the world. They are motile with asexual and sexual spores. They have posterior flagella.

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Zygomycota—these are the Zygomycetes that have thick-walled zygospores formed during sexual reproduction. Black bread mold is an example of this type of mold.

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Ascomycota—these are called the Ascomycetes that have spores inside a sac known as an ascus. There are eight sexual spores in an ascus.

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Basidiomycota—these are fungi that have spores on the outside of a clubshaped structure known as a basidium.

There are a few fungi that do not fit well into any of the fungi phyla. The AM fungi (which stands for arbuscular mycorrhizal fungi) live only in the mycorrhizae of plants. They have large spores and only reproduce sexually. There are also the Fungi Imperfecti or “deuteromycetes” that do not have a sexual state within their life cycle and slime molds, which are similar to fungi but are not true fungal organisms. Most fungi are beneficial to life; however, there are those that cause certain crop diseases and health problems to humans and other animals. Crop diseases such as smuts and rusts are from fungal organisms, while human diseases include those from aflatoxins (caused by moldy fruit and grains). Other human diseases, such as “sick building syndrome” and ringworm are from fungi. Yeast infections are from fungi as well. Certain psychoactive and hallucinogenic substances can be extracted from fungal fruiting bodies of some fungi.

FUNGAL ANATOMY Fungal anatomy can be thought of in microscopic and macroscopic terms. Microscopically, these organisms form hyphae, which are cylindrical, thready-appearing structures that are only about two to ten micrometers in diameter but can be several

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centimeters long. These structures grow at their tips with new hyphae forming as branches off of existing hyphae or forking off from an existing hypha. They can fuse together with other hyphae to form anastomoses. An interconnected group of hyphae come together as a mycelium. Hyphae can be septate (developing septa), forming internal cell walls within the hypha, or coenocytic (having non-compartmentalized hyphae). These septa have large pores in them so that very large nuclei and other organelles can pass through. Coenocytic hyphae are like multinucleated cells or “supercells”. These are mainly saprophytic, living off of decomposing matter. They have haustoria, which are specialized food-uptake structures in parasitic strains of fungi. Some will have structures called arbuscules that can penetrate host cells in order to consume nutrients. Fungi are considered opisthokonts, which is an evolutionary group that is characterized by having a single flagellum in the posterior section of the organism; however, except for the chytrids, the major species of fungi have lost his particular feature. The key feature is the cell wall, which contains glucans and chitin. Septa will form in most filamentous fungi, particularly in the Ascomycota and Basidiomycota phyla. These are basically barriers across the filament. Some will have septa at regular intervals, while others are irregularly spaced. These allow the different “cells” or different compartments of the hypha to rapidly communicate. The main structure of the hypha is referred to as a thallus. Pores can close off in order to enable differentiation within the thallus. Secondary septa can form that prevent movement of cytoplasm out of damaged hyphae; these septa will not have pores. These secondary septa are irregularly spaced and so their appearance depends on stressors within the mycelium. As mentioned, these secondary septa can also form between the sexual structures and the main thallus. They will increase the rigidity of the hypha as it provides structural support for the hyphae that might otherwise rupture. In yeast cells, the septum functions in reproduction. Their reproduction differs from that of hyphal organisms. In the ascomycetous yeasts, bud cells will separate from parent cells with a septum dividing the bud from the main yeast organism. There is a 191

wall deposited within the septum with subsequent dissolution of the septum so that the bud can separate off. This leaves a scar behind in the parent cell that will not be able to bud again. This will limit the number of buds that a single yeast cell can develop. The pores will close off for a variety of reasons with blockage occurring sometimes rapidly. This leads to two separate functional units so that the thallus can grow differently on either side of the blockage. If a hypha is damaged, the pores will close in order to prevent the thallus from losing cytoplasm. The goal of pore closure is to keep the living thallus separate from that part which is damaged and that will die off. Hyphal structure can be complex with things like fruiting bodies developing in some areas. There are three different types of hyphae. There are generative hyphae that have thin walls and septa. There are skeletal hyphae that are unbranched, having no septa and thick cell walls. Binding hyphae are highly branched and are also aseptate. Macroscopically, fungal mycelia can be large enough to be seen by the naked eye. Spoiled food and damp surfaces can develop molds. These will have increased pigmentation and/or spores that make them visible. Figure 46 shows the macroscopic structure of a mushroom, which is a fruiting body of a fungus:

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Some fungi are only noticeable when they produce spores as mushrooms or molds. The fruiting body is part of the sexual phase of the fungal life cycle. The sporocarp is a multicellular spore-forming structure seen only during the sexual phase of the life cycle of the fungus. Dimorphic fungi have the capability to form two different shapes, depending on the circumstances. One dimorphic fungus, called Histoplasma capsulatum, has two different shapes depending on the temperature. In colder temperatures, the fungus forms a brown mycelium that looks like threads. In warmer temperatures, such as the human body temperature, they are single-celled organisms, causing the human disease called histoplasmosis.

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FUNGAL PHYSIOLOGY While the common fungus such as the mushroom is readily visible and synonymous with the term “fungus”, many fungi do not form mushrooms at all. Fungal cells are more similar to animal cells than they are to plant cells. There are about 100,000 identified species of the 1.5 million probable species of fungi. Typical fungi include the yeasts, molds, and edible or inedible mushrooms. Fungi are not capable of photosynthesis. Instead, they are heterotrophic, getting their food from complex organic compounds. As mentioned, many are spore-forming, with spores being haploid cells that can undergo mitosis to form multicellular haploid structures. They are essential to the ecosystem because they are decomposers that break down complex organic molecules for fuel. Most land plants have symbiotic relationships with fungi. Roots of many plants will form what are called mycorrhizae, in which the fungus and plant exchange water and nutrients. Another symbiotic relationship is that with algae or other photosynthetic organisms, forming lichens. Infections by fungal organisms can cause human, animal, and plant diseases. Dutch elm disease is a fungal infection of the elm trees that infect the tree’s vascular system with the elm bark beetle being a vector. Fungi are eukaryotic single or multicellular organisms that have the typical cell structure we’ve already discussed. They do not have chloroplasts because they don’t undergo photosynthesis. The bright colors seen in fungal organisms come from cell wall pigments that protect the fungus against ultraviolet radiation. The cell wall consists of both chitin and glucans. Chitin is the same polysaccharide that is found as part of the exoskeleton of insects. It protects the cell from predators and from drying out. The cell membranes are different from animals in that they do not have cholesterol in them but have ergosterol, another steroid molecule. As mentioned, the vegetative body of the fungus is called a thallus (whether it be unicellular or multicellular). Many dimorphic fungi can go from unicellular to multicellular to form two shapes. The two main morphologies seen in multicellular fungi are called vegetative and reproductive morphologies. The vegetative state is the hyphal

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state while the reproductive state is the fruiting body state. There are cases where the vegetative state can be quite large—in one case, a single organism covers more than 2,000 acres of hyphae. Fungi are considered heterotrophs that live off of other organic compounds. Many are saprophytic, meaning they live off of dead or dying organisms. They don’t fix carbon dioxide in photosynthesis and they don’t fix nitrogen from the atmosphere. They do not ingest and then digest, like animals and many other organisms. Instead, they do the opposite. They send out exoenzymes outside of the hyphae that process the food outside of the organism. Then they absorb the smaller molecules. These exoenzymes will be able to break down the cellulose and lignan of plant cells. Similar to animals, their storage molecule is glycogen rather than starch.

FUNGAL REPRODUCTION There are many ways that fungi can reproduce asexually, including budding, fragmentation, and spore formation. Sexual reproduction can also occur. The so-called perfect fungi can reproduce both sexually and asexually, while the “imperfect fungi” can only reproduce through mitosis. They do not undergo binary fission. Spores can be produced and can be dispersed through other animals or the wind. These spores tend to be lighter and much smaller than plant seeds with trillions of spores released at one time in certain species. This huge number of spores will ensure that some of them will find the right habitat in order to start hyphal growth again. Asexual fungal reproduction can be through budding, spore formation, or fragmentation. Fragmentation involves the breaking off of a hypha from the main mycelium. Yeast cells will bud off in a sort of cytokinesis process with mitosis occurring to send a copy of the genome to the daughter cell. The most common asexual reproductive strategy is through spore formation. One parent will make spores that will be genetically identical to the parent organism. The spores can be released from the parent thallus or can make a sporangium, which is a special reproductive sac. Figure 47 shows the fungi life cycle:

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In the fungi life cycle, there are spores that are given off from the hyphae through mitosis and spore formation. The mycelium is a haploid structure with germination happening when the habitat is right. In the process of plasmogamy, two different mycelia will combine to form a diploid organism with two or more nuclei. In karyogamy, the nuclei fuse to make a true diploid organism. This makes a diploid zygote that undergoes meiosis to make a haploid organism and haploid cells that develop into another haploid mycelium. Sexual reproduction generally happens under the conditions of increased stress. The mating of hyphae can be homothallic or heterothallic. Homothallic reproduction happens within the same mycelium, while heterothallic reproduction happens when two mycelia in close proximity to one another that are genetically compatible combine sexually.

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Asexual spores come in many forms. There are conidiospores that can be multicellular or unicellular and that are directly released from the tip or side of the hyphae. Others will bud off from the vegetative part of the organism. Those spores that are released from a sporangium are called sporangiospores.

ECOLOGY OF FUNGI Fungi have an important role to play in ecology as they are the major decomposers in nature. Organic matter is broken down that would otherwise be unable to be recycled because no other organism type can recycle these nutrients. Fungi prefer dark and moist conditions and live in hostile environments that other organisms can’t. The forest floor is a common place for them, where there is a lot of decaying debris. As mentioned, they send out exoenzymes that decompose many structures to make nutrients that other organisms can use. Two main elements, nitrogen and phosphorus are necessary for life and yet are not readily available to many organisms without the action of fungal organisms. The way that fungi participate most in the cycle of nutrients is through the action of their exoenzymes. These are released into the environment to break down cell walls and other nutrients of decaying matter. This requires water so the presence of water and damp environments is crucial to their digestive process. The mutualistic relationship to other organisms includes relationships between plants, animals, and cyanobacteria. Mutualistic relationships are also called symbiotic relationships when both members in the relationship receive benefit from the others. As mentioned, mycorrhizae are extremely common, affecting 90 percent of terrestrial plants. In this association, the hyphae branch out and come in contact with the soil in order to channel minerals and water toward the plant, increasing the ability of plants to take up nutrients. The tradeoff is that the fungi benefit from the products of photosynthesis coming from the plants. Mycorrhizae do not diversify much as they do not participate in sexual reproduction. In many ways, they are quite primitive and cannot live outside of the mycorrhizae. There

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are several types of mycorrhizae. One is called ectomycorrhizae, in which the fungal hyphae form a sheath around the roots called a mantle with a net of hyphae that extend outward from the roots. Another type of mycorrhiza is called the glomeromycete fungi or endomycorrhizae. In such cases, the fungi form arbuscules (vesicles) that penetrate the root cells, resulting in metabolic exchange between the fungus and plant. A third type involves those seen in orchids. The orchid plant forms seeds that need a mycorrhizal exchange between the fungal organism and the seed. The fungus provides nutrients to the seed until it can germinate. Lichens have the ability to survive in very hostile environments and are basically everywhere. Lichens are not single organism but, as mentioned, are the combined efforts of fungi and cyanobacteria or algae. These are hardy relationships, surviving cold and desiccation in order to come alive in more prosperous situations. They are important in ecology because they are highly sensitive to air pollution. The fungi responsible can be Basidiomycota or Ascomycota species—with no member of the lichen able to survive outside of the symbiotic relationship. The body of the lichen is referred to as a thallus, which involves hyphae that are wrapped around a photosynthetic partner species. Sometimes, when cyanobacteria are involved, the cyanobacteria will take nitrogen from the air and fix it for the hyphal partner. The fungus will protect the photosynthetic partner from desiccation and excessive light and will provide minerals to the cyanobacterial organism. The fungus can also form the attachment of the lichen to the underlying substrate. These lichens will form soredia, which are clusters of the algae or cyanobacteria surrounded by mycelia that are dispersed by wind and water in order to make new lichens. Fungi have mutualistic relationships with animals as well—particularly insects. The fungus provides protection from pathogens and predators, while the fungus gets a way to disseminate spores and gets nutrients from the insect. The fungus will cover the insect colonies and, in some cases, the fungi will digest the cellulose that cannot be broken down by the insects. When this happens, the insect eats the fungus that has the

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broken-down nutrients in it. The insects, in return, will protect the area from invading and competing fungal organisms.

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KEY TAKEAWAYS •

Fungi have a kingdom of their own based on the uniqueness of their cell walls.

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The basic form of a fungus is a called a hypha. Many hyphae will together form a mycelium.

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The fungus that is seen macroscopically is usually the fruiting body, including that seen in mushrooms.

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The hyphae can be multinucleated or can be septate with septa that separate the different aspects of the hypha.

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The fungi often form mutualistic relationships—with animals, cyanobacteria, algae, or plants.

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QUIZ 1. What is the fungal cell wall made from? a. Cellulose b. Chitin and glucans c. Lignans d. Peptidoglycans Answer: b. The cell wall of fungi is made from chitin and glucans, which makes them relatively unique among the different species of cell-walled organisms. 2. What are the different phyla of the kingdom fungi based on? a. Cell wall characteristics b. Metabolic pathways c. Spore characteristics d. Type of fruiting bodies Answer: c. The different phyla are based on the characteristics of their spores. Some have asexual spores, others have sexual spores, and still others have both asexual and sexual spores. 3. What is not a major function of the septa in the hyphae of a fungal mycelium? a. To block off areas that have been damaged b. To allow for branching of the hyphae c. To allow for rapid communication between the compartments d. To improve the rigidity of the hypha Answer: b. The septa have several functions that involve each of the above except for branching of the hyphae.

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4. How do fungi get their nutrition? a. They are photosynthetic b. They engulf food into their cells c. They get food from the soil d. They take in food from decaying organisms Answer: d. Many fungi are saprophytic and take in food from the environment by digesting the contents of decaying organisms. 5. In looking at hyphae, what is a coenocytic fungus? a. A highly branched hypha b. A hypha with a fruiting body attached c. An aseptate fungus that is multinucleated d. A single-celled fungus Answer: c. A coenocytic fungus is an aseptate fungus that is multinucleated. 6. Fungi are often considered saprophytic. What does that mean? a. It can form symbiotic relationships with other organisms b. It can live off of dead or decomposing organisms c. It can have two or more different morphologies d. It can cause animal or plant diseases Answer: b. Many fungi are saprophytic, meaning that they can live off of dead or decomposing organisms. 7. What is not true of sexual reproduction of fungal hyphae? a. The true mycelium is a haploid organism b. The hypha fuse with another hypha to form a multinucleated cell. c. The zygote is a diploid organism. d. The spores will combine in sexual reproduction.

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Answer: d. The sexual reproduction does not involve spores combining. It is the hyphae that combine in order to form a diploid organism that then undergoes meiosis in order to form haploid spores. 8. In the sexual reproduction of fungi, what is karyogamy? a. The fusion of two nuclei to make a diploid nucleus b. The meiotic process that occurs in the spores c. The combining of cells in order to form a multinucleated cell d. The mitosis that occurs in the zygote Answer: a. Karyogamy is the fusion of two nuclei from different organisms into a diploid nucleus. 9. What is not usually a member of the lichen relationship? a. Cyanobacteria b. Methanogenic archaea c. Ascomycetes d. Basidiomycetes Answer: b. Any of these can participate in the formation of a lichen relationship except for methanogenic archaea, which do not survive well in this type of relationship. 10. In a lichen, what is not something that the fungus will do to help the cyanobacterial partner? a. Help the lichen attach to the substrate b. Help protect the cyanobacteria from excessive sunlight c. Help fix nitrogen from the atmosphere d. Protect the cyanobacteria from desiccation Answer: c. In a lichen relationship, it is the cyanobacteria that fix nitrogen and not the other way around. The fungi will do each of the other things in this relationship.

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CHAPTER 11: ANIMAL FORM AND FUNCTION The focus of this chapter is the various systems that make up complex animals. All animals must have some way of obtaining nutrients through digestive systems, must circulate nutrients, and need to use respiration to have oxygen for energy. These will be different, depending on the animal species. Animal cells will have nervous systems of some sort and need strong immune systems to defend against pathogens. These systems as well as the endocrine systems and hormones in animal systems are discussed in this chapter.

CIRCULATORY SYSTEMS The circulatory system is a way for larger organisms to have oxygen and nutrients travel throughout the organism. In animals, the circulatory system transports oxygen to the tissues and gets rid of the CO2, which is a waste product of metabolism. Evolutionarily speaking, circulatory systems evolved when organisms became too large to accommodate simple diffusion of nutrients and gases. The circulatory system normally must coordinate with the respiratory system in order to have a way to get the gases in and out of the body. In animals, the key feature of the human circulatory system is the heart. In humans and higher order animals, it is a structure with electrically-active cells that have automaticity in order to beat and pump blood throughout the organism. Endocrine organs and the central nervous system will have input into the way the heart beats. While the heart does not participate in gas exchange, the rest of the circulatory system is intricately involved—coordinating with the respiratory system to engage in the exchange of oxygen needed by the animal and carbon dioxide, a waste product of the animal’s metabolism. The circulatory system can be open or closed. It depends on whether the blood is in vessels versus in a type of circulatory system. In a closed system, there is a heart that pumps blood in one direction away from and finally back to the heart. In arthropods, which have an open circulatory system, blood is pumped into a hemocoel (a cavity that

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surrounds the organs, returning the blood back to one or more hearts through openings called ostia. The blood and interstitial fluid are together in arthropods, where it is called hemolymph. While the heart is essential in animals, so are the arteries, veins, and capillaries (cylindrical vessels) that emanate from the pump. In closed systems, the blood does not flow in a cavity but is completely contained in either the heart or vessels. Figure 48 shows a closed circulatory system in humans:

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Insects, crustaceans, and many mollusks have an open circulatory system and many have more than one heart. The blood flows because of the movement of the animal and the pumping of the heart or hearts with blood passing through ostia from the central cavity back to the heart. This does not take as much energy as a closed system but cannot allow for the transport of oxygen to highly metabolically active areas of the animal. Simple animals like sponges and rotifers do not need a circulatory system because they have systems in place that allow for diffusion of substances across the organism. Comb jellies and jellyfish have diffusion through a gastrovascular compartment so that things can diffuse both inside and outside of the organism. Fish have a single blood flow circuit and a two-chambered heart. There is a single atrium (the receiving chamber of the heart) and a single ventricle (that pumps blood out of the heart). Blood is pumped to the gills and re-oxygenated, then returned to the atrium after flowing through the body. The end result is a limit in the amount of oxygen that can reach the organs and tissues of the fish organism. Amphibians, reptiles, birds, and mammals have two types of circulatory systems: a pulmonary circulation and a systemic circulation. Amphibians have a three-chambered heart that has two atria and one ventricle. The two atria get blood from both circulatory systems but the blood gets mixed into the ventricle, leading to a reduced oxygenation efficiency. There is a ridge in the ventricle that diverts blood preferentially to the pulmonary-cutaneous circuit (that is deoxygenated blood) or to the systemic circuit (that is oxygenated blood). Most reptiles have a similar three-chambered heart with a partial septum in the ventricle to divert mixed blood in separate directions with less mixing. Alligators and crocodiles have a four-chambered heart with crocodiles shunting blood toward the intestinal organs while submerged and waiting for prey. Birds and mammals have a four-chambered heart that separates the oxygenated from deoxygenated blood. It is believed to have evolved independently from the three-chambered heart. In a four-chambered heart system, the blood goes from one atrium to one ventricle that pumps deoxygenated blood from the tissues to the lungs. This is the pulmonary circuit.

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The blood gets oxygenated and enters a second atrium and onto a second ventricle that pumps oxygenated blood to the tissues in a systemic circulation.

NERVOUS SYSTEMS Animal nervous systems ultimately have some type of complex controlled system (the brain) and electrically-excitable nerve tissue that sends signals from one place to another in the organism. There are two divisions to the nervous system in animals: a central nervous system or CNS and a peripheral nervous system or PNS. The central nervous system consists of the brain and spinal cord. Mammals will have four major lobes to the brain: the frontal lobe, the parietal lobe, the temporal lobe, and the occipital lobe. Other major structures deeper in the brain are the thalamus, hypothalamus, basal ganglia, limbic system, cerebellum, and brainstem. Most higher functions depend on the activity of more than one brain area. The spinal cord sends information from the brain to bridge the gap between the CNS and the PNS (or peripheral nerves). Motor reflexes are the responsibility of the spinal cord. There are three protective coverings over the brain and spinal cord, called meninges. The outer layer is called the dura mater, which is primarily protective but also has veins that carry blood back to the heart. The middle layer is web-like and is called the arachnoid mater. The part that is intimately associated with the brain is referred to as the pia mater. Between the arachnoid mater and the pia mater is the cushioning cerebrospinal fluid or CSF. The CSF will circulate chemical substances throughout the brain and spinal cord. The peripheral nervous system involves nerves that send motor signals to the muscles and organs of the body and receive sensory information, sending it to the central nervous system. The peripheral nervous system does not have a barrier between itself and the rest of the body with the PNS exposed to injury and toxins that aren’t a major factor in the CNS. The autonomic nervous system is part of the PNS and is responsible for the unconscious control of things like the gastrointestinal system, blood pressure, heartbeat, and

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breathing rate. It is important in the animal’s fight-or-flight response that is necessary for animal survival. Digestion is also a part of the autonomic nervous system. There are two types of cells in the nervous system of animals. There are neurons, which are conducting cells, and neuroglia or glial cells, which are supporting and nonconducting cells. Neurons are non-mitotic cells that cannot be replaced if destroyed. Figure 49 shows the anatomic structure of the neuron or nerve cell:

Neurons have three cell parts: a cell body or soma, at least one dendrite, and a single axon. The cell body has the main structures that other cells have with the organelles and nucleus of the cell. They do not have centrioles, which are necessary for mitosis because these cells don’t undergo mitosis. The dendrites are the “receiving” part of the neuron. The extend out from the soma and transmit signals from the other nerve cells to the rest of the neuron. There is usually just one axon that sends a signal out to other nerves in the body. Axons can be myelinated or nonmyelinated. Myelin is a white, fatty substance made by glial cells that helps speed up the transmission of the nerve signals. In the peripheral nervous system, the myelin as made by special glial cells called Schwann cells. It wraps tightly around the axon. The equivalent myelin-producing cell in the CNS is called the oligodendrocyte. While it is possible for nerve cells to

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regenerate axons peripherally, it is not possible in the CNS. This is because the PNS nerves have a covering called a neurilemma that creates a path for the nerve axon to regenerate. Neurons can be divided into being afferent neurons, efferent neurons, or interneurons. Interneurons connect two neurons together and can go to or from the CNS. Afferent neurons are sensory neurons that carry peripheral signals to the CNS. They have long dendrites and shorter axons. Efferent neurons send signals from the CNS to the periphery—often to muscles or glands. They tend to have short dendrites and very long axons. The peripheral nervous system can be afferent (sensory) or efferent (motor).

DIGESTIVE SYSTEMS The digestive system of animals has a major digestive tract and several accessory organs. It takes larger molecules through ingestion, and processes them to make smaller molecules that can be absorbed in the GI tract. The major functions of the digestive system are to ingest food, break it down mechanically, break it down chemically, and absorb the small, absorbable molecules. The final act of the digestive tract is the elimination of waste products that are not digestible. The digestive tract, while diverse throughout the system, is basically a continuous tube from mouth to anus. It starts with ingestion through some type of mouth. In many cases, there are teeth that start the process of mechanical digestion (or breakdown). In mammals, there is a small amount of chemical digestion (via saliva) in the mouth as well. The stomach also participates in both the mechanical and chemical digestion, breaking up proteins and churning food into chyme. Most chemical digestion takes place through the action of hydrolysis in the upper small intestine using pancreatic enzymes and brush border enzymes along the intestinal wall to break down proteins, carbohydrates, and fats into absorbable nutrients. The swallowing action of the mouth is called deglutition. This is voluntary. Outside of that, there are involuntary muscles that undergo peristalsis in order to pass food through the GI tract. Besides peristaltic movements, there are segmental movements in the small intestine that move chyme back and forth so it can be maximally absorbed. It 209

is in the small intestine where the vast majority of food is absorbed, particularly the jejunum, which is the middle segment of the small intestine. The food that is not absorbed is eliminated through the large intestine and the anus.

RESPIRATORY SYSTEMS The goal of the respiratory system is to exchange oxygen and carbon dioxide between the animal and the environment. Animals breathe both voluntarily and involuntarily. The amount of air taken in and the rate of breathing is regulated mainly by the brain’s respiratory system. There is inhalation and exhalation. Inhalation fills the lungs with oxygenated air. The oxygen reaches alveoli which are small sacs that exchange the oxygen with carbon dioxide, deep within the lungs. Outside of the lungs, cellular respiration takes place, in which oxygen participates in the breakdown of glucose into CO2, making ATP in the process. Evolutionarily speaking, there has been a change in the way organisms allow for oxygen and carbon dioxide exchange. As the animal complexity and size has increased, the respiratory system developed structures (the alveoli) with a large surface area in order to allow for the maximal rate of diffusion. The diffusion process is completely passive and goes from an area of high concentration of oxygen and carbon dioxide to a lower concentration of these gases. For small multicellular organisms, diffusion across an outer membrane is enough to meet their oxygen needs. This works only up to a one-millimeter distance from the cell to the exterior of the animal. This is how flatworms and cnidarians operate; they are flat or tubular so every cell participates in gradual diffusion across the cells. Other than lungs and diffusion, animals have developed other effective ways to have gas exchange. Earthworms and amphibians respire through their skin. There is a dense interconnected capillary network just below the skin that helps participate in gas exchange. It requires that the skin be moist in order to have gases dissolve and diffuse across this surface. Water-living organisms use oxygen dissolved in water. Fish and other aquatic organisms will use gills in order to extract oxygen from the surrounding water. Water passes over 210

the gills and oxygen diffuses into the fish’s circulatory system. Gills are folded and branched so that they take in a great deal of oxygen. Gills are also seen in crustaceans, mollusks, and annelids but these will have coelomic fluid rather than blood. Figure 50 shows the respiratory system of fish:

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Insects use tracheal systems in order to respire. The respiratory systems and the circulatory systems in these organisms are separate. Instead, there are tubes that carry oxygen to the entire body efficiently. The tubes are made of chitin as is the rest of the exoskeleton of the insect. Insect bodies have respiratory openings called spiracles along the thorax and abdomen that allow oxygen to pass through the body, regulating the diffusion of oxygen and carbon dioxide. The air enters and exits the tracheal system through the spiracles. Amphibians have evolved many different ways of breathing in order to survive the different aspects of their life cycle. Younger amphibians like tadpoles have gills in order to breathe; they are confined to water. The gills disappear as the animal grows so that lungs take their place (in many cases). The lungs are more primitive than higher animals with an inefficient or absent diaphragm and the need for additional respiration through the skin. Birds have a unique respiratory system that differs from other vertebrates. They have small lungs and few air sacs. They do not have diaphragms nor do they have a pleural cavity. The gas exchange does not occur through the alveoli but happens between the air capillaries and the blood capillaries. Because flight takes a great deal of oxygen, they have evolved a relatively sophisticated way to exchange gas. Besides lungs, they have air sacs (a posterior air sac and an anterior air sac) that allows for efficient oxygen uptake, particularly during high altitude situations. Mammals have lungs that participate in gas exchange. There is air inspired through the nose that is warmed and filtered as it enters the respiratory tract. There is a conducting zone of the upper respiratory tract and a respiratory zone that participates in gas exchange. The latter zone is primarily made up of the alveoli in the lungs. Figure 51 is an image of the human respiratory system:

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Gas exchange occurs in the alveoli. Incoming air is taken in by the contraction of the diaphragm with air taken in. The oxygen diffuses across the thin alveolar membrane, which has fused with the capillary membrane so that the gases can exchange across the combined “respiratory membrane”. The alveoli contain surfactant that maintains the opening of the alveoli so that they do not collapse. The alveoli provide a very large surface area for gas exchange in mammals.

IMMUNE SYSTEMS There are two main immune systems in mammals with the innate immune system being older evolutionarily-speaking. Higher animals will have both an innate immune system and an adaptive immune system. Together, their role is to defend against pathogens. Pathogens for higher organisms include microorganisms such as bacteria, protists, and fungi. These can be found in the water, in the air, and on surfaces. The goal of the immune system is to recognize self from non-self and to get rid of those things that are recognized as non-self. The innate immune system functions since birth and is relatively nonspecific when it comes to its activity against pathogens. The adaptive immune system stores information about past infections, mounting pathogen-

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specific defenses that are remembered for long periods of time—usually the lifetime of the individual. The innate immune system involves both chemical and physical barriers that act as the first line of defense against pathogens. It does not respond to vaccinations as it has no memory. It starts with having barriers, such as the skin, respiratory tract, mucous membranes, and the GI tract. These types of systems have been in place evolutionarily for about a billion years. Things like tears and mucus will trap pathogens and will remove them from the animal’s system. If a microorganism breaches the skin or other barriers, there are other defenses. The stomach provides a chemical barrier by having a low pH that kills many pathogens. The blood-brain barrier will prevent the pathogens from entering the brain. Urination will help flush organisms out of the bladder. When a pathogen truly enters the body, the animal will have the ability to detect pathogen-associated molecular patterns or PAMPs, which are the different receptors and proteins on pathogens that characterize them as being foreign to the self. These PAMPs are found on viruses, bacteria, and parasites. Macrophages and related cells have phagocytic properties; that is, they can eat pathogens they recognize as foreign in order to get rid of them as soon as possible. Macrophages are a key player in the innate immune system. They come from monocytes, which is a type of white blood cell that can move into tissues when necessary. The main thing that the innate immune system does is to activate the inflammatory response in response to a breach in the barrier system or to a pathogen that has entered the tissues. Cells that participate in this include the following: •

Mast cell—these cells dilate blood vessels and release histamines and heparin as inflammatory mediators. They help recruit neutrophils and macrophages to the breached area.

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Macrophage—these are phagocytic cells that kill pathogens and cancerous cells.

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NK cells—these are natural killer cells that kill virally-infected cells and cancerous cells.

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Dendritic cells—these will phagocytize the pathogens and will put out antigens from the pathogen, presenting them to cells of the adaptive immune system.

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Neutrophil—these are roving cells that can exit the bloodstream to go to the site of infection in order to participate in phagocytosis.

So, the NK cells, macrophages, neutrophils, and dendritic cells all participate in phagocytosis in order to get rid of pathogens or to present antigens (that come from the pathogens) on their surfaces in order to activate the adaptive immune system. Cytokines are also important in the immune system of animals. These are basically chemical messengers that regulate the proliferation of cells, cell differentiation, and gene expression in order to affect the immune response. There are forty different cytokines in humans alone. There are the interleukins that involve white blood cell activity, interferons that are released by infected cells to warn nearby cells, and other messenger molecules that cause systemic responses to infection. Cytokines tend to be initially pro-inflammatory so that the signs of inflammation are present (such as redness, swelling, and localized heat). Other important molecules to this system are the molecules of the complement system, which are proteins that are activated early on in the infection, setting off a cascade of biochemical reactions that mark cells for phagocytosis. They are complementary to the antibody system by marking a pathogen so that both macrophages and B cells can be activated in order to engulf the pathogen. When complement proteins mark the cells for killing, this process is called opsonization. Some complement proteins will form attack complexes on the microbe in order to have pores open up in the microbial cell membranes. The adaptive immune system involves a slower immune response than the innate immune response but it has memory and is highly specific to a particular pathogen. When antigens are presented to the cells of the adaptive immune system, they are triggered to make antibodies that ultimately mark a pathogen for killing. It is the B cells that make antibodies. There are plasma cells, which are activated B cells, and memory cells that retain the memory of the pathogen so that, years from the infection, the

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memory B cells can be activated in order to prevent an infection from developing a second time. B cells and the adaptive immune system respond to antigens. So, what is an antigen? This can be anything—a carbohydrate or protein or virus particle—that is recognized as foreign and that can have an antibody made to it. The antibodies bind to a specific antigen that they’ve been made against. Once made, antibodies can facilitate the killing of the pathogen by causing their agglutination or by triggering other cells to recognize the pathogen as foreign so it can be killed. Figure 52 shows the route that B cells go through when activated:

https://www.shutterstock.com/image-vector/activation-bcell-leukocytes-lymphoblastmemory-bleukocyte-748304221?src=mkKSbIA4bKMxh6K30mACkA-1-51

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T cells also participate in the adaptive immune response. Both B cells and T cells are lymphocytes, differentiating them from other white blood cells in the body. T cells don’t directly recognize a pathogen. Instead they recognize specific antigens that are attached to MHCs (major histocompatibility complexes) that are basically self-identifying complexes. These MHCs are necessary for T cells to recognize the antigen. When a cell is infected, antigens from the pathogen will be found on the outside of the cell, linked to MHCs that identify the cell as belonging to the self but being infected as well. These antigen-presenting cells will trigger a T cell and a B cell response that is specific to the pathogen. While the B cell will be triggered to make antibodies, the activated T cell will directly kill anything that contains the antigen they’ve been activated to kill. This is called cell-mediated immunity. T cells only kill self-cells that have been identified as being infected or possibly cancerous. There are cytotoxic T cells that do the killing of infected cells and T helper cells that aid in the process but do not do any infected cell killing. T helper cells will secrete cytokines when in contact with an infected cell. This stimulates NK cells and macrophages to kill the pathogen. So, how do vaccines work? They are given to humans and animals in order to prevent an infection. These represent killed bacterial cell wall parts, killed viruses, or live but harmless viruses that can generate an immune response against the infection they represent. These vaccines basically contain antigens that allow the adaptive immune system to kick in and to develop a memory for having an infection that the individual never actually had in the first place. This memory prevents the infectious organism from taking hold in the body by tricking the immune system into thinking the person has already had the infection. These will confer a long-term response against infection.

ENDOCRINE SYSTEMS Some aspect of an endocrine system exists in animals of all types. It represents several glands that secrete hormones. Hormones can be simple molecules, modified amino acids, and peptides that act over long distances to affect the body in some way. Hormones are secreted by a variety of endocrine glands that have no ducts but secrete

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the hormone directly into the immune system. Figure 53 illustrates the aspects of the endocrine system that are seen in humans. In mammals and humans, there is the hypothalamus and pituitary gland, which together secrete most of the hormones that affect the other endocrine glands in the body. There are hormones secreted by the pituitary that affect growth, alter metabolism, generate the sexual and reproductive responses in males and females, regulate blood sugar, and regulate salt and water balance in the body. Some of this is a direct response (as is the case with growth hormone), while most act on other glands (like the adrenal gland and the thyroid gland) that do the actual end-organ action in the body. The main endocrine glands in the body are the pituitary gland, the pineal gland, the thyroid gland, the parathyroid glands, the adrenal glands, the pancreas, the ovaries, and the testes. The pituitary gland is a pea-sized gland near the base of the brain that secretes these hormones: •

Growth hormone—this regulates the growth of the body.

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Follicle stimulating hormone—this regulates the development of the gametes (sex cells) in males and females.

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Prolactin—this controls milk production in the body.

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Thyroid stimulating hormone—this regulates the output of the thyroid gland.

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Adrenocorticotropic hormone (ACTH)—this regulates cortisol secretion in the adrenal cortex, which is part of the adrenal gland.

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Melanocyte stimulating hormone—this helps to produce melanin, which darkens the skin.

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Luteinizing hormone—this regulates sex hormone production in males and females.

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Antidiuretic hormone—this increases blood pressure and regulates water loss.

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Oxytocin—this contributes to the let-down reflex when milk is secreted by the females that are lactating or breastfeeding. 218

The other hormones and the glands that secrete them include the following: •

Pineal gland—located in the brain and makes melatonin in response to darkness so that it helps to regulate the sleep-wake cycle.

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Thyroid gland—this is located in the neck and secretes two hormones (thyroxine and triiodothyronine) that regulate metabolism on a cellular level.

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Parathyroid glands—these are located behind the thyroid gland and make parathyroid hormone that increases the calcium level in the bloodstream.

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Adrenal glands—the adrenal glands are located above the kidneys. They make mineralocorticoids that regulate salt excretion and blood pressure, sex hormones, and cortisol, which has many effects on the immune system and on blood sugar values.

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Pancreas—this is located in the abdomen and regulates blood sugar by secreting insulin to lower blood sugar and glucagon to raise blood sugar.

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Ovaries—these are located in the female pelvis and are responsible for producing estrogen and progesterone under the influence of the pituitary gland.

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Testes—these are located in the scrotum of males. They secrete testosterone, which is the major male hormone.

REPRODUCTIVE SYSTEMS There is both sexual and asexual reproduction in the animal kingdom. There are advantages and disadvantages to both methods of reproduction. Asexual reproduction has the capacity to release large numbers of offspring that are genetically identical to the parent organism. It leads to highly adapted offspring during situations where the environment is stable. If the environment is unstable; however, the offspring might not be able to adapt to the changing environment. Sexual reproduction produces an organism that requires two parents but that creates a genetically unique organism. This creates diversity in the environment, which is potentially helpful in ensuring survival of the population. Usually, this involves the

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presence of a female (offspring-bearing organism) and a male (which donates only the genetic material to make the offspring). This type of system leads to fewer offspring, which might be a reproductive disadvantage over asexual reproduction. We’ve talked a little about asexual reproduction, which occurs in prokaryotes and many single-celled eukaryotic organisms. Some animals can reproduce asexually and there are those that can do both asexual and sexual reproduction. Binary fission does not generally occur in animals in the way we’ve discussed in the past. With animal binary fission, what’s meant by that is that the organism can regenerate a missing part. This can happen to certain types of flatworms (called planarians), sea anemones, and sea cucumbers, which can be split in half longitudinally in order to regenerate another half. Budding can happen in which an outgrowth of the main body will separate from the organism to grow a smaller version of itself. This can happen in invertebrate animals, such as hydras and corals but is otherwise a rare phenomenon in animals. Fragmentation involves the breaking of an individual animal, after which it regenerates the missing parts. If the part broken off is big enough, it can grow a separate individual in each part. Reproduction using this method can be seen in echinoderms, annelids, sponges, some turbellarians, and some cnidarians. Sea stars can regenerate a whole new sea star with just one arm and a portion of the central disc remaining. Parthenogenesis involves the development of an individual organism from an unfertilized egg. This can result in a diploid or haploid individual, depending on the species. This can occur in several types of insects, including aphids, stick insects, water fleas, wasps, bees, and ants. Ants, wasps, and bees will use parthenogenesis to create a haploid drone insect (which is always male). Female workers and queen bees are diploid and come directly from a fertilized egg. Larger vertebrate animals can also reproduce via parthenogenesis, including fish, amphibians, and reptiles. It can happen when females of certain species are isolated from males, and has happened in sharks and Komodo dragons.

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Sexual reproduction is the combination of reproductive cells from two organisms of the same species to create a unique offspring organism. There will be two sexes in one individual (called hermaphroditism) or two separate sexes. Some animals are hermaphrodites, having male and female reproductive systems. This is the case in slugs, tapeworms, and snails. They may self-fertilize but will usually mate with another. Self-fertilization can happen in organisms that do not move, such as clams and barnacles. Self-breeding, however, does not confer an ecological advantage as it causes inbreeding and offspring that are potentially not as fit as with true sexual reproduction. In mammals, there are two sexes. The female sex has two X chromosomes, while the male sex has an X and a Y chromosome. This system is seen in plants and in insects but is not seen in all animal species. In birds, there is a ZW system, in which the ZZ genotype results in a male and the ZW genotype results in a female. Insects, reptiles, crustaceans, and fish (some species) also follow the ZW system. There can be more complicated three-chromosome systems as is seen in swordtail fish, which have three sex chromosomes instead of two. Some species will have the determination of sex not by the chromosome situation but by some environmental factor. Alligators, tuataras, and some turtles will have a sex determination based on the temperature of the environment during incubation. Cool temperatures in some turtle species will produce males while warm temperatures will produce females. The reverse can be true in other turtle species. In some crocodiles, moderate temperatures favor both genders being produced while extremes in temperatures produce mainly females. Some species will change gender during their lifetime. Protogyny means the animal is female first and then male, while protandry means the animal is male first and then female. Oysters are all born male and then grow to become females that lay eggs. Certain reef fishes are also considered “sequential hermaphrodites” and will switch gender. Some fish will have a group of females and a single male of the species but, if the male dies, one of the females will grow and develop into a male.

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Fertilization involves the fusion of a sperm and egg. This process can be internal (happening within the female) or external (happening outside the female). Humans and most mammals have internal fertilization. The frog and the duck billed platypus will lay eggs that will be fertilized outside of the female body. External fertilization will often happen in aquatic environments in which the eggs and sperm are released in the water. This is what happens when animals spawn. In spawning, there is the release of the eggs in large numbers as well as the release of sperm in the same vicinity. This is what happens in fish, crabs, oysters, shrimp, squid, sea urchins, sea cucumbers, frogs, mosquitos, corals, and mayflies. Internal fertilization happens in many terrestrial animals, although it can be seen in aquatic animals. The male may deposit sperm in the female directly or can happen with sperm deposited into the environment, which the female later picks up and deposits. After internal fertilization, the offspring can be produced in several ways. In oviparity, the fertilized eggs are laid and develop outside of the body (as in birds, a few mammals, some fish, some reptiles, some amphibians, and some cartilaginous fish). Most reptiles and insects produce eggs with a leathery cover, while birds and turtles have hard-shelled eggs. The duck-billed platypus lays leathery eggs. In ovo-oviparity, fertilized eggs are retained in the female and are hatched inside of her or are laid just prior to hatching. This happens in some bony fish, some snakes, some sharks, lizards, some vipers, and in certain invertebrate animals. In viviparity, the young are born alive. This is seen in some cartilaginous fish, some reptiles, and almost all mammals.

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KEY TAKEAWAYS •

A circulatory system is necessary when diffusion is insufficient in getting oxygen to all animal tissues.

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The respiratory system is different in different animals but involves structures that exchange oxygen and carbon dioxide.

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The animal digestive system involves ingestion, mechanical digestion, chemical digestion, absorption, and elimination of waste.

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Animal organisms will have an innate and sometimes an adaptive immune system, the latter of which is evolutionarily younger.

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The endocrine system involves endocrine glands that send hormones through the circulatory system to act on distant organs.

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Reproduction can be asexual or sexual in animals, with a variety of mechanisms of reproduction possible.

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QUIZ 1. What system contributes least to the beating rate of the heart in animals? a. Respiratory system b. Endocrine system c. Nervous system d. Cardiac system Answer: a. The heart’s rate is determined partially by the automaticity of the heart inherent in the cells of the heart, as well as by input from the central nervous system (via the autonomic nervous system) and the endocrine system (via hormonal input). 2. Which type of organism is most likely to have an open circulatory system? a. Mammal b. Arthropod c. Fish d. Bird Answer: b. An arthropod is a type of animal that has an open circulatory system, in which hemolymph gets circulated into a large cavity rather than a system of vessels. 3. What part of the nervous system in animals will control the fight-or-flight response? a. Spinal cord b. Cerebrum c. Brainstem d. Autonomic nervous system Answer: d. The autonomic nervous system is mainly responsible for the animal’s fight-or-flight response.

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4. What aspect of the nerve cell is efferent, sending signals from the body of the neuron to other neurons? a. Dendrites b. Axons c. Soma d. Myelin Answer: b. It is the axons that send signals out of the nerve cell to other parts of the nervous system. There is usually just one axon per nerve cell. 5. How are oxygen and carbon dioxide exchanged in the lungs? a. It involves the active transport of oxygen and carbon dioxide across alveolar cells. b. It involves a direct oxygen-carbon dioxide exchange in the alveolar cells. c. Oxygen is actively pumped in but carbon dioxide passively leaves. d. Both oxygen and carbon dioxide passively move across the alveolar cells. Answer: d. Oxygen and carbon dioxide are passively diffused across the alveolar cells with both gases going from an area of high concentration to an area of low concentration (in opposite directions). 6. Besides lungs, animals have evolved several other systems for respiration. Which is not a major system used for respiration in animals? a. GI tract b. Tracheal system c. Gills d. Skin Answer: a. Each of these are ways that an animal can have gas exchange; however, they generally do not use the GI tract for this purpose.

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7. What cell is not associated with the innate immune system? a. T cell b. Macrophage c. Dendritic cell d. NK cell Answer: a. The T cell is distinctly connected to the adaptive immune system and not to the innate immune system. The others are cells that are connected to the innate immune system. 8. Which type of cell does not actively participate in the phagocytic process as part of the innate immune system? a. Dendritic cell b. Mast cell c. NK cell d. Macrophage Answer: b. The mast cell will participate in the innate immune system but it does not actively engage in phagocytosis. The other cells are phagocytic cells of the innate immune system. 9. What is not a feature of sexual reproduction? a. It produces genetically unique individuals b. There can be an advantage in unstable environments c. It involves two types of parents d. Large numbers of offspring can be created Answer: d. A potential disadvantage of sexual reproduction is that large numbers of offspring cannot be created so this is not as successful in some ways when compared to asexual reproduction.

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10. Which animal can regenerate a new organism when parts of it have been split in half longitudinally? a. Coral b. Sea anemones c. Wasps d. Water fleas Answer: b. Sea anemones and a few other species can reproduce by binary fission, which in animals, involves splitting the organism longitudinally to create two identical offspring.

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CHAPTER 12: ECOLOGY Ecology is the subject of this chapter in the course. This is the study of ecosystems in the world as well as the biosphere, which are the regions of the earth inhabited by living organisms. The ecology of populations is covered in this chapter as well as the important and timely topic of global ecological changes that have happened, are happening, and will happen to the earth as a planet.

NITROGEN CYCLE The nitrogen cycle is important in ecology because it shows how different organisms in the world interact to take nitrogen out of the environment and to put it into the proteins, RNA, and DNA necessary for all living organisms. While we’ve talked about life mainly being carbon-based, it is also clear that all living things also need nitrogen. Nitrogen is extremely available in the atmosphere but this nitrogen is not available to living things. This is because nitrogen gas or N2 gas is extremely tightly bound so that it would take a great deal of chemical energy to break the chemical bonds apart. In order for plants and animal species to use nitrogen, the N2 gas bond must be broken and converted into either ammonium (NH4), nitrate (NO3), or organic nitrogen, such as urea. But, because of the inertness of N2 gas, nitrogen in ecosystems becomes a limiting factor in the growth of plant species. The nitrogen cycle involves the movement of nitrogen between the atmosphere, the biosphere (where life lives), and the geosphere. It is a major biochemical cycle in which there are reserves of nitrogen and various processes that are involved in exchanging nitrogen from the different areas. Figure 53 shows what the nitrogen cycle looks like on earth:

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There are five main processes that take place on earth. These include nitrogen fixation, nitrogen mineralization through decay, nitrogen uptake in organisms, nitrification, and denitrification. Much of these processes take place because of bacteria and other microorganisms in the environment. Nitrogen fixation happens when N2 gas becomes ammonium or NH4. This is the only method that can get to the vast quantities of nitrogen gas in the atmosphere. The few microorganisms that can do this are referred to as nitrogen-fixing organisms, which are mainly bacterial species. They will take nitrogen gas and make it organic. This sometimes requires a symbiotic relationship with host organisms, usually plants. It is commonly seen in the symbiotic relationship between Rhizobium species and members of the legume family (clover, peas, and beans).

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In the symbiotic relationship between nitrogen-fixing bacteria and legumes, the bacteria reside in the legume root nodules and will get carbohydrates from the host plant. In the aquatic environment, however, there are cyanobacterial species that are not symbiotic and will fix nitrogen as a free-living organism. Small amounts of nitrogen get fixed in non-living situations, such as when lightning strikes, during forest fires, and in lava flows. These share the fact that they are highenergy situations that have the energy necessary to break the strong N2 gas bond. Human activity will fix nitrogen through the burning of fossil fuels, using synthetic nitrogen fertilizers, and through the cultivation of legumes as crops. These human activities have doubled the amount of fixed nitrogen in the biosphere each year. Another step involves what’s called nitrogen uptake. This is when ammonium ion becomes organic nitrogen compounds. The ammonium ion comes from the nitrogenfixing bacteria but is quickly taken up to make proteins and nucleic acids. Animals and other larger organisms take in food that has already been turned into organic nitrogenous molecules. Ultimately, plants, animals, and bacteria die and the process of nitrogen mineralization occurs. This is when things decompose after death. There are decomposing bacteria and fungi that consume organic matter and lead to the transfer of organic nitrogen to NH4 (ammonium ion) again. This leaves the ammonium ion available for nitrification by plants. Nitrification involves the biochemical transfer of NH4 to NO3 ions. Bacteria do this in order to get oxygen in a process that requires oxygen by the bacteria. It happens in high oxygen environments, such as the surface of an area of soil or decomposition. It involves a change from a positively charged ion to a negatively charged ion. The ammonium charge is positive so it can’t be leached out of the soil through rainfall but the NO3 ion is negatively charged; this leads to it being easily leached out of the soil. The nitrate (NO3) ion gets into the groundwater. Then comes denitrification, which takes nitrate (NO3) and turns it back into N2 gas plus nitrous oxide gas, which is N2O. This is an anaerobic reaction, which takes place in low oxygen environments by denitrifying bacteria. An intermediary is nitric oxide or NO

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gas, which contributes to smog. Another intermediary is the nitrous oxide (N2O) gas. This is considered a greenhouse gas, contributing to global warming. The goal is to make all N2 gas, which ultimately happens. It starts the process all over again. As you have probably surmised, man has contributed directly to greenhouse gases. The use of synthetic nitrogen fertilizers from chemically fixed nitrogen and the burning of fossil fuels has led to a lot of fixed nitrogen in the environment that hasn’t been there before. In addition, the groundwater has a lot of nitrogen in it. Drinking this groundwater with NO2 and NO3 in it (nitrite and nitrate, respectively) increases the cancer risk in humans. It has also led to the coastal fish-kill events from algae blooms in polluted ocean water. This has also led to an increase in NO gas, which is a component of smog and an increase in N2O gas, which is a greenhouse gas. This is where acid rain comes from, which leads to forest death and the decline in forests in parts of the US and Europe.

ECOSYSTEMS All of the different bacteria, animals, plants, and other organisms do not live in isolation. They live together in an ecosystem. An ecosystem, briefly, can be all the organisms living together in a small pond or tide pool; it can also be the entirety of the rainforest or grassland. An ecosystem is the combination of the organisms plus the physical environment. There are many populations or communities within an ecosystem that interact with the environment. The ecosystem is different from the community in that it involves the physical environment itself. A community is the living or “biotic” aspect of the totality of the ecosystem, making the ecosystem a combination of abiotic (environmental) and biotic factors. Ecosystems can be quite small or very large, depending on the circumstances. Ecosystems can be freshwater, marine-based, or terrestrial. The most common ecosystems are ocean ecosystems because oceans cover 75 percent of the earth’s surface. Freshwater ecosystems are the least common, comprising just 1.8 percent of the Earth’s surface. The rest are terrestrial.

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The terrestrial ecosystems can be divided into different “biomes” based on the climate of the area. There are several different biomes, such as savannas, tropical rain forests, deserts, coniferous forests, tundra, and deciduous forests. There is diversity within the biomes such that different deserts and different forests of the world are structurally different. Ecosystems have food webs, which are networks of organisms that ultimately feed on one another. They also have their own ways of participating in different biogeochemical cycles, which include the carbon cycle and the nitrogen cycle. Energy and matter are always conserved so that things like nitrogen get transferred from one state to another by organisms in the ecosystem. It’s important to know that matter simply gets recycled through the Earth’s ecosystems. It can stay within a given ecosystem but just as easily can leave one ecosystem, such as a forest, to go to another ecosystem, such as a river during rain runoff situations. The same atoms on earth get recycled by getting assembled into different chemical forms in order to be used by different types of organisms As for carbon, you can easily see that it is recycled like nitrogen. It’s in the atmosphere in the form of CO2 and gets fixed through photosynthesis. It then goes into making plants that get eaten and used in cellular respiration. The end result is CO2 formation through cellular respiration and the sending of CO2 back into the atmosphere. Waste products from animals also get excreted and used by bacteria and fungi as decomposers, leaving behind simple molecules that can be taken up by other organisms. Energy, on the other hand, cannot be recycled. It is a one-way street in an ecosystem— going from light into heat. Energy enters the ecosystems as sunlight, getting captured by plants through photosynthesis. This energy gets stored into molecules that get turned into heat and ATP in order to drive chemical reactions. When these things die, the energy is lost. Energy doesn’t get destroyed, what isn’t used gets given off as heat energy. The sun is required to drive energetic processes at all times. Ecosystems are highly dynamic with a continual recycling of phosphorus, nitrogen, and carbon. An ecosystem would die if it weren’t dynamic. Populations in ecosystems are always dying and being born or created, so that there are changes in the relative

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numbers of organisms within an ecosystem. Climate is always changing, which changes the ecosystem over time. Despite the dynamic nature of ecosystems, they are always in equilibrium, in which there is a balance of organisms in the ecosystem with relatively steady levels of the different organisms in the system. The problem happens when there is a disturbance to an ecosystem, which disrupts the balance of organisms. A disruption can be a major fire, acid rain, algal blooms, deforestation, and the introduction of a new species into the system. Some ecosystems will recover, while others will fall apart. Ecosystems can be resistant to a disturbance and will be able to recover despite the change. The system can also be resilient so that it stays steady over a long period of time. A key factor in the ecosystem is the biodiversity in the ecosystem. It means that, while some organisms do not recover after a disturbance, others will survive and will continue the ecosystem, even though it may take a while to recover.

POPULATION ECOLOGY There are many factors in the study of ecology, including the effects of the environment and the changes in the genetics of the ecosystems. Population ecology is a branch of the study of ecology and involves the different biological populations within an ecosystem, such as their structure and dynamics. This study is similar to community ecology, which studies the structure and dynamics of the different communities in an ecosystem as well as the study of population genetics, which is the study of gene frequencies within the ecosystem. Populations will differ in their level of stability. Some will be stable for many thousands of years, while others will die off and become extinct. Other populations will be transient, such as larval forms of insects that survive only until they get past that stage of their life cycle and leave the ecosystem to go to another ecosystem. Populations are groups of different individual organisms that share the same characteristics. Even though the organisms are unique within the population, they are considered ecologically “equivalent”. This means basically that they have the same life cycle, live in the same ecological environment, and react the same to the environment. 233

The population density is the number of individuals in a population per unit area. It can be numbers of organisms or weight of organisms per area (or volume in oceanic ecosystems). There is the crude density, which is the number or biomass per unit space. The ecological density, on the other hand, is the density per unit of habitat space (which is the available space that can be colonized by the members of the population). This is an important distinction because not all space in an ecosystem reflects an appropriate habitat for a specific organism. Population dispersal is possible. There are three possible dispersal patterns. In regular dispersion the individuals are regularly spaced. This is primarily seen in crops and with territorial animals. There is also random dispersion, in which there is no relationship between the different members of the population. This is also rare. Clumped dispersal is the most common, with individuals aggregated into patches with less populated areas in between. Populations are made from organisms of different age. The proportion of different animals or plants of different age groups is called the age structure of the population. This determines the reproductive status of the population. The population can be mainly pre-reproductive, reproductive, or post-productive. The duration of these different stages depends on the organism. There are three different age structures, including the following: •

Pyramidal shape—this involves a broad base of young individuals and a narrow apex of older individuals. The birth rate needs to be high and is something seen in many lower-order animals, like paramecium and insects.

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Bell-shaped polygon—this is an equal group of young and middle-aged individuals with a small number of older, post-productive organisms.

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Urn-shaped structure—this is a low percentage of young individuals and a low birth rate so that the population dwindles because many are in the postproductive years.

The number of individuals in a population depends on the birth rate and the death rate of the different organisms in the population. There is a wide variation among species as

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to the average age at which they reproduce, the number of offspring produced, and their total lifespan.

THE BIOSPHERE The biosphere or “ecosphere” is the worldwide sum of all of the ecosystems. It is the zone of life on earth, different from the atmosphere, geosphere, hydrosphere, and lithosphere. The biosphere has not always been on earth, having evolved from the rest of the elements on earth about 3.8 billion years ago. The earliest evidence for the biosphere has been found in 3.7 billion-year-old sedimentary rocks found in Greenland and in nearly as old sandstone rocks in Western Australia. Some rocks have been found indicating the possibility of life more than 4 billion years ago in Australia. Every part of the earth has some form of life, including the polar ice caps. The biosphere may extend to areas deep within the terrestrial earth and as high as 7 miles into the atmosphere. This extends the biosphere to far greater than the part that any given person can actually see. The biosphere has been found in soil, the air, hot springs, inside rocks deep underground, and in the deep ocean. Microorganisms have been found to survive in deep space but are not found there naturally. The total amount of bacterial carbon alone is about 5 times 10 to the seventeenth power grams. Prokaryotes make up the vast majority of the mass of the biosphere. In total, the biosphere is the sum of all of the biomes on earth.

GLOBAL ECOLOGICAL CHANGES Global ecological change basically involves climate change that can take place over many decades or over millions of years. It is caused by biotic processes (by living organisms), changes in solar radiation received by the sun, volcanic eruptions, and plate tectonics. In today’s time, humans have been considered primary players in climate change leading to global warming. Even without human involvement, there have been changes in the earth’s climate over the millennia since life has come on earth.

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Factors that shape climate are called climate forcings or forcing mechanisms. These can be internal or external mechanisms. Internal mechanisms are changes within the climate itself because of natural processes. Thermohaline circulation (which is a part of the large-scale ocean circulation that is driven by global salt density gradients created by surface heat and freshwater fluctuations) is an internal forcing mechanism. External forcing mechanisms include human changes (such as emissions of greenhouse gases), changes in solar input, changes within the earth’s orbit, and volcanic eruptions. Human changes that force climate change are called anthropogenic forcing mechanisms. Other climate forcings include variations in solar radiation, changes in the earth’s orbit, changes in the oceans, continental drift, greenhouse gas concentrations, and atmospheric changes. By definition, climate change happens over long periods of time, and does not involve things like El Niño, which is just a transient change in weather patterns. Climate change is not necessarily the same thing as global warming as it represents the changes that have occurred over the past billions of years that earth has been formed along with the changes that will happen in the next billions of years with human inhabitants on earth. Global warming is just a part of this. Climactic change is another related term. It involves climate changes that have occurred over time scales on the order of decades. So, how have anthropogenic factors influenced climate? The scientific consensus is that climate is definitely changed

and that these changes have been in a large part due to

human activities. The consensus is also that the changes that have happened are largely irreversible so that nothing we do now will reverse what’s already happened. The biggest change is an increase in CO2 levels in the atmosphere from burning fossil fuels, the use of aerosols, and the release of CO2 by cement manufacturers. Things like land use, the depletion of the ozone layer, the raising of cattle that produce methane, and deforestation have all affected the climate.

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KEY TAKEAWAYS •

There are different cycles of nutrients with the nitrogen cycle being an important one as nitrogen is a limiting nutrient in the formation of living things.

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There are nitrogen fixing bacteria that take nitrogen from the atmosphere and denitrification bacteria that put the nitrogen back into the atmosphere.

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Ecosystems can be large or small but involve the interaction of organisms in a specific area with the physical characteristics of the environment.

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Population ecology is the study of different organisms and their growth or lack of growth in numbers in a specific area.

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The biosphere is the totality of the ecosystems and encompasses areas deep within the earth and parts of the atmosphere but not in deep space.

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Climate change has happened for billions of years, even when humans did not inhabit it the earth

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Humans have affected the climate in irreversible ways through an increase in greenhouse gases, deforestation, and other human activities.

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QUIZ 1. Which process least affects nitrogen fixation on earth in modern times? a. Cyanobacteria b. Symbiotic nitrogen-fixers c. Fossil fuel burning d. Lightning strikes Answer: d. Each of these is a major way that nitrogen fixation occurs; however, lightning strikes play a minor role in this process. 2. What molecule gets made by nitrogen-fixing bacteria? a. Nitrate b. Nitrite c. Ammonium d. N2 Answer: c. Nitrogen-fixing bacteria get N2 from the atmosphere and make ammonium out of it in the process. 3. Which nitrogen cycle process contributes to greenhouse gases? a. Denitrification b. Nitrogen fixation c. Nitrogen mineralization d. Nitrification Answer: a. Denitrification takes the NO3 and turns it ultimately back into N2 gas. This process has intermediaries such as N2O gas, which is a greenhouse gas that contributes to global warming. It ultimately means that all of the burning of fossil fuels and the use of nitrogencontaining fertilizer is contributing to the N2O getting into the atmosphere.

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4. Which form of nitrogen is what most contributes to smog? a. N2 b. b. NH4 c. N2O d. NO Answer: It’s the NO gas that contributes to smog and the N2O gas that contributes to greenhouse gases. Ultimately, it gets transferred into N2 gas but these intermediaries have led to things like acid rain, smog, and greenhouse gases that have been a direct consequence of using synthetic nitrogen fertilizers. 5. What is the most common ecosystem on earth? a. Ocean b. Freshwater c. Rain forest d. Desert Answer: a. The ocean ecosystem is the largest ecosystem, primarily because the oceans comprise about 75 percent of the surface of the earth. 6. In an ecosystem, what does not get recycled as part of the metabolic processes in animals and plants? a. Nitrogen b. Carbon c. Energy d. Phosphorus Answer: c. All of the major atoms in the bodies of plants, animals, bacteria, and other species get recycled over and over again; however, energy goes in one direction and gets lost, requiring continual input by the sun in order to have a steady supply of energy.

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7. What is not a feature of ecosystems? a. They are resilient against disturbances b. They are static c. They are resistant to disturbances d. They are biodiverse Answer: b. Each of these is a feature of ecosystems except that ecosystems are dynamic and are not static. The would fall apart if they are not dynamic. 8. What is the main thing that happens when a population is urn-shaped with a greater population of post-reproductive organisms and few reproductive organisms? a. The population grows exponentially. b. The population grows at a steady state (or basically stays the same). c. The population declines. d. The population ultimately becomes extinct. Answer: c. In this type of population, the population declines but does not necessarily become extinct because there are fewer productive organisms. 9. What is least likely to contain the biosphere of the earth? a. Deep space b. Deep oceans c. Deep within rocks d. Deep into hot springs Answer: a. Life has naturally been found in each of these areas, making them part of the biosphere, except for the deep space environment, which can allow the survival of bacterial organisms although these have been artificially introduced into the deep space environment by astronauts and aren’t found there naturally.

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10. What is an example of an internal climate forcing? a. Emission of greenhouse gases b. Volcanic eruptions c. Changes in the solar output d. Thermohaline circulation Answer: d. Each of these is an example of external climate forcing with the exception of thermohaline circulation, which involves a forcing change that takes place within the climate itself rather than externally.

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SUMMARY OF THE COURSE The purpose of this course was to introduce the vast world of biology to the inquiring student. Biology, as you have come to understand in this course, is simply the study of living things. In this course, you learned about what constitutes a “living thing” versus nonliving organisms. Each of the main categories of living things were discussed, including the biology of viruses, bacteria, protists (including fungi), animals, and plants. You have also come to learn that biology is also concerned with genetics, evolution, and ecology—each of which is important to the way that biological organisms appear to us in today’s time and in the future, which is why they were covered in this course. Chapter one in the course began the discussion of living things by explaining what constitutes a living thing. There are certain characteristics of living things that make humans, plants, and even viral particles called living things. The biochemistry of life is something that unifies life and involves molecules that are only seen, at least in concert, in things that are considered living organisms. Life exists, for the most part, in an aqueous environment and so the physiology of life in relation to water was discussed as part of this chapter. Virus anatomy and function were the focus of Chapter two in the course. Viruses are the most basic structures in life and, some would argue, they barely qualify as truly representing life. As you saw in the first chapter, however, viruses are basic living things that have structure and that replicate. The way viruses multiply and cause disease in other living things was introduced as part of this chapter. Chapter three covered the topic of bacteria. Bacteria are single-celled organisms that, compared to viruses, are remarkably complex. These are prokaryotes as opposed to the typical animal and plant eukaryotic cells with the ability to divide and grow independently of other organisms. You learned that there are many types of bacteria, some of which are motile. The physiology of bacteria, particularly the way they can become motile, was discussed in this chapter.

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Chapter four in the course explained the biology of animal cells, including their anatomy and physiology. These were the cells and cell types people are more familiar with, with multiple organelles that unite to create basic animal cell physiology. The structure and function or “physiology” of the animal cell was presented to you in detail in this chapter along with the ways that genetic material divide. Both mitosis and meiosis, important in cellular and animal reproduction, were covered as part of this chapter. Chapter five talked about the inner workings of cellular metabolism. Animal cell metabolism involves primarily cellular respiration and the use of oxygen to break down nutrients for use as fuel or energy, usually resulting in the making of ATP, the universal energy currency of the cell. There are processes within cells in place for anaerobic respiration and fermentation, which was discussed in this chapter. Plants use their cellular machinery to participate in photosynthesis, which yields oxygen and utilizes carbon dioxide. This process was also discussed as part of this chapter. Genetics was the topic of discussion in Chapter six in the course. Genetics is the study of how traits are passed from one generation to the next, which involves the building blocks of genetics, DNA and RNA. These are divided into chromosomes and genes that together write the code that determines the offspring’s genotype (or genetic code) and phenotype (or physical appearance). Genes are tightly regulated so that some genes are expressed, while others are suppressed. This process of gene regulation was also covered in this chapter. The focus of Chapter seven in the course was evolution and evolutionary processes, whereby individual species and populations gradually change over time because of the natural selection of the species that have inherited advantages over other species. Much of this involves Darwinian evolutionary principles, which was covered in this chapter. The history of evolution on earth and the origin of species has been largely uncovered by those who study evolution and these were topics of discussion in this chapter. The Chapter eight in the course explained the main divisions in nature and living things, outlining the six major kingdoms and their subdivisions. The way that biological species are defined was discussed in this chapter. The major features of each kingdom

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and how kingdoms and their subdivisions are determined were important topics in this chapter. Because archaea and Protista hadn’t yet been covered, they were also discussed in separate sections. Chapter nine in the course involved an extensive discussion of the cellular structures, basic anatomy, and reproductive functions of plants. Plants use much different nutrients when compared to animals and use these nutrients to participate in photosynthesis and in making nutritional substances used by many animal species. Plants have been the subject of a great deal of discussion in the world when it comes to biotechnology and genetic modification. This hot topic was covered in this chapter. Chapter ten in the course talked about fungi, their anatomy and physiology. Fungi are a broad category of organisms, ranging from microscopic organisms to the commonlyknown fungi, such as mushrooms. What they have in common and how they differ from one another were covered in this chapter. Fungi have their own unique way of reproducing themselves, which was explained as part of this chapter. The focus of Chapter eleven was the various systems that make up complex animals. All animals must have some way of obtaining nutrients through digestive systems, must circulate nutrients, and need to use respiration to have oxygen for energy. These will be different, depending on the animal species. Animal cells will have nervous systems of some sort and need strong immune systems to defend against pathogens. These systems as well as the endocrine systems and hormones in animal systems were discussed in this chapter. Ecology was the subject of Chapter twelve in the course. This is the study of ecosystems in the world as well as the biosphere, which are the regions of the earth inhabited by living organisms. The ecology of populations was explained in this chapter as well as the important and timely topic of global ecological changes that have happened, are happening, and will happen to the earth as a planet.

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COURSE TEST QUESTIONS 1. What is a characteristic of the responsiveness of living things that differs from nonliving things? a. There is an external stimulus involved in the behavior of the thing. b. The thing must follow the laws of physics. c. The thing follows a predictable pattern. d. The thing must expend energy in order to respond. Answer: d. In living things, there must be the expending of internal energy of the thing in order to respond to a stimulus. This is not the case in nonliving things. They follow a predictable pattern in response to a stimulus and follow the laws of physics but do not themselves expend energy from within. 2. What is not a feature of asexual reproduction of living things? a. The production of two or more cells from a parent cell. b. The potential for differentiation of a daughter organism. c. The presence of DNA from two separate organisms to create a unique organism. d. The duplication of genetic material to create two identical cells. Answer: c. Asexual reproduction involves a single parent cell that divides its genetic material to make two identical daughter cells, although there is always the potential for differentiation of one or more cells. Sexual reproduction, on the other hand, involves the combining of genetic material to make a unique organism.

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3. What is the definition of entropy when it comes to living things? a. A measure of disorder within the organism. b. The interaction of an organism with their environment. c. The usage of energy to cause reactions to happen. d. The ability to digest nutrients to build structure. Answer: a. Entropy is a measure of disorder within a system. While it appears that life contradicts the laws of entropy, this is not truly possible because living things need energy to counteract entropy and when living things die off, the entropy becomes positive again—toward the direction of increasing disorder. 4. What aspect of hierarchy does not apply to both unicellular (single-celled) organisms and multicellular organisms? a. Molecules b. Organelles c. Atoms d. Organ systems Answer: d. Organ systems are only aspects of multicellular living things; they cannot apply to single-celled organisms as these are confined to just one independently-functioning cell. 5. When does a group of organisms in a hierarchy first diverge to involve members of a different species? a. Ecosystem b. Community c. Biosphere d. Population Answer: a. An ecosystem is the smallest hierarchical category that involves organisms of different species interacting in the same physical space. Both populations and communities involve members of the same species, while a biosphere is all of the ecosystems together.

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6. What is the largest biosphere known? a. The solar system b. Earth c. The oceans d. The atmosphere Answer: b. Because there are no known sources of life outside of the earth, the earth is the largest biosphere. This is larger than the oceans and the atmosphere and represents the combined effects of all of the ecosystems together. 7. What is not one of the top four atoms seen in living structures? a. Oxygen b. Hydrogen c. Nitrogen d. Phosphorus Answer: d. Each of these are seen in a living organism’s molecules; however, phosphorus is not one of the top four organic atoms seen in life. 8. Which atom defines a molecule as being “organic” and belonging to life? a. Carbon b. Oxygen c. Hydrogen d. Nitrogen Answer: a. Life is basically carbon-based because all organic molecules contain carbon. Carbon is the core atom found in all organic molecules.

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9. What is the chemical formula for methane? a. NH3 b. CH3 c. CO d. CH4 Answer: d. Methane or CH4 is a gaseous molecule that binds one carbon atom with four hydrogen atoms, which is a stable molecule found in rare situations in living things. Methanobacteria are not bacteria but are unicellular organisms that use CH4 and CO2 to make carbon-based organic molecules without the presence of oxygen. 10. How many free electrons are there available for combining with other atoms when it comes to carbon? a. 2 b. 3 c. 4 d. 6 Answer: c. Carbon just has six electrons in total. Of these, four of them are available for bonding. This makes carbon a versatile molecule that can combine in all four “corners” of the molecule (even though they are not technically corners as the electrons must be as far apart from one another in 3 dimensions as possible). 11. Which common atom does not make up the structure of carbohydrates? a. Nitrogen b. Carbon c. Hydrogen d. Oxygen Answer: a. Carbohydrates are different combinations of carbon, hydrogen, and oxygen. They do not have nitrogen as part of their structure.

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12. Which of the following sugars is not a monosaccharide? a. Galactose b. Sucrose c. Glucose d. Fructose Answer: b. Sucrose is a disaccharide and is not a monosaccharide. The others are the three hexose monosaccharides seen in living things. 13. Which sugar is considered a pentose instead of a hexose molecule? a. Glucose b. Galactose c. Ribose d. Fructose Answer: c. Ribose is a pentose sugar found in RNA and is a 5-carbon sugar rather than a 6-carbon sugar like the other three molecules. 14. What molecule makes up a membrane bilayer? a. Phospholipids b. Triglycerides c. Cholesterol d. Polysaccharides Answer: a. Phospholipids have a hydrophobic side and a hydrophilic side. This allows for a central hydrophobic section that is “sandwiched” between the hydrophilic outer layers. 15. What do the different lipid types have in common? a. They all contain nitrogen. b. They all contain a 4-carbon ring. c. They are not water-soluble. d. They all have hydrophobic and hydrophilic ends.

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Answer: c. Lipids are not water-soluble, although things like phospholipids have hydrophobic and hydrophilic ends. Others are completely hydrophobic. Only steroids have a 4-carbon ring. None of them contain nitrogen. 16. How many amino acids are there in nature? a. 12 b. 20 c. 22 d. 34 Answer: c. There are 22 amino acids in nature although two are synthesized by other amino acids. The rest are encoded for by nucleic acids as part of the genetic code. 17. What is the simplest amino acid with the simplest side chain? a. Glycine b. Phenylalanine c. Histidine d. Cysteine Answer: a. Glycine is the simplest amino acid, with a side chain that is just a carbon atom, giving it the chemical formula of HCHOOHNH2. 18. Which molecule is smaller? a. Oligopeptide b. Polypeptide c. Amino acid d. Peptide Answer: c. An amino acid is the smallest molecule, made from just one amino acid. Polypeptides are the longest, made from multiple amino acids together.

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19. In a DNA molecule, there is a combination of nitrogenous bases that link the double helix together. Which molecule attaches to an adenine (A) base, forming a base pair in the DNA molecule? a. Cytosine b. Guanine c. Uracil d. Thymine Answer: d. A thymine molecule always forms a base pair with adenine in a DNA double helix molecule. Uracil is in RNA and not in DNA. 20. What is not a part of the nucleic acid molecule? a. Phosphate group b. Carbon chain c. Pentose sugar d. Nitrogenous base Answer: b. A carbon chain is not a part of the nucleic acid molecule; it does contain a phosphate group, pentose sugar, and nitrogenous base. 21. What is not an argument for viruses being considered living organism? a. They have organelles b. They reproduce c. They undergo evolution d. They contain genetic material Answer: a. Each of these, except for having organelles, represents an argument for viruses being considered living organism. Additionally, viruses are not cellular species.

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22. Which entity in the viral line is least like life because it does not contain a protein coat? a. Satellite virus b. Plasmid c. Viroid d. Virion Answer: b. Plasmids do not contain protein coats and are considered just free pieces of DNA or RNA that can be transported between cells. They are least like life because they don’t contain any protective protein coat. 23. What is the main function of the protein tail on a complex virus particle? a. To allow for mobility of the viral particle b. To house the nucleic acids in the virus particle c. To inject the nucleic acid into the cell it infects d. To stabilize the icosahedral structure of the virus particle Answer: c. The virus that has a protein tail uses it to inject nucleic acid into the cell it infects. The proteins “contract” so that the nucleic acid can be directly injected into the cell. 24. What shape do enveloped viruses look like? a. Icosahedral b. Pleomorphic c. Spherical d. Helical Answer: a. Enveloped viruses are generally icosahedral but tend to look more spherical because there are many faces on the viral particle’s icosahedron.

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25. What type of genome is mainly seen in plant viruses (and most other viruses). a. Single-stranded DNA molecules b. Double-stranded DNA molecules c. Double-stranded RNA molecules d. Single-stranded RNA molecules Answer: d. Single-stranded RNA molecules make up the genome of most plant viruses and RNA is considered the most common type of genome in viral particles. 26. Which type of viral nucleic acid structure can be directly translated without an intermediary action? a. Double-stranded RNA b. Plus-strand RNA c. Minus-strand RNA d. Double-stranded DNA Answer: b. Plus-strand RNA involves RNA that is immediately translated into proteins without having an intermediary step, such as turning a minus-strand RNA molecule into a plus-strand RNA. 27. What is the reason why people get infected by the influenza virus every year? a. There are many types of influenza viruses in the world. b. Two influenza viruses fuse together. c. There is antigenic drift because of mutations of the nucleic acids. d. The immune system cannot mount an attack against such a small viral particle. Answer: c. There are mutations of the nucleic acids that lead to antigenic drift—a drift in the shape of proteins on the outer surface of the viral particle that makes it unidentifiable to the host.

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28. What is the most accurate way to describe the proliferation of viral particles in a cell? a. Division b. Replication c. Multiplication d. Assembly Answer: d. Viral particles make multiple copies of themselves through assembly of viral particles in the cells they infect. 29. In an HIV infection, what is the last thing that happens in the virus replication cycle? a. Penetration b. Replication c. Budding d. Assembly Answer: c. Budding out of the infected cell in order to have an enveloped virus happens as the last part of the virus replication cycle. 30. What do the late genes do in the making of new virus particles? a. They get incorporated into the host genome. b. They make the viral structural proteins. c. They cause lysis of the host cell. d. They make the viral nucleic acid particles. Answer: b. The late genes generally make viral structural proteins that are assembled to make the total viral particle. 31. What is involved in maturation of a virus? a. The modification of proteins in the viral capsid b. The development of a viral envelope c. The release of viral particles from the host cell d. The changing of a provirus to a virus

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Answer: a. Modification of proteins of the viral capsid after the capsid has been made is also referred to as maturation. It generally occurs after the virus has been released from the host cell. 32. How do most bacteriophages get inside the bacterial cell to infect them? a. Through endocytosis of the viral particle into the cell b. By binding to receptors and fusing the envelope with the bacterial cell membrane c. By degrading the cell membrane to gain entry d. By the injection of viral genome into the bacterial host Answer: d. These bacteriophages will inject the viral genome into the bacterial host cell via a complex mechanism involving protein tails. 33. Which virus is not known to pass vertically? a. Hepatitis B b. Chickenpox c. HIV d. Herpes simplex Answer: d. Herpes simplex is a cold sore virus that doesn’t get passed from mother to child. The other viruses can get passed from mother to child in utero or at the time of birth. 34. What is the best way to reduce the number of susceptible individuals in a viral infection? a. The use of vaccines b. The use of antiviral medications c. The use of disinfectants d. Improved sanitation Answer: a. Vaccines will directly reduce the numbers of susceptible individuals to a particular viral infection.

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35. When is a person most likely to pass on a viral infection without knowing it? a. Incubation period b. Communicative period c. Symptomatic period d. Recovery period Answer: c. During the communicative period, a person is likely to pass on a viral infection without knowing it because they are infected and incubating but are not symptomatic. 36. Which virus is known to cause cervical, anal, and penile cancer? a. HIV b. Hepatitis B c. Epstein-Barr virus d. Human papillomavirus Answer: d. Human papillomavirus causes many types of cancer, including cervical, anal, and penile cancer. 37. In understanding viral diseases, what are vectors? a. Live attenuated viruses that give disease in immunocompromised individuals. b. Viral particles that are transmitted vertically from parent to child. c. Vaccines that prevent viral infections. d. Carriers of viruses from host to host. Answer: d. Vectors are carriers of viral particles from host to host, causing diseases between individuals. 38. In understanding viruses, what is a bacteriophage? a. A virus that is as large as a small bacterium b. A live, attenuated viral particle c. A virus that infects only bacteria d. A virus that uses bacteria to infect animals or plants

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Answer: c. A bacteriophage is a virus that infects only bacteria. 39. Which type of organism uses restriction endonucleases in order to fight off viral infections? a. Humans b. Bacteria c. Plants d. Animals Answer: b. Bacteria have restriction endonucleases that destroy nucleic acids from virus particles because they are foreign to the cell. This is not the case with the other species. 40. Which type of organism is most prominent in the oceanic ecosystem? a. Phytoplankton b. Archaea c. Bacteria d. Viruses Answer: d. There are more than 10 times the numbers of viruses than there are archaea and bacteria, which are the next most common organism in the oceans. 41. What shape bacteria are the bacilli? a. Spiral b. Spherical c. Comma-shaped d. Rod-shaped Answer: d. Bacteria that are bacilli are basically rod-shaped organisms.

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42. What shape of bacteria are the vibrio bacterial species? a. Spiral b. Spherical c. Comma-shaped d. Rod-shaped Answer: c. Vibrio bacteria are basically comma-shaped bacteria. Spirochetes are spiral; cocci are spherical, and bacilli are rod-shaped. These are the main shapes that bacteria come in. 43. Which bacterial species tends to be seen as diploid pairs of bacterial organisms? a. Neisseria b. Myxobacteria c. Actinobacteria d. Streptomyces Answer: a. Neisseria is found in pairs of organisms—often referred to as diploid pairs. Bacteria can form filaments, chains, bunches, and other complex aggregates of microorganisms. 44. What are the bacterial structures called in which there are dormant bacteria resistant to drying and other adverse conditions? a. Bacterial mats b. Bacterial spores c. Biofilms d. Microcolonies Answer: b. Bacterial spores are organizations of bacteria in which certain bacteria go dormant and resist adverse conditions around them, such as drying. They can become activated again when the environmental conditions are right.

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45. What are the photosynthetic structures called in photosynthetic bacteria? a. Carboxysomes b. Chlorosomes c. Liposomes d. Peroxisomes Answer: b. The chlorosomes are structural components of bacteria that come from invaginated cell membranes of photosynthetic bacterial species. 46. What is the cell wall in bacterial structures made from? a. Peptidoglycan b. Phospholipids c. Chitin d. Cellulose Answer: a. Peptidoglycans are polysaccharides that are crosslinked with small peptide molecules, forming a layer that protects the cell membrane of bacterial cell walls. 47. Which is the cell wall structure of Gram-positive species of bacteria? a. A double layer of lipids and no teichoic acid b. A thick phospholipid-containing cell wall c. A thin peptidoglycan cell wall d. A thick peptidoglycan and teichoic acid cell wall Answer: d. Gram-positive bacterial organisms have very thick cell walls consisting of multiple layers of teichoic acids and peptidoglycans.

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48. Which structure is used in bacteria to confer motility to the organism? a. Attachment pili b. Cilia c. Flagellae d. Fimbriae Answer: c. Flagellae are structures on the surface of the bacterial cell that confer motility to the bacterial organism. 49. Bacteria that use organic molecules to gain energy as nutritive substances are called what? a. Lithotrophs b. Phototrophs c. Aerobes d. Organotrophs Answer: d. Organotrophs are bacteria that use organic substances in order to gain energy. 50. Which is a type of bacteria that specifically uses oxygen as a terminal electron receptor in the metabolic processes of the cell? a. Anaerobes b. Lithotrophs c. Aerobes d. Phototrophs Answer: c. Aerobes are organisms that have oxygen as the terminal electron receptor in the cellular metabolic processes. 51. Where does carbon come from to build organic molecules in organisms called “autotrophs”, mainly certain types of bacteria? a. Carbon dioxide b. Methane gas c. Other organic molecules d. Sunlight 260

Answer: a. Autotrophs are bacterial species that fix carbon dioxide in order to make organic molecules. 52. What is the carbon source for the making of organic molecules in microorganisms that are referred to as heterotrophs? a. Carbon dioxide b. Methane gas c. Other organic molecules d. Sunlight Answer: c. Heterotrophs will get carbon from other organic molecules as sources of nutrients to make structural cellular molecules. 53. In understanding bacteria, what is quorum sensing? a. Cell-to-cell transfer of DNA b. Inter-cellular communication process c. The ability to confer antibiotic resistance d. Forming spores to protect the bacteria from the environment Answer: b. Quorum sensing is an inter-cellular communication process in which cells set up ways to interact with one another as a unit. 54. Bacterial species that live within or on a host without affecting the host either way are referred to as what? a. Mutualists b. Pathogens c. Commensalists d. Predatory Answer: c. Commensal bacteria or commensalists will behave in a neutral way when growing within or on another host organism.

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55. The relationship between humans and the bacteria residing in the human gut is one of what type? a. Predatory b. Pathogenic c. Commensalistic d. Symbiotic Answer: d. Bacteria of the GI tract in humans are symbiotic or mutualistic, whereby humans rely on the bacteria and the bacteria rely on the humans to survive. 56. How are bacterial species classified in modern science? a. On the basis of their genomes b. On differences in structural morphology c. By their different staining techniques d. By virtue of their metabolic properties Answer: a. Modern science uses polymerase chain reaction techniques in order to identify genomic differences in different bacterial species. 57. When a group of bacteria first encounter a high-nutrient environment, what phase of growth do they enter? a. Death phase b. Lag phase c. Logarithmic phase d. Stationary phase Answer: b. The organisms first adjust to their environment in the lag phase so they can biosynthesize proteins and prepare for exponential growth.

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58. What is the bacterial phase of growth called that is also referred to as the exponential phase? a. Lag phase b. Stationary phase c. Logarithmic phase d. Death phase Answer: c. The logarithmic phase is also referred to as the exponential phase in which there are large amounts of bacteria produced and binary fission happening at a continual rate. 59. What ultimately powers the flagellum used by bacteria in order to have movement? a. An electrochemical gradient across the membrane b. Anaerobic respiration that generates ATP molecules c. The electron transport across the cell membrane that creates energy d. The movement of the cell’s cytoskeleton Answer: a. There is ion flow across an electrochemical gradient that powers a motor at the base of the flagellum. 60. A bacterial organism that has clusters of flagella at each end of the cell is said to be what type of cell? a. Monotrichous b. Lophotrichous c. Peritrichous d. Amphitrichous Answer: b. A lophotrichous bacterium has clusters of flagella located at each end of the cell that help to engage the cell in motility in its environment.

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61. Which are the parts of the cytoskeleton that are responsible for muscle contraction? a. Microfilaments b. Intermediate tubules c. Intermediate filaments d. Microtubules Answer: a. Microfilaments are the thinnest structures of the cytoskeleton. They are responsible for muscle contraction in muscle cells as they are made of actin and interact with myosin to contract the muscle cell. 62. Which are the parts of the cytoskeleton that allow the formation of cilia and flagella in animal cells? a. Microfilaments b. Intermediate tubules c. Intermediate filaments d. Microtubules Answer: d. Microtubules are thick filaments that form cilia and flagella in animal cells. These structures use the microtubules in order to protrude from the cell itself and to move. 63. What is the cell structure made in the nucleolus of a cell? a. DNA b. Messenger RNA c. Ribosomal RNA d. Proteins Answer: c. Ribosomal RNA is made in the nucleolus of the cell. The rRNA goes on to participate in the protein-making process in the ribosomes of the cell.

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64. What is the main function of smooth endoplasmic reticulum in the animal cell? a. To package proteins for transport b. To make lipids and hormones c. To make RNA for the cell d. To translate proteins Answer: b. Smooth endoplasmic reticulum or SER is responsible mainly for making lipids and hormones for the cell. 65. What is the function of ribosomes in the animal cell? a. They package molecules for transport b. They make carbohydrates c. They make proteins d. They make lipids and hormones Answer: c. Ribosomes are strictly protein-making structures within the cell because they act with messenger RNA and transfer RNA to translate the DNA/RNA messages within the cell into proteins. 66. What is the main function of lysosomes? a. They are storage molecules inside the cells. b. They digest macromolecules and microbes for the cells. c. They transport proteins within the cell to the outside of the cell. d. They modify lipids and proteins so they are more functional. Answer: b. Lysosomes will act to digest macromolecules and microbes for the cell, acting as “garbage disposals” for the cell. 67. Which is the major byproduct of metabolism in peroxisomes? a. Hydrogen peroxide b. CO2 c. Peroxidase d. Glucose

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Answer: a. Hydrogen peroxide is a major end-product of metabolic processes in the peroxisome of the animal cell. 68. Which cell membrane transport system is considered a passive form of transport, requiring no cellular energy? a. Phagocytosis b. Exocytosis c. Pinocytosis d. Osmosis Answer: d. Osmosis is the passive transport of molecules across a membrane; this is different from the active transportation methods of phagocytosis, pinocytosis, and exocytosis. 69. Which molecule does not cross the cell through active transport? a. Glucose b. Amino acids c. Water d. Potassium Answer: c. Each of these requires cellular energy in the course of active transport except for water, which passes through the cell via osmosis, not an active process. 70. Which cellular process is also referred to as endocytosis? a. Pinocytosis b. Exocytosis c. Active transport d. Phagocytosis Answer: d. The processes of phagocytosis and endocytosis are basically the same because substances are taken in by the cell for different purposes. In phagocytosis, the substance is often a pathogen that is later destroyed by the cell.

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71. What is the main purpose of cellular respiration? a. To make cellular energy b. To use up oxygen by the organism c. To give off CO2 d. To generate heat for the organism Answer: a. The main purpose of cellular respiration is to make cellular energy in the form of ATP, although all of the other processes do happen as part of cellular respiration. 72. Which organelle in the cell contains digestive enzymes? a. Vacuoles b. Lysosomes c. Golgi apparatus d. Ribosomes Answer: b. The lysosomes in the cell contain digestive enzymes in order to break down the different macromolecules needing breakdown within the cells. 73. What molecule does not participate in the translation process in a cell? a. Transfer RNA b. DNA c. Messenger RNA d. Amino acids Answer: b. Translation involves the taking of the mRNA molecule and adding one amino acid at a time through the combined messaging system between mRNA and tRNA. DNA is not involved directly in this process.

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74. What phase is the part of the cell cycle in which the cell does not participate in the division process? a. Gap 1 phase b. M phase c. Gap 2 phase d. Gap 0 phase Answer: d. The Gap 0 phase involves cells that are not dividing and are in a quiescent, resting state. 75. What is the last part of the cell cycle referred to as? a. Karyokinesis b. Interphase c. Cytokinesis d. Metaphase Answer: c. Cytokinesis is the last part of the cell cycle, when the cell divides its cytoplasm and organelles to make daughter cells. 76. What three phases of the cell cycle are not among those that are collectively referred to as being in interphase? a. M phase b. G1 phase c. S phase d. G2 phase Answer: a. M phase is the mitosis phase; interphase involves mainly the G1 phase, S phase, and G2 phase. 77. What is the end result of one cell undergoing meiosis? a. Two diploid cells b. Two haploid cells c. Four haploid cells d. Four diploid cells

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Answer: c. There are four haploid cells made from one cell in animal, plant, and fungal cells that undergo the meiotic process. 78. How many ova are created from a single female germ cell in animals? a. One b. Two c. Three d. Four Answer: a. There are four haploid cells created from a germ cell; however, three of these are extruded as polar bodies with only one ovum created from a female germ cell. 79. What is involved in genetic recombination in meiosis? a. DNA is duplicated and separates to opposite sides of the cell. b. Gene segments are exchanged to ensure unique haploid properties. c. Cell division occurs without DNA division. d. The germ cell divides at once into four haploid cells. Answer: b. Gene segments are exchanged in recombination in order to have unique haploid cells produced when meiosis is finished. 80.During what phase of meiosis does genetic recombination occur to create genetic diversity? a. Prophase of Meiosis II b. Before meiosis begins at all c. During prophase of Meiosis I d. During metaphase of Meiosis II Answer: c. Genetic recombination occurs as soon as Meiosis I starts, during prophase of Meiosis I, when there is a diploid cell with chromosomes that are lined up together in close proximity to each other.

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81. How many net ATP molecules are made in the glycolysis portion of the breakdown of glucose? a. 1 b. 2 c. 3 d. 4 Answer: b. The net number of ATP molecules is 2 because two are used up in the beginning but four are made in the reaction to lead to a net of 2 molecules. 82. Which enzyme starts the entire process of glycolysis? a. Hexokinase b. Phosphoglucose Isomerase c. Aldolase d. Phosphofructokinase Answer: a. All of these enzymes act in the glycolysis pathway but the first molecule that starts this process is called hexokinase, which takes the glucose (hexose) molecule and adds a phosphate molecule to it (remember that all kinases add phosphate groups to organic molecules). 83. Many reactions in the glycolysis pathway require something to block the negative charge involved in the reaction. Remember that many reactions do not like to have a negative charge (or a positive charge) left over. What ion is necessary to shield these negative ions in glycolysis? a. Sodium b. Magnesium c. Potassium d. Zinc

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Answer: b. Many of these reactions are magnesium-dependent, requiring magnesium to shield the negative ions seen when ATP is involved in the glycolysis pathway. 84. What molecule ends the process of glycolysis? a. Acetic acid b. Lactate c. Phosphoenolpyruvate d. Pyruvate Answer: d. Pyruvate is the end of glycolysis. These molecules go on to the Krebs cycle after an intermediary step in order to further transform and ultimately lead to CO2 and water. 85. Which is the molecule that enters the Krebs cycle in order to break down itself to make CO2 and energy? a. Oxaloacetate b. Citrate c. Acetyl CoA d. Pyruvate Answer: c. Acetyl CoA enters the Krebs cycle and gets broken down into 2 CO2 molecules for a total of the four glucose carbon atoms from the initial glucose molecule. 86. Where does the Krebs cycle take place in the cell? a. Mitochondrial cristae b. Mitochondrial matrix c. Cytoplasm d. Mitochondrial membrane Answer: b. The mitochondrial matrix is where the Krebs cycle takes place. Molecules from the cytoplasm and from glycolysis diffuse into the matrix for this cycle to take place.

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87. What molecule becomes the final electron acceptor in the process of oxidative phosphorylation? a. Oxygen b. Carbon dioxide c. Water d. ADP Answer: a. Oxygen is the final electron acceptor in the electron transport chain, forming water as an end-product of these reactions. 88. Which molecule is being driven by the electron transport chain? a. Pyruvate kinase b. Enolase c. Hexokinase d. ATP synthase Answer: d. The whole purpose of the electron transport chain is to drive ATP synthase so that it is in the biochemical position to make ATP molecules out of ADP and phosphate. 89. Approximately how many ATP molecules are actually generated by the oxidation of one molecule of glucose? a. 12 b. 24 c. 30 d. 38 Answer: c. Theoretically, a total of 38 molecules should be made from this process; however, ATP is expended for many reasons so that only 30 to 32 molecules is the actual yield.

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90. What is the main end product of fermentation in mammalian muscle cells? a. Butyric acid b. Ethanol c. Acetate d. Lactic acid Answer: d. The end product of fermentation in mammalian muscle cells is lactic acid, although the others are also possible fermentation waste products in other types of organisms. 91. What is not an end product of the fermentation process? a. Acetate b. Methane c. Ethanol d. Lactate Answer: b. Methane is not a direct end product of fermentation; rather, it is the end product of metabolism in methanogenic Archaea species that take up the end-products of fermentation and take it a step further to make methane gas in the absence of oxygen. 92. What gas is made when dough rises? a. Carbon monoxide b. Oxygen c. Carbon dioxide d. Nitrogen Answer: c. In the alcohol fermentation process that happens when yeast is added to dough, carbon dioxide is given off in the process.

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93. Which type of organism is least likely to participate in photosynthesis? a. Cyanobacteria b. Algae c. Plants d. Fungi Answer: d. Fungi do not routinely participate in photosynthesis; however, the other organisms do participate in this process. 94. What is the substrate that ultimately goes into the photosynthetic process? a. Carbon dioxide b. Methane c. Glucose d. Acetate Answer: a. The initial substrate in photosynthesis is carbon dioxide, which interacts with water in order to make higher-order organic molecules. 95. What temporary energy storage molecule is made as part of the lightdependent reactions in photosynthesis? a. ADP b. O2 c. NADPH d. CO2 Answer: c. NADPH and ATP are two temporary energy storage molecules that are made from light dependent reactions as part of photosynthesis. This energy gets used to make sugars.

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96. In oxygenic photosynthesis, what is the source of hydrogen atoms necessary to reduce carbon dioxide into sugars? a. Acetate b. Water c. Carbon dioxide d. Ethanol Answer: b. These reactions need water to deliver the hydrogen atoms in reducing carbon dioxide, leaving oxygen gas behind as a waste product. 97. What is the evolutionary equivalent of the mitochondrial cristae in plants? a. Chloroplast membrane b. Thylakoid membrane c. Chloroplast stroma d. Chlorophyll Answer: b. The thylakoid membranes are stacked discs that are membranous. Like mitochondrial cristae, they have protein complexes that undergo electron transport, although for different reasons than is seen in mitochondria. 98. What is the main function of the Calvin cycle in plants? a. Carbon fixation b. H2O splitting c. Chlorophyll photon absorption d. Electron transport Answer: a. The main function of the Calvin cycle in photosynthesis is the fixation of carbon in the light-independent photosynthetic reactions.

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99. What is the end-product of the Calvin cycle in plants? a. Glucose b. ATP c. Triose phosphate d. NADPH Answer: c. Triose phosphate, a 3-carbon sugar is made from the Calvin cycle and, if not used to continue the cycle, is used from the Calvin cycle to build six-carbon sugars like glucose. 100.

What is the main storage molecule when the photosynthetic process has

taken place in plants? a. Fructose b. Cellulose c. Sucrose d. Starch Answer: d. Starch is a collection of glucose molecules that form the storage molecule for plants after glucose is created from triose phosphate in the Calvin cycle. 101.

Mendel’s Law that states that, for each trait, the alleles are separated so

that one allele gets passed onto the offspring, with the specific pair getting passed on being completely random is called what? a. Law of Inheritance b. Law of Dominance c. Law of Independent Assortment d. Law of Segregation Answer: d. Mendel’s Law of Segregation involves the separation of alleles into two separate alleles that get passed onto the offspring randomly.

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If a woman has an x-linked recessive trait but not the disease, what are

the chances that she’ll pass the trait but not the disease to her sons? a. 0 percent b. 33 percent c. 50 percent d. 100 percent Answer: a. She will pass the disease onto 50 percent of her sons but, because there is no matching X-chromosome on the male, there is no chance that she’ll just pass on the trait to her sons. It will always be the disease or no disease. 103.

What is the rarest type of inheritance pattern in animal traits?

a. Autosomal dominant b. Autosomal recessive c. X-linked dominant d. X-linked recessive Answer: c. X-linked dominant traits do exist but they are extremely rare in nature. 104.

If a homozygous dominant parent mates with a homozygous recessive

parent for a specific trait, what percentage of the offspring will have the recessive characteristic or trait? a. 0 percent b. 25 percent c. 50 percent d. 75 percent Answer: a. As long as there is a homozygous dominant genotype for a trait in the parents, there will be no chance that the offspring will have the recessive trait as it will always be masked by the dominant trait inherited by the autosomal dominant parent’s alleles.

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A female is a carrier for an X-linked recessive trait. What percent of her

sons will be affected by the disease? a. 0 percent b. 25 percent c. 50 percent d. 100 percent Answer: c. If the female parent is a carrier for an X-linked recessive trait, a total of half of her sons will inherit the recessive allele and, because this is their only X allele, they will have the disease themselves. Half of her daughters will have the allele but will only be carriers for the trait (unless the male parent is affected by the disease, in which half of the daughters will have the disease). 106.

What percent of mitochondrial DNA is inherited from the maternal side in

animal reproduction situations? a. 0 percent b. 25 percent c. 50 percent d. 100 percent Answer: d. The ovum is the only gamete that contains mitochondrial DNA. This is the reason that a hundred percent of mitochondrial DNA is inherited from the maternal side of the parents. 107.

Genes are transcribed by transferring the DNA message onto the RNA

molecule. How are these genes transcribed? a. From the three-prime end to the five-prime end b. From the middle of the gene out to both sides c. All nucleotides are added randomly until the gene is transcribed d. From the five-prime end to the three-prime end Answer: d. Genes are transcribed from the five-prime end to the threeprime end exclusively.

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How many bases form a codon in a gene structure?

a. Two b. Three c. Four d. Five Answer: b. There are three base pairs forming a codon or reading sequence in a DNA molecule. 109.

Genes make up the coded segments of DNA. What are the coded segments

of DNA referred to in general? a. Introns b. Histones c. Exons d. Telomeres Answer: c. Exons are the coded segments of genes, while introns are the noncoding segments. The gene may have an exon in it that is spliced out of the RNA after it is transcribed. 110.

What mutational change is most likely to lead to a nonsensical protein?

a. Point mutation b. Chromosome inversion c. Frameshift mutation d. Chromosome deletion Answer: c. While any of these can be serious mutations to a gene, the frameshift mutation will lead to the greatest chance of having a nonsensical protein as a result. Chromosome deletions and inversions can lead to the absence of a protein completely. Point mutations lead to a change in just one amino acid and are not always very serious.

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When talking about genes and alleles, there is the concept of the wild type

allele. What is the definition of this? a. The oldest allele in the population b. The newest allele in the population c. The evolutionarily fittest allele in the population d. The most common allele in the population Answer: d. The wild type allele is the allele most commonly seen in a given population. It may not be the fittest, oldest, or newest allele. 112.

What is a synonymous mutation in a gene?

a. A mutation that provides a genetic advantage to the organism b. A mutation that does not change the amino acid translated c. A mutation that does not confer a genetic advantage d. A mutation that results in a longer than normal protein Answer: b. A synonymous mutation is one that does not change the amino acid being translated because there are codons that code for the same amino acid. Even if the codon changes, the amino acid might still be the same as was originally intended. 113.

What are ribozymes made of?

a. RNA b. DNA c. Glycoproteins d. Peptides Answer: a. Ribozymes are RNA molecules that act as enzymes to drive specific reactions in the ribosomes of the cell.

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In gene regulation, what does a growth factor connect to or bind with?

a. A DNA promotor region b. A ribosome c. An external cellular receptor d. A messenger RNA molecule Answer: c. Growth factors bind to external cellular receptors and cause transcription factors to be made that will bind to the DNA promotor region. 115.

In gene regulation, what does microRNA bind to in order to regulate gene

output? a. Promotor region of DNA b. Proteins getting translated c. Nuclear envelope pores d. Messenger RNA Answer: d. Micro RNA will bind to messenger RNA, causing it to be chopped up in the cytosol rather than being translated into proteins. 116.

What is the most important factor in natural selection of organisms?

a. The environment the organisms live in b. The number of organisms in the population c. The rate of reproduction in the population d. The development of random mutations Answer: a. The environment the organisms live in is the most important factor in natural selection as it determines what the different variations in the species must adapt to.

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What is the most obvious difference between artificial selection and

natural selection? a. Natural selection is faster than artificial selection. b. Artificial selection does not involve heritable changes in the population. c. Natural selection can happen to any population, whereas artificial selection happens only in mammals. d. Artificial selection is entirely intentional whereas natural selection depends primarily on the environment. Answer: d. Artificial selection is intentional by breeders and does not depend mainly on the environment, which is the main factor behind natural selection. 118.

What is the most important thing involved in survival of the fittest?

a. The length of time the organism lives must be longer to survive b. There must be an improvement in the fitness over time c. The fittest organism reproduces more efficiently and has more offspring d. There must be competition between species Answer: c. Survival of the fittest means that the organism must reproduce more efficiently and must have more offspring than other variants in the species. 119.

What is it called in natural selection when more than one extreme is

favored over an intermediate species? a. Bidirectional selection b. Disruptive selection c. Stabilizing selection d. Directional selection Answer: b. In disruptive selection, there is the favoring of more than one extreme versus an intermediate species.

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What evolutionary theory was proposed and called saltationism?

a. Evolution by blending of two organism’s characteristics. b. Evolution by the gradual development of successive mutations. c. Evolution in jumps rather than gradually. d. Evolution by natural selection between organisms. Answer: c. Evolution in jumps rather than gradually is the major theory of saltationism. 121.

What is not considered one of the major differences between modern

synthesis in evolution and Darwin’s theories? a. That inheritance comes in the form of genes. b. The existence of natural selection. c. That mutations exist that are generally random. d. That there is punctuated equilibrium in evolution. Answer: b. Modern synthesis does believe that natural selection exists; however, it indicates that there are more things in play to cause evolution to occur besides natural selection. 122.

What theory contradicts the microevolution-to-macroevolution theory?

a. Natural selection b. The presence of different alleles in a population c. The presence of random mutations d. The fact of punctuated equilibrium Answer: d. The fact that there is punctuated equilibrium or the fossil evidence of rapid speciation goes against the microevolution-tomacroevolution theory, although both situations could occur at the same time.

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When is it believed that life first took hold on earth?

a. 7 billion years ago b. 3.8 billion years ago c. 2.5 billion years ago d. 1.7 billion years ago Answer: b. It is believed that life began on earth about 3.8 billion years ago. 124.

In terms of evolution, which were the first photosynthetic organisms?

a. Algae b. Small plants c. Archaea d. Cyanobacteria Answer: d. Cyanobacteria were the first photosynthetic organisms on earth, believed to have participated in the building up of oxygen in the earth’s atmosphere. 125.

What structure evolved in eukaryotic cells from photosynthetic bacteria

about 2 billion years ago? a. Mitochondria b. Chloroplasts c. Golgi apparatus d. Nucleus Answer: b. Chloroplasts evolved from the engulfing of photosynthetic bacteria, making eukaryotic cells that could undergo photosynthesis. 126.

When did plants, fungi, and animals separate into different lineages?

a. 3.1 billion years ago b. 2.7 billion years ago c. 1.5 billion years ago d. 500 million years ago

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Answer: c. About 1.5 billion years ago, there were separate lineages that separated the plant, fungi, and animal lines. The bacteria and archaea were already on earth as the original separation that occurred from an evolutionary standpoint. 127.

Which form of animal is considered the oldest surviving type?

a. Fish b. Placozoa c. Amoeba d. Sponges Answer: d. Sponges are the oldest form of animal that still survives. About 800 million years ago, sponges broke off to become sponges and the rest of animals were called Eumetazoa before later dividing off. 128.

About 590 million years ago, there was a major split of the Bilateria group

in evolution into protostomes and deuterostomes. What organism is of the deuterostome category? a. Crabs b. Insects c. Fish d. Worms Answer: c. Vertebrates, like fish belong to the deuterostome category. This category and protostomes are differentiated by the way their blastomeres first form their blastopore in embryonic development. 129.

Which organism are we as humans evolutionarily closer to?

a. Starfish b. Insects c. Crabs d. Worms

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Answer: a. Starfish are deuterostomes, which make them distant relatives of vertebrates, while the others are protostomes that are further away from vertebrates evolutionarily speaking. 130.

What did the first vertebrates look like in terms of modern animals?

a. Turtles b. Eels c. Starfish d. Snakes Answer: b. The first vertebrates were believed to look like eels, lamprey, or hagfish. 131.

About 460 million years ago, there was a split between cartilaginous fish

and bony fish. Which fish type belongs to the bony fish category rather than the cartilaginous fish category? a. Sharks b. Skates c. Tuna d. Manta rays Answer: c. Each of these is of the cartilaginous fish category except for tuna, which are bony fish. They diverged about 460 million years ago. 132.

Which animal type is most unrelated to the others?

a. Reptiles b. Mammals c. Birds d. Dinosaurs Answer: b. The mammals are of the synapsid group, while the reptiles, dinosaurs, and birds are of the sauropsid group. These groups split apart along evolutionary lines at around 310 million years ago.

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A major split occurred 180 million years ago in evolution, such that there

were mammals that laid eggs instead of bearing live young. These monotremes include what animal today? a. Alligator b. Bird c. Duck-billed platypus d. Turtle Answer: c. Of these, only the duck-billed platypus is actually a mammal. It is a monotreme that lays eggs instead of bearing live young. 134.

What species is closest in evolutionary respects to primates and humans?

a. Dogs b. Horses c. Elephants d. Rodents Answer: d. Rodents are closer cousins to primates than any of these other species because of a major split in the animal kingdom occurring around 100 million years ago. 135.

When did the Cretaceous-Tertiary (K/T) extinction occur that wiped out

the dinosaurs? a. 110 million years ago b. 65 million years ago c. 35 million years ago d. 10 million years ago Answer: b. The K/T extinction that killed the dinosaurs happened 65 million years ago and paved the way for mammals to be dominant on the earth.

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The study of what aspect of living cells has made the differentiation

between the different domains of life? a. Cell membrane b. Cell wall c. Ribosomal RNA d. DNA Answer: c. The differences in ribosomal RNA have made the division into the three domains from a molecular and biochemical status. 137.

The term Homo sapiens refers to what aspect of taxonomy or the hierarchy

of life? a. Kingdom and phylum b. Family and order c. Subphylum and species d. Genus and species Answer: d. The genus and species are defining the organism when the term Homo sapiens is used to indicate humans when using taxonomy or “systematics”. 138.

How do the Archaea species most relate to eukaryotic species?

a. They have similar cell membranes b. They have similar cell walls c. They have similar transcription and translation enzymes d. They have similar chromosome shapes Answer: c. The main similarity to eukaryotes is the similarity in their transcription and translation enzymes. 139.

What metabolic feature is unique to archaea as a domain?

a. Fermentation b. Anaerobic metabolism c. Photosynthesis d. Methanogenesis 288

Answer: d. Methanogenesis is unique to archaea species and is not seen in other domains. The others can be seen in both eukaryotes or bacteria. 140.

Why are phototrophs in the Archaea species not truly photosynthetic?

a. Because they do not use sunlight as a form of energy. b. Because they do not give off oxygen gas. c. Because they do not fix carbon in the same way. d. Because they use methane gas to fix carbon. Answer: b. These archaea are phototrophic because they use sunlight but are not truly photosynthetic as they do not give off oxygen or O2 gas in the process. 141.

What is not a way that archaea can replicate?

a. Binary fission b. Budding c. Fragmentation d. Mitosis Answer: d. Archaea do not participate in mitosis or meiosis but participate in the other forms of reproduction. Remember that binary fission is different from mitosis, although it looks basically the same. 142.

What is the major method of locomotion of amoebas?

a. Cilia b. Pseudopodia c. Flagella d. They are not motile Answer: b. The amoeba sends out pseudopodia in order to be motile.

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The species of foraminiferans or “forams” form tests. What are the tests

that these organisms make? a. Holes in the organisms b. Pseudopodia they send out c. The shells they make d. Vacuoles inside the cells Answer: c. The shells these organisms make are called tests. They are called foraminiferans because they make holes within the shells or tests. 144.

What is contained in the contractile vacuoles of many single-celled

Protista? a. Air b. Water c. Nutrients d. Waste products Answer: b. Water is contained in the contractile vacuoles and is released into the cell in order to regulate the osmotic pressures within the cell under different osmotic situations. 145.

How does the paramecium move in an aqueous environment?

a. Through the movement of flagella b. Through pseudopodia c. Through the movement of cilia d. By twisting through the water Answer: c. The paramecium has multiple cilia that beat in the same direction in an aqueous environment to allow for movement of the organism.

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What is the largest phylum among the kingdom of Animalia?

a. Chordata b. Mollusca c. Nematoda d. Arthropoda Answer: d. Arthropoda, which includes the insects and related species, is the largest phylum, containing millions of different species. 147.

What phylum does mankind belong to?

a. Chordata b. Nematoda c. Rotifera d. Cnidaria Answer: a. The phylum Chordata includes many species, including members of Mammalia, which is the class that involves humans. 148.

Which type of cell in a plant transports most of the water from the roots to

the rest of the plant? a. Parenchymal cells b. Xylem cells c. Collenchyma cells d. Phloem cells Answer: b. The xylem cells are responsible for carrying the water from the roots of the plant up to the leaves and other structures in the plant. 149.

Which cell in a plant is basically dead?

a. Phloem cells b. Collenchyma cells c. Sclerenchyma cells d. Xylem cells

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Answer: c. The sclerenchyma cells are basically the dead supportive cells of larger plants that support the structure of the plant with thick cell walls. 150.

What part of the chloroplast contains the chlorophyll pigment?

a. Intermembrane space b. Stroma c. Inner membrane d. Thylakoids Answer: d. The thylakoids are stacked membranous structures inside the chloroplast. Inside the thylakoids are the pigments, the majority of which is chlorophyll. 151.

What is the main purpose of the large central vacuole in plant cells?

a. To maintain the turgor pressure of the cell b. To store water during times of low water conditions c. To store nutrients for the cell d. To store starch within the cell Answer: a. The large central vacuole is designed to maintain a high turgor pressure in the cell, which keeps the cell plump. Because of the cell wall, it is difficult for this situation to burst or lyse the plant cell, which is not the case in animal cells. 152.

What part of the stem of a plant is the outer protective layer of the plant’s

stem? a. Ground tissue b. Dermal tissue c. Phloem tissue d. Xylem tissue Answer: b. The dermal tissue is the outer protective layer of the plant stem, basically meaning the outer skin of the stem.

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Where is the mature ovary in the plant?

a. The roots b. The flowers c. The fruit d. The leaves Answer: c. The fruit of the plant is where the ovary on the plant is located. The flower is the reproductive structure of the plant, containing male and female parts. 154.

In a flower, what are the petals and its surrounding bud structures called

together? a. Perianth b. Stamen c. Corolla d. Pollen sac Answer: a. The perianth is the collective petals and bud structures together. They do not participate in reproduction except to attract the pollinators to the flower structures. 155.

In a flower, what is the male part of the flower, having the pollen in or on

them? a. Carpel b. Gynoecium c. Filament d. Stamen Answer: d. The stamen structure forms the androecium, which is the male part of the flower. The carpel is the female part of the plant.

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What is the scientific name for a cluster of flowers?

a. Inflorescence b. Staminate c. Angiosperm d. Receptacle Answer: a. An inflorescence is a flower or cluster of flowers on an angiosperm, which is the name for a flower-producing plant. 157.

Which animal is responsible for most of the cross-pollination of flowers?

a. Beetles b. Mosquitos c. Bees d. Birds Answer: c. The bees are the major pollinating animal among the different animal species, sending pollen from one plant of the same species to another and feeding off the nectar the flowers have. 158.

Which fruit or vegetable is actually a modified stem of the plant?

a. Carrot b. Beet c. Pineapple d. Onion Answer: d. The onion is a modified stem structure and is not a root or flower part. The carrot and beet are modified root structures, while the pineapple is a fruit that comes from a whole inflorescence.

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In a fruit of a plant, what is the outer layer of the fruit called?

a. Seed b. Exocarp c. Pericarp d. Endocarp Answer: b. The exocarp of the fruit is the outer layer, such as the outer layer of an orange, pumpkin, or tomato. 160.

Where does most of the water go when it is taken up by the roots of the

plant? a. Used for cell metabolism b. Used for achieving cell turgor c. Used to maintain the stem structure d. Lost in transpiration Answer: d. The vast majority of water is lost in transpiration or evaporation to allow for cooling of the leaves and to pull water upward. 161.

What is the most necessary thing in the transportation of water against

gravity in plants? a. The photosynthetic process b. The transpiration process c. Active transport of water across cell membranes d. Pumping action of the xylem Answer: b. It is the negative pressure exerted by the transpiration process that pulls the water up the plant against gravity. This is why most of the water is lost through transpiration. 162.

In studying plants, what does the cohesion theory state?

a. That water is cohesive, helping to draw water up the plant. b. That plant roots are cohesive to one another. c. That plant nutrients are easily dissolvable in water. d. That nitrogen is cohesive to the roots of the plant. 295

Answer: a. The cohesion theory involves the fact that water is cohesive in a small tube so that it is drawn upward along with the negative pressure brought on by transpiration. 163.

What sugar molecule is made for the most part in the plant cell and that

gets transported through the phloem? a. Starch b. Fructose c. Glucose d. Sucrose Answer: d. The main sugar molecule made by plants that goes up and down the phloem is sucrose, a combination disaccharide made from glucose and fructose. 164.

Which of the following does not happen when man introduces genetic

modification to crops? a. The crops are more resistant to herbicides b. The crops have decreased spoilage c. The crops are more resistant to pests d. The crops grow at a greater rate Answer: d. Each of these are things that happen when plants are genetically modified except that the actual rate of growth is not yet affected by genetic manipulation. 165.

Which type of fungal organism is not actually a part of the fungi kingdom?

a. Slime molds b. Chytrids c. Ascomycetes d. Basidiomycetes Answer: a. Slime molds are not actually fungal organisms although they do share some of the features of true fungal organisms.

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What is the main microscopic feature of fungal cells?

a. Multinucleated b. Amorphous cells c. Microscopic spores d. Branching hyphae Answer: d. From a microscopic standpoint, the main feature seen in fungal cells is the presence of branching hyphae, which may be septate or may appear to be multinucleated. 167.

What cell feature does not have the capability to enter through the pores in

microscopic septa within fungal hyphae? a. Cell wall b. Nucleus c. Macromolecules d. Ribosomes Answer: a. These pores in the septa of fungal hyphae are so large that even nuclei can pass through them. The cell walls cannot pass through, however. 168.

In studying fungi, what is a mycelium?

a. Fungal spores b. Fungal fruiting body c. A group of hyphae d. A hyphal septum Answer: c. A collection of hyphae is called a mycelium, with the pleural being mycelia.

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Mycorrhizae are a cooperative effort between fungi and what other type of

organism? a. Plants b. Algae c. Bacteria d. Protists Answer: a. Plants and fungi form mycorrhizae that will take nutrients and water, sharing them for the benefit of both. 170.

Lichens are a cooperative effort between fungi and what other type of

organism? a. Plants b. Algae c. Bacteria d. Protists Answer: b. Algae are photosynthetic organisms that will combine with fungi for the benefit of both types of organisms. 171.

Fungi can be highly pigmented. What part of the fungal cell is associated

with the pigments? a. Within chloroplasts b. Within pigment granules c. Within the nucleus d. Associated with the cell wall Answer: d. The pigment is affiliated with the cell wall of the fungal cell in order to protect the fungus from UV radiation.

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In studying fungi, what is a thallus?

a. The vegetative body of the fungus b. The fruiting body of the fungus c. The reproductive structure of the fungus d. The area of anastomosis of the hyphae Answer: a. The main vegetative body of the fungus is called the thallus. It is basically the main hypha that branches off to have other hyphae as part of it. 173.

What is the storage molecule in fungi that have ingested more food than

they need? a. Glycogen b. Starch c. Cellulose d. Chitin Answer: a. Similar to animals, the storage molecule of fungi is glycogen—made when there is more food available than they need. 174.

Fungi are known to eat in a unique way. What is true of the way they eat?

a. They have no digestive enzymes and only eat small molecules. b. They only eat carbohydrates and fix nitrogen from the atmosphere. c. They use phagocytosis to take in macromolecules before digesting them. d. They send out exoenzymes that digest first and then absorb the small molecules made. Answer: d. Fungi send out exoenzymes that digest first and then absorb the small molecules that are made outside of the body and then absorbed into the cells.

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What is not considered a type of asexual reproductive mechanism of

fungi? a. Mitosis with budding b. Binary fission c. Fragmentation off the main hyphae d. Spore formation Answer: b. Each of these is an asexual reproductive mechanism that is done by certain fungi, except for binary fission that does not occur in fungal organisms. 176.

What is the primary way that yeast will reproduce?

a. Through binary fission b. Through spore formation c. Through budding and mitosis d. Through fragmentation Answer: c. Yeast undergo mitosis and budding as their primary means of reproduction. They can only bud off a few times as they will have a scar at the site of budding that prevents further budding at the site of the scar. 177.

In the sexual reproduction of fungi, what is plasmogamy?

a. The fusion of two nuclei to make a diploid nucleus b. The meiotic process that occurs in the spores c. The combining of hyphal cells in order to form a multinucleated cell d. The mitosis that occurs in the zygote Answer: c. The process of plasmogamy happen when two different hyphal cells combine to form a multinucleated cell.

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What nutrients are released by fungi that would otherwise be tied up in

organic matter and would not be available? a. Zinc and iron b. Nitrogen and phosphorus c. Carbon and oxygen d. Carbon dioxide and phosphorus Answer: b. Nitrogen and phosphorus are tied up in organic matter yet are broken down by fungi in order to be used by organisms that need them in a smaller form. 179.

What role do fungi play in the mycorrhizal relationship between plants

and animals? a. They use oxygen from the plants to aid in respiratory metabolism. b. They participate in photosynthesis by providing CO2 to the plants. c. They fix nitrogen in the soil to make it available to plants. d. They increase the surface area in the soil for the uptake of water and nutrients. Answer: d. The fungal organisms will participate in mycorrhizae by increasing the surface area in the soil in order to bring more nutrients and water into the plant’s roots. 180.

The type of mycorrhizae in the exchange between plants and fungi that

involve the fungi forming a mantle around the root is called what? a. Ectomycorrhizae b. Endomycorrhizae c. Arbuscular mycorrhizae d. Glomeromycete fungi Answer: a. It is the ectomycorrhizae that form a mantle of fungal cells outside of the root with a net of fungal hyphae that get nutrients for the hyphae and plant cells.

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181.

In a mutualistic relationship between insects and fungi, what is one way

that the fungi do not benefit? a. They get the benefit of spore disbursement. b. They get protection against competing organisms. c. They get some nutrients from the insects. d. They can break down the insects’ exoskeletons for food. Answer: d. The fungi get each of these features from the insects with the exception that they do not break down the insects’ exoskeletons for food. In fact, the insects eat the fungi for use in metabolism. 182.

In the fish circulatory system, where does the oxygenated blood go after it

leaves the gills? a. To the lungs of the fish b. To the atrium of the fish heart c. To the ventricles of the fish heart d. To the tissues of the fish body Answer: d. Fish have a simple two-chambered heart. The blood gets pumped to the tissues before going back to the atrium and ventricle of the heart in a single loop. They do not have a separate pulmonary circulatory system. 183.

What type of heart does an amphibian have?

a. It has two atria and two ventricles b. It has one atrium and two ventricles c. It has two atria and one ventricle d. It has two atria and one ventricle that has a septum in it Answer: c. Amphibians have a three-chambered heart that has two atria and one ventricle that has a ridge that attempts to prevent a lot of mixing of the blood that goes to the pulmonary and systemic circulatory systems.

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184.

What part of the nervous system in vertebrates is responsible for motor

reflexes? a. Spinal cord b. Brainstem c. Thalamus d. Cerebellum Answer: a. The motor reflexes come from the spinal cord and bypass the brain altogether. The remainder of the structures mentioned in the question are parts of the brain and not the spinal cord. 185.

What aspect of the area around the brain is most responsible for

cushioning the brain and spinal cord? a. Dura mater b. Arachnoid mater c. Cerebrospinal fluid d. Pia mater Answer: c. The cerebrospinal fluid is designed mainly to cushion the brain and will also help circulate nutrients throughout the central nervous system. 186.

What is not considered a main function of the digestive system in animals?

a. Absorption b. Ingestion c. Metabolism d. Elimination Answer: c. The main functions of the digestive tract are ingestion, digestion, absorption, and elimination. It does not include metabolism, which takes place at a cellular level.

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187.

Where in the digestive tract of mammals does most chemical digestion

take place? a. Mouth b. Large intestine c. Stomach d. Small intestine Answer: d. Most chemical digestion takes place in the upper small intestine and involves the pancreatic enzymes and brush border enzymes that completely break down the absorbable food. 188.

Where in the digestive tract does chyme get made?

a. Stomach b. Mouth c. Large intestine d. Small intestine Answer: a. Chyme is made in the stomach by the churning of the stomach and acid that breaks down the protein in part, which creates the semi-solid chyme. 189.

What part of the digestive tract in humans is where most of the nutrients

are absorbed? a. Stomach b. Duodenum c. Jejunum d. Large intestine Answer: c. Most of the absorption takes place in the jejunum after the nutrients have been digested in the stomach and duodenum.

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190.

What is the main method of gas exchange in earthworms?

a. They have lungs b. They have a tracheal system c. They use a type of gills d. They respire through the skin Answer: d. Earthworms have a capillary network beneath the skin that participates in gas exchange through the earthworm’s moist skin. 191.

Which type of animal has spiracles as part of their respiratory system?

a. Mollusks b. Annelids c. Insects d. Crustaceans Answer: c. Insects have a specialized tracheal system with spiracles that are open to the exterior to allow gas to enter and leave the animal. 192.

Amphibians use multiple ways of respiring. What is not one of the ways

that these animals respire? a. Through lungs b. Through tracheal systems c. Through gills d. Through the skin Answer: b. Amphibians have all of these capabilities to respire with the exception of tracheal systems.

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193.

In the immune system of higher organisms, what is considered a first

defense against pathogenic organisms? a. Antibodies b. Memory cells c. Phagocytes d. Barriers Answer: d. Barriers, such as the skin, GI tract, and respiratory tract will be the first line of defense against pathogens as they attempt to breach them and get into the organism. 194.

Which cells of the immune system are responsible for making antibodies?

a. Cytotoxic T cells b. NK cells c. B cells d. T helper cells Answer: c. B cells are the adaptive immune cells that actively make antibodies. 195.

Which type of immune cell only kills infected cells after recognizing their

infection? a. T helper cells b. NK cells c. B cells d. Cytotoxic T cells Answer: d. Cytotoxic T cells will recognize an infected cell and will kill it after identifying it as being a self-cell that is infected or possibly cancerous.

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196.

Which hormone is not secreted by the pituitary gland?

a. Cortisol b. Follicle stimulating hormone c. Growth hormone d. Thyroid stimulating hormone Answer: a. Each of these hormones is secreted by the anterior pituitary gland with the exception of the cortisol, which is secreted by the adrenal cortex. 197.

Which gland of the endocrine system is most responsible for blood sugar

regulation? a. Pineal gland b. Thyroid gland c. Pancreas d. Parathyroid gland Answer: c. The pancreas secretes both glucagon and insulin, which together help to regulate the blood sugar levels in the body. 198.

Which animal is least likely to be hermaphroditic?

a. Sea slug b. Snail c. Whale d. Barnacle Answer: c. Each of these species can be hermaphroditic; however, the whale will not have characteristics of both genders under normal circumstances.

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199.

What species of organism in animals produce a different gender

depending on the temperature when eggs are incubating? a. Turtles b. Birds c. Crustaceans d. Fish Answer: a. Turtles will have different genders made when the temperature changes during egg development. 200. Which type of animal does not undergo spawning? a. Mosquito b. Bird c. Fish d. Crabs Answer: b. These species will all lay eggs; however, unlike the others, birds will not undergo spawning, which is a type of external fertilization.

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College Level Biology

Articles inside

Summary of the Course

Quiz

Key Takeaways

Ecosystems

Population Ecology

Quiz

Key Takeaways

Respiratory Systems

Endocrine Systems

Immune Systems

Reproductive Systems

Digestive Systems

Nervous Systems

Quiz

Key Takeaways

Fungal Reproduction

Fungal Physiology

Fungal Anatomy

Ecology of Fungi

Quiz

Plant Biotechnology

Key Takeaways

Transpiration

Fruits

Pollination

Soil Utilization and Plant Nutrition

Flowers

Quiz

Reproduction of Plants

Plant Morphology

Key Takeaways

Protista

The Different Animal Phyla

Quiz

Archaea

History of Evolution on Earth and Origin of Species

Key Takeaways

Modern Synthesis in Evolution

Natural Selection

Quiz

Genome

Regulation of Gene Expression

Gene Mutations

Chromosomes and Genes

DNA and Genetics

Dominant Inheritance

Quiz

Key Takeaways

Chloroplasts

Photosynthesis

Fermentation

Oxidative Phosphorylation

Glycolysis

Quiz

Krebs Cycle or Citric Acid Cycle

Meiosis

Mitosis

The Cell Cycle

Mitochondrial Physiology

Endoplasmic Reticulum

Nucleus

Organelles

Cytoskeleton

Key Takeaways

Bacterial Motility

Quiz

Prokaryote Cell Division

Classifying Bacteria

Bacterial Genetics

Bacterial Physiology

Bacterial Communication

Quiz

Prokaryote Structure

Non-Human Viral Infections

Epidemics from Viruses

The Virome

Virus Replication

Viruses and Disease