College Level Molecular Biology by AudioLearn

Molecular Biology

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TABLE OF CONTENTS Preface........................................................................................................ 1 Chapter One: Chemical Foundations of Life ................................................ 5 Types of Chemical Bonds ................................................................................................. 9 Ionic Bonds ...................................................................................................................... 9 Covalent Bonds ............................................................................................................... 11 Polar Bonds .................................................................................................................... 13 Hydrogen Bonds ............................................................................................................ 13 Chemical Building Blocks of Life ................................................................................... 14 Chemical Reactions in Living Things ............................................................................ 20 Key Takeaways ............................................................................................................... 22 Quiz ................................................................................................................................ 23 Chapter Two: Cell Structures .................................................................... 25 Prokaryotic Cell Structures ............................................................................................ 25 Eukaryotic Cell Structures ............................................................................................. 28 Cell to Cell Communication ........................................................................................... 37 Tissue Differentiation .................................................................................................... 38 Key Takeaways ............................................................................................................... 44 Quiz ................................................................................................................................ 45 Chapter Three: Integrating Cells into Tissues ............................................ 47 Cell-Cell Connections ..................................................................................................... 47 Tight Junctions .............................................................................................................. 47 Desmosomes .................................................................................................................. 49

Adherens Junctions ....................................................................................................... 51 Gap Junctions ................................................................................................................ 51 Cell-Matrix Connections ................................................................................................ 52 Basement Membrane ..................................................................................................... 52 Connective Tissue and Connective Tissue Proteins ...................................................... 53 Plant Cell Adhesions ...................................................................................................... 56 Key Takeaways ............................................................................................................... 58 Quiz ................................................................................................................................ 59 Chapter Four: Biomembranes ................................................................... 61 Fatty Acid Synthesis ....................................................................................................... 61 Composition of Membranes .......................................................................................... 63 Membrane Proteins ....................................................................................................... 65 Key Takeaways ............................................................................................................... 67 Quiz ................................................................................................................................ 68 Chapter Five: Transmembrane Transport ..................................................71 Osmosis ...........................................................................................................................71 Diffusion ......................................................................................................................... 73 Active Transport ............................................................................................................ 75 Sodium-Potassium ATPase Pump ................................................................................. 79 Resting Membrane Potential ......................................................................................... 79 Key Takeaways ............................................................................................................... 81 Quiz ................................................................................................................................ 82 Chapter Six: Proteins and Protein Chemistry ............................................ 85 Structures of Proteins .................................................................................................... 85

Protein Synthesis ........................................................................................................... 87 Post-Translational Modification.................................................................................... 91 Enzymology .................................................................................................................... 92 Protein Detection and Characterization ........................................................................ 95 Key Takeaways ............................................................................................................... 97 Quiz ................................................................................................................................ 98 Chapter Seven: Molecular Genetics .......................................................... 101 Structure of DNA ..........................................................................................................101 Types and Function of RNA ......................................................................................... 107 DNA Replication ........................................................................................................... 112 DNA Repair ................................................................................................................... 114 Key Takeaways .............................................................................................................. 116 Quiz ............................................................................................................................... 117 Chapter Eight: Genes and Chromosomes ................................................. 119 Prokaryotic Genes ......................................................................................................... 119 Eukaryotic Genes ......................................................................................................... 123 Transposable DNA ....................................................................................................... 126 Genomics.......................................................................................................................127 Gene Mutations ............................................................................................................ 128 Key Takeaways ............................................................................................................. 130 Quiz ............................................................................................................................... 131 Chapter Nine: Cellular Energetics ........................................................... 133 Overview of Chemoorganotrophy ................................................................................ 133 Glycolysis ..................................................................................................................... 135

Mitochondrial Respiration ...........................................................................................137 Citric Acid Cycle ........................................................................................................... 140 Fatty Acid Oxidation .................................................................................................... 143 Photosynthesis ............................................................................................................. 144 Key Takeaways ............................................................................................................. 148 Quiz .............................................................................................................................. 149 Chapter Ten: Vesicular Traffic, Secretion, and Endocytosis .....................152 Vesicular Budding and Fusion ..................................................................................... 152 Secretory Pathways in Nerve Cells .............................................................................. 156 Receptor-Mediated Endocytosis.................................................................................. 159 Key Takeaways ............................................................................................................. 162 Quiz .............................................................................................................................. 163 Chapter Eleven: Signal Transduction by the Cell ..................................... 165 Signal Transduction ..................................................................................................... 165 Receptors...................................................................................................................... 166 Ligands ......................................................................................................................... 169 Signaling Processes ...................................................................................................... 170 G Protein-coupled Receptors ........................................................................................172 Key Takeaways ............................................................................................................. 174 Quiz ...............................................................................................................................175 Chapter Twelve: Cell Organization and Movement ................................... 177 Cytoskeleton .................................................................................................................. 177 Microfilaments ............................................................................................................. 178 Cell Migration .............................................................................................................. 183

Microtubules ................................................................................................................ 184 Intermediate Filaments ............................................................................................... 185 Cilia, Centrioles and Flagella ....................................................................................... 186 Key Takeaways ............................................................................................................. 187 Quiz .............................................................................................................................. 188 Chapter Thirteen: Eukaryotic Cell Cycle .................................................. 190 Cell Cycle and Cell Cycle Control ................................................................................. 190 Cell Cycle Regulators ................................................................................................... 193 Mitosis and its Regulation ........................................................................................... 194 Meiosis ......................................................................................................................... 195 Apoptosis ...................................................................................................................... 197 Key Takeaways ............................................................................................................. 199 Quiz ............................................................................................................................. 200 Summary ................................................................................................ 203 Course Questions and Answers ............................................................... 207 Answers to Quiz ...................................................................................... 249 Answers to Chapter One .............................................................................................. 249 Answers to Chapter Two .............................................................................................. 251 Answers to Chapter Three ........................................................................................... 252 Answers to Chapter Four ............................................................................................. 253 Answers to Chapter Five .............................................................................................. 255 Answers to Chapter Six ................................................................................................ 256 Answers to Chapter Seven ........................................................................................... 257 Answers to Chapter Eight ............................................................................................ 258

Answers to Chapter Nine ............................................................................................. 259 Answers to Chapter Ten ...............................................................................................260 Answers to Chapter Eleven .......................................................................................... 262 Answers to Chapter Twelve ......................................................................................... 263 Answers to Chapter Thirteen ....................................................................................... 264 Answers to Course Questions ...................................................................................... 265

PREFACE This course involves the study of the molecular structures associated with living things. It combines the related subjects of biophysics, biochemistry, and genetics in order to give a clearer picture of the molecules that interact on a cellular level. The major macromolecules studied in the course include proteins, which make up structural molecules and enzymes, as well as nucleic acids, the underlying biochemical structures seen in ribonucleic acid (or RNA) and deoxyribonucleic acid (or DNA). The course also looks into the molecules used in the making of biomembranes, such as those that comprise the outer cell membrane and organelles. The molecular basis of the functions of prokaryotic and eukaryotic cells, including animal and plant cells, is also covered in this course. Chapter one in the course introduces molecular biology by talking about the basics of biochemistry as it applies to life and living things. All of human life is based on water, which is a polar molecule that acts as a solvent for many biological molecules in living things. The bonds that make up biochemical molecules are also important in the discussion of molecular biology. The types of molecules that make up living organisms is also covered as are the different biochemical reactions that take place inside and outside the cell. In chapter two of the course, the discussion moves from biochemistry to the biology of cells and cell structures. There are two major types of cells: prokaryotic cells and eukaryotic cells. These are quite different from one another in structure and function, which will be covered in the chapter. Cells inside multicellular organisms must communicate with one another through different mechanisms. Animals that are complex and multicellular (such as are seen in the human body) have different cell types that form tissues. The tissues together form organ systems. The different types of tissues are covered in this chapter. The focus of chapter three is the integration of cells into tissues. This chapter looks specifically into intercellular connections and how some of these connections create cell-

to-cell communication. In epithelial cell tissues, there is the basal lamina, the structure and function of which will be covered in the chapter. In addition, the structure and function of connective tissue structures are discussed as are the adhesions seen in plant cells. Chapter four in the course talks about the synthesis and structure of biomembranes. It covers fatty acid synthesis, which is how the basic molecules of biomembranes get created and incorporated into things like cell membranes and the membranes seen in organelles. The composition of membranes is also introduced, including the phospholipids and membrane proteins that together make up the cell membrane structure. The main focus of chapter five is the different things that happen in transmembrane support. Water, for example, can pass through the membrane by osmosis—from a high concentration of water to a low concentration of water. Other types of membrane transport include simple and facilitated diffusion, as well as active transport. The sodium-potassium ATPase pump is particularly important in cell membrane transport. Symporters and antiporters also aid in the transport of certain molecules across the membrane. Ion transport helps account for a difference in electric potential between the inside and outside of the cell. Chapter six in the course mainly covers proteins and their biochemistry. Proteins have several different characteristics, based on how they are made and on post-translational modification of the protein structures. The different factors that play a role into making proteins from amino acids is introduced in this chapter. Some proteins are functional enzymes; how these behave is covered in the chapter as are the different methods of detecting and characterizing proteins in molecular biology. The structure and molecular processes of DNA and RNA are the topics of chapter seven. DNA and RNA have similar structures, although DNA is usually double-stranded and RNA is usually single-stranded. There are different types of RNA that vary according to their function. The chapter also talks about DNA replication, DNA repair, and the process of recombination.

There is a difference between prokaryotic genes and eukaryotic genes, which is part of the discussion of chapter eight in the course. Genetic material is divided up into genes, which are the readable segments of DNA in the organism. Transposons or transposable DNA are also covered, which is DNA that does not stay in the same place throughout the lifespan of the cell. Also included is a discussion of genomics, which is the collection of all the genes that exist as part of a given organism’s genetic material. Cellular energetics is the subject of chapter nine in the course. There are hundreds of enzymes and reactions that take place as a result of cellular metabolism. Amino acids, fatty acids, and carbohydrates all get metabolized by the cell to varying degrees, usually with a common final pathway. Prokaryotic cells and eukaryotic cells have both similarities and differences in the way nutrients are metabolized. In addition, photosynthesis is covered as a metabolic process that plants and other photosynthetic organisms participate in. The focus of chapter ten is the function of vesicles in exocytosis and endocytosis. Vesicular budding and fusion is a process where by small vesicles break off or fuse with the cell membrane or other membranes in order to dump or take up contents within the vesicles. This process can happen either to rid the cell of substances or take on substances by the cell. The process of receptor-mediated endocytosis is covered as part of this chapter as is the complex process of neurotransmitter secretion by nerve cells, which also involves vesicles. Chapter eleven in the course introduces the topic of signal transduction or cell signaling. There are several signaling pathways that involve the ways that cells send and receive signals from other cells in multicellular organisms. There are ligands and receptors involved in signal transduction, of which there are many types. The largest family of membrane receptors is the G-coupled protein receptor family, which involves a specific protein type that many cells make use of in cell signaling. The ways this receptor operates in the cell membrane and within the cell are covered as part of this chapter. Chapter twelve places a focus on cell organization and on how aspects of cell organization control movement within the cell. There are many different types of molecules involved in cellular organization, many of which contribute to the cell

cytoskeleton. Organelles and substances move along the cytoskeleton so that the cell can have order and proper placement of intracellular structures. Some of these same fibrous proteins play a role in the cilia and flagella of different types of cells. In addition, cells migrate both as part of cell division and outside of cell division by virtue of the activity of the cell cytoskeleton. Chapter thirteen in the course is about the eukaryotic cell cycle. There is a natural progression to the lifespan of a cell. It goes through growing phases, dividing phases, and the phases of death or apoptosis. There are specific controls over the eukaryotic cell cycle. The different phases of mitosis and meiosis are discussed along with the process of cell death, which is also called apoptosis.

CHAPTER ONE: CHEMICAL FOUNDATIONS OF LIFE This chapter introduces molecular biology by talking about the basics of biochemistry as it applies to life and living things. All of human life is based on water, which is a polar molecule that acts as a solvent for many biological molecules in living things. The bonds that make up biochemical molecules are also important in the discussion of molecular biology. The types of molecules that make up living organisms is also covered as are the different biochemical reactions that take place inside and outside the cell. Water Biochemistry Water is the common solvent found in all forms of life. Humans are about 70 percent water, while many marine organisms, such as jellyfish, are as much as 95 percent water. The oxygen that humans and animals breathe ultimately come from the water—turned into oxygen by the activities of photosynthetic plants. Plants and other organisms that are photosynthetic will take water and sunlight to make food, with oxygen as a waste product. Water is extremely abundant with about 350 million cubic miles of water on earth. About 97 percent of this is in the oceans of the earth, covering two-thirds of the planet’s surface. About 90 percent of all of the fresh water on earth is frozen in the poles and in glaciers. Only 1 percent of the water on the planet is drinkable, mostly found in underground aquifers. While water is a simple molecule, its characteristics are extremely important in molecular biology. Its chemical structure, H2O, means that it contains two atoms of hydrogen and one atom of oxygen, bonded in a V shape. Figure 1 shows what the molecular structure of water is:

Figure 1.

Water has a really small size but it has unique biochemical properties that make it easy to bond with other molecules through hydrogen bonding, which will be explained in a few minutes. Water is so important that it is involved in practically every chemical reaction and biological activity of the cell. It is the solvent that dissolves nearly every biological substance because it binds to other molecules and can exist on earth in every form: solid, liquid, and gaseous forms. It takes a great deal of energy to change the inherent temperature of water because it has a high specific heat. The specific heat of something is the number of calories it takes to change a gram of a substance to a different temperature level. The specific heat of water is 1 calorie per gram or 4.18 joules per gram per degree Celsius, meaning that it takes 1 calorie to raise the temperature of a gram of water one degree Celsius. This is much higher that the specific heat of other common substances, meaning it plays a big role in temperature regulation in living things. Water also transmits light well. This means that it allows for photosynthesis to occur under the water. Water is polar. This means that the positively negatively charged oxygen atom, having eight electrons around the molecule. The electrons orbit the eight protons in areas called orbitals. Two of the electrons fit within the first orbital and the six remaining electrons orbit the second orbital. Hydrogen has one proton and one electron. Because of the negatively charge pull of the oxygen electrons, the hydrogen atom donates and shares its atom with the oxygen in the second orbital of the oxygen molecule. The term “polar” means that there is a net negative charge on the oxygen molecule and a net positive charge on the hydrogen molecules. This bond between the hydrogen and 6

oxygen atom is called a “covalent bond”, which will be discussed in a few minutes. Covalent bonds involve the sharing of electrons. The oxygen molecule is V shaped because of the way the orbitals around the oxygen molecule are shaped. Because water is polar, it is able to dissolve other polar substances, including ions. Ions are atoms that have gained or lost an electron. One that has lost an electron is a cation and is positively charged. One that has gained an electron is an anion and is negatively charged. The polarity of water allows cations and anions to reside within the water solvent. Cations and anions are ions that are known as “hydrophilic”, which means water-loving. Even molecules that are not officially charges and are neutral can be hydrophilic. Examples of hydrophilic substances include glucose and any type of salt or ion. On the other hand, fats and some proteins are hydrophilic, which means “water-hating”. They do not easily dissolve in water but will dissolve in nonpolar substances. The terms “hydrophilic” and “hydrophobic” are important in the molecular biology of membranes or layers of hydrophobic and hydrophilic parts of molecules. Membranes can exist in water because they have atoms that are hydrophilic on the outside and atoms that are hydrophobic sandwiched between the hydrophilic parts. Water is so small that it can pass through most membranes without destroying the membrane itself. Figure 2 shows what a membrane looks like in water. Note that it is arranged in layers:

Figure 2.

Water has a high surface tension because the molecules stick together. This high surface tension means that it takes a great deal of force to separate the molecules and to break into the surface of the liquid. Think about insects that can walk on the surface of water in a lake, for example. Rain falling results in a droplet of liquid that stays on the surface of the earth, allowing more water to absorb into the soil for use by plants and other photosynthetic organisms. Because the specific heat of water is so high, the temperature of oceans and lakes changes slowly, leaving a stable temperature on the earth’s surface. This stable environment is important for plants. It also helps maintain the temperature of an organism, which means that the organism’s biochemical reactions can happen in a stable environment. The energy of vaporization of water is high. This means that it takes a great deal of heat to turn liquid water into water vapor. The water molecule vaporized takes the with it, leaving the remaining liquid water cooler. This is referred to as evaporative cooling. Evaporative cooling is used by animals to maintain their body temperature. This is the process that happens when humans sweat. It is a necessary process when exposed to the heat of the sun. As mentioned, water is found in three states on this planet. Water is denser as a liquid, which is an unusual property of water. It means that the lattice of solid water floats on the surface of liquid water. Water is densest at 4 degrees Celsius and become solid at 0 degrees Celsius. Water also expands when it freezes into a lattice shape. These properties of water help animals survive in cold temperatures under the water. As mentioned also is the ability of water to transmit light. What’s good about water is that it transmits certain wavelengths of light and scatters other wavelengths of light. Small wavelengths of light, such as UV light, can damage cells and are scattered by water vapor molecules surrounding the earth. On the other hand, blue and green wavelengths are transmitted easily through water; these are the wavelengths of light used most effectively by photosynthetic plants. What will absorb red light, which causes it to retain heat. This keeps the planet warm for the existence of light.

TYPES OF CHEMICAL BONDS Most of the time, atoms are not isolated. They tend to form certain stable patterns with other atoms. We talked a little bit about the bonds that exist in a molecule of water. The bond oxygen has with the hydrogen atoms is called a covalent chemical bond because it involves the sharing of electrons in a shared orbital between the atoms. This force that keeps the molecules together is called a chemical bond. There are several types of chemical bonds.

IONIC BONDS Ionic bonding happens when one atom transfers an electron to another atom. As we talked about, this type of bonding creates an anion and a cation. Because these are charged particles of opposite charges, they are attracted to one another and form an ionic molecule. The bond between them is called an ionic bond. An example of an ionic bond is between sodium and chlorine, which together form table salt or sodium chloride. This ionic molecule is extremely important in the molecular biology of living things. Figure 3 shows table salt in its lattice or crystalline form:

Figure 3.

Most ionic compounds dissolve easily in water because water is polar. Ionic compounds have high melting points and conduct electricity when they are dissolved in water. This is why ionic compounds are referred to as electrolytes. Ionic compounds and their ability to conduct electricity is extremely important in molecular biology. They allow for electrical potentials or differences in the electric charge between membranes, such as cellular membranes. The biggest difference between ionic bonding and covalent bonding is that ionic bonding has a difference in electronegativity of the atoms in the bond. They do share electrons, as is seen in covalent bonding but the sharing of electrons is unequal. One atom has more electronegativity than the other atom in the molecule. As you can see by figure 3, ionic compounds in solid form will form a lattice. There is a specific lattice energy of an ionic compound. The lattice energy of the compound is measure of its bond strength in solid form. Another way to describe it is that is the energy it takes to make solid ionic lattices from the molecule in gaseous form. For sodium chloride, for example, the lattice energy is -787 kilojoules per mole. This is quite high, meaning there is a strong lattice energy in this molecule. Notice the negative sign before the number. This signifies that the reaction is exothermic or that it gives off heat. This is a favorable reaction. The actual lattice energy of an ionic molecule cannot be measured because it would be difficult to have something like table salt in its gaseous form. What you should know is that the lattice energy of a molecule increases as the charge of the ions increase. In the same way, the lattice energy decreases with an increased size of the ions. When writing the chemical symbol for an ionic compound, the cation precedes the anion, just as sodium and chlorine come together to make sodium chloride. The suffix ide is added to signify that the molecule is an ionic compound. If the ionic compound is made from more than two atoms, the suffix -ate or -ite is used as you will see when you write the names of molecules like sodium phosphate and calcium nitrite.

COVALENT BONDS As we have talked about, covalent bonds are those that involve the sharing of electrons between atoms of the same molecule. Glucose is a sugar that is involved in multiple covalent bonds. This is also true of the bonding in water. There are orbitals around each atom that contain electrons. In covalent bonding, the atoms form a new orbital that contains the shared electrons. Figure 4 shows the covalent bonding seen in the methane molecule, which is an organic molecule not seen in most organisms:

Figure 4.

Covalent bonding changes the characteristics of the molecule. At normal room temperature and normal atmospheric pressure, covalent molecules may be solids, liquids, and gases. Ionic compounds are instead only solids at room temperature and pressure. Covalent compounds do not conduct electricity when dissolved in water. Compared to covalently bonded substances, ionic substances have a very high melting and boiling points.

You should know that covalent bonds can be single bonds or multiple bonds. Think of saturated fats, which contain only single bonds, and unsaturated fats, which have double bonds. Single bonds or sigma bonds are strong bonds, involving the sharing of a single pair of electrons. A sigma bond is seen in the bonds between oxygen and hydrogen in water or between two hydrogen atoms in the making of H2 or hydrogen gas. Double bonding in covalently bonded molecules involves the sharing of four electrons, while triple bonding involves the sharing of six electrons in sigma and pi orbitals. These bonds will make the connection between two atoms stronger. There is mixing of orbitals into hybrid orbitals that what are called “hybrid orbitals”. Multiple bonds always contain a single sigma bond plus other pi bonds between the atoms. Figure 5 shows what these bonds look like:

Figure 5.

Covalent bonds are named according the bond strength or the energy it takes to break the bond. There is more energy in the bonding between two oxygen atoms in O2 gas than there is in the bonding between two hydrogen atoms in H2 gas. Double bonds are stronger than single bonds and triple bonds are the strongest. The double bond strength of O2 is about 497 kilocalories per mole, while the triple bond strength of N2 is about 945 kilojoules per mole. 12

There is a difference too in the bond length between single, double, and triple bonds. Triple bonds have the shortest bond length, followed by double bonds and single bonds, which are longer than the rest. You should remember that atoms like to have eight atoms in each of their valent shells. This is called the “octet rule”. This makes the atom more stable. It will lead to a molecule that shares electrons in order to have stability of each atom that makes up the molecule. While covalent bonds are very strong, the intermolecular forces between these types of molecules is weak so they can have very low melting and boiling points. This is why they can be found in all the different states of matter. There are no ions in these molecules so they don’t conduct electricity and the strong double and triple bonds have shorter bond lengths than single bonds.

POLAR BONDS A polar bond is sort of a hybrid between a covalent bond and an ionic bond. It is a type of covalent bond in which there is an uneven distribution of the charge between the two atoms in the bond. The atom that is more electronegative will take on more of the negative charge. This is what is actually the case in the water molecule, where the oxygen atom is more electronegative than the hydrogen atom. The overall charge on the molecule is zero; however, at close range, these charge differences can help create interactions between the polar molecule and other polar molecules.

HYDROGEN BONDS Hydrogen bonding can happen between molecules of substances that are polar. It is a bond in which one of the atoms in the bond is hydrogen, which is less electronegative than oxygen, in the case of water. Hydrogen bonding is the weakest of all bonds, being just one-twentieth of the strength of a covalent bond. It is strong enough, however, to alter the molecular properties of water and to account for the high specific heat, high surface tension, and high heat of vaporization of water. It is also an important bond in the structure of DNA.

Related to hydrogen bonding is what are called van der Waals forces but van der Waals forces are even weaker than hydrogen bonds. Van der Waals forces attract neutral molecules to one another in the same way as is seen in hydrogen bonding. Because of the polarity of these types of molecules, the atoms that are more electronegative will attract atoms that are more electropositive. You can determine the electronegativity of a substance by looking at the periodic table. Those atoms in the upper right-hand corner of the table are considered the most electronegative.

CHEMICAL BUILDING BLOCKS OF LIFE There are four elements that make up the most common elements in living things. The largest contribution by weight is oxygen, followed by carbon, hydrogen, and nitrogen. Others that are less commonly seen include phosphorus, calcium, iron, and other metals or ions. There are four classes of biomolecules seen in the biochemistry of living things. These include lipids, carbohydrates, protein, and nucleic acids. As you will see, these tend to be polymers made up of certain monomers linked together. As you will see, when monomers turn into polymers, they do so by participating in dehydration reactions. Carbohydrates are molecules that are used for the storage and production of energy. Carbohydrates are made from sugars linked together. These molecules are the most abundant of the different biomolecules on earth. The simplest carbohydrate is called a monosaccharide. Two monosaccharides together will yield a disaccharide, while many together make a polysaccharide. They are made from carbon, hydrogen, and oxygen atoms only. A monosaccharide involves just a few different sugars. There are the six-carbon sugars, including glucose, fructose, and galactose, and five-carbon sugars, including ribose and deoxyribose. The five-carbon sugars are used to make RNA and DNA, respectively. Monosaccharides can be in an open-chain form or a closed-chain or “cyclic” form. Figure 6 shows the structure of several monosaccharides and disaccharides:

Figure 6.

As mentioned, two monosaccharides undergo a dehydration reaction to make a disaccharide. Examples of disaccharides include lactose, sucrose, and maltose. Sucrose is ordinary table sugar, made from glucose and fructose together. It takes a hydrolysis reaction to separate a disaccharide into two monosaccharides. A few sugars together make an oligosaccharide, which is used in chemical signaling. Many monosaccharides together make a polysaccharide, which can be linear or

branched. Cellulose, chitin, and glycogen are common polysaccharides. Of these, glycogen is used as an energy storage molecule in various animals. Lipids include thing like fatty acids and sterols like cholesterol. Triglycerides are free fatty acid molecules attached to glycerol. These look different from one another but share the fact that they are water-insoluble or hydrophobic. Some lipids have ring structures, like cholesterol, while others are linear, like fatty acids. Figure 7 shows the structure of the cholesterol molecule:

Figure 7.

Saturated fatty acids have no double bonds in the molecule, while unsaturated fatty acids have at least one double bond. A polyunsaturated fatty acid has many double bonds. Figure 8 shows what some unsaturated fatty acids look like:

Figure 8.

In general, fatty acids are nonpolar. When they are attached to a phosphate molecule, the molecule, called a phospholipid, becomes amphipathic, which means that it is hydrophobic on one end and hydrophilic on the other end. In this case, the phosphate component of the phospholipid is hydrophilic and the long tail is hydrophobic. Lipids are seen in the membranes of cells and are a common part of the human diet. Things like vegetable oils have polyunsaturated fatty acids, while butter contains saturated fatty acids. These are broken down in the diet and made into triglycerides in the body. Proteins and amino acids are called nitrogenous compounds because they contain nitrogen. Amino acids are the building blocks of proteins. Amino acids have a carboxyl group or a -COOH group and an amino group or NH3. Peptides are short proteins,

while proteins can consist of hundreds of amino acids strung together. There are twenty standard amino acids used in living things. They have different degrees of lipophilicity and hydrophilicity, which contribute to their three-dimensional shape. Amino acids can be modified or unmodified to make neurotransmitters in neurologic systems. Glutamate is an amino acid that also acts as a neurotransmitter. Figure 9 shows the structure of amino acids in neutral and zwitterion form:

Figure 9.

Proteins can be found in all biological systems. Things like actin and myosin, used to contract muscles, are made from proteins, albumin, and antibodies are all made from amino acids and are considered proteins. Glycoproteins are mixtures of proteins and sugars in one molecule. Enzymes are made from proteins. As you will see in a later chapter, there are different ways to describe the structure of proteins.

Proteins are important parts of the human diet. Proteins are consumed and are broken down into amino acids. They get absorbed by the GI tract and get reconfigured to make new proteins. In the cell, the pentose phosphate pathway and the citric acid cycle, which will be discussed later, are used to create new amino acids. There are nine amino acids that are considered essential to humans because they cannot be synthesized. Nucleic acids are found in the nuclei of cells as well as in the mitochondria. DNA and RNA are the polymers that are made from monomers called nucleotides. The consist of purines and pyrimidines, which are the “nitrogenous bases”, a sugar group, and a phosphate group. Figure 10 shows what a nucleotide looks like chemically:

Figure 10.

When making a nucleic acid like DNA or RNA, the phosphate group of one monomer binds covalently with the sugar group to make the polymer. The nitrogenous bases bind to each other loosely in hydrogen bonding to make the double helix seen in DNA. RNA is mostly single-stranded but can be double-stranded. In DNA, the adenine base binds with the thymine and the cytosine bonds with guanine, using hydrogen bonding to create the double strand. In RNA, the thymine is replaced with uracil. Nucleic acids can also be messengers and energy-producing molecules. Adenosine triphosphate is an energy-producing molecule that has energy in the phosphate linkages so when ATP (adenosine triphosphate) becomes ADP (adenosine diphosphate) the phosphate link breakage releases energy that is used to drive reactions.

CHEMICAL REACTIONS IN LIVING THINGS There are several types of reactions that can happen in biochemistry and cellular systems. One of these is a neutralization reaction. In this type of reaction, acids and bases react in order to form salt and water as a byproduct. The acids dissolve to make hydrogen or H+ ions. Bases dissolve in water to make hydroxyl or -OH ions. Neutralization reactions will control the pH of a solution by neutralizing the acidic and basic substances. Neutral pH in many systems is about 7 to 7.5, which is the pH that most enzymes react with the greatest intensity. Condensation or dehydration reactions take two molecules or two parts of molecules, binding the molecules together and remove water from the equation. An example is when sugars make a glycosidic linkage, giving off water in the process. Hydrolysis reactions are actually the reverse of condensation or dehydration reactions. Water is added to a system in order to divide or split two molecules or parts of molecules. Soap can be made by the hydrolysis of fats and corn syrup is made from the hydrolysis of corn starch. An oxidation-reduction reaction or redox reaction, there is a change in the oxidation state of an atom. Oxidation means the atom has lost some electrons and reduction happens when the atom has gained some electrons. The reason that this is called a redox reaction is because they happen together. Oxidation always happens with reduction. 20

The reducing agent loses electrons and is oxidized, while the oxidizing agent gains electrons, becoming reduced itself. Applications of redox reactions include the reactions that happen in cellular respiration and photosynthesis. The production of free radicals can happen in these reactions. Free radicals can damage cellular structures. The reactions that take place with enzymes will be discussed in a later chapter. Suffice it to say that enzymes reduce the energy of activation of a reaction so that the reaction can occur more easily. The beginning and ending energies of the reaction are the same with and without the enzyme. The enzyme just acts as a catalyst to facilitate the reaction. Without an enzyme, the reaction would occur too slowly. Enzymes act like a lock and key, making the enzyme specific for a given substrate. The enzyme can change the orientation of a molecule in order to have a bond form, can change the placement of electrons to enhance the reactivity of the substrate, or can induce physical stress in order to cleave a molecule more easily. Enzyme activity can be affected by the concentration of the substrate and enzyme, by the pH, by pressure, and by temperature occurring at the time of the reaction. There can be competitive inhibition, whereby a substance or enzyme is blocked from reacting.

KEY TAKEAWAYS •

Water is the universal solvent because it has many properties that allow it to be used in biological systems.

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Ions are involved in ionic bonding because of the inequality that exists with regard to holding onto electrons between the cation and anion.

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Covalent bonds are extremely strong and exist when two atoms roughly equally share electrons in a shared orbital.

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Hydrogen bonds are weak bonds between two atoms or molecules that are slightly polar and therefore attract each other.

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There are several core molecules in biochemistry, including carbohydrates, proteins, and nucleic acids.

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There are different reactions that can occur in biological systems, including acidbase, hydrolysis, dehydration, and redox reactions.

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Enzymes reduce the activation energy of a reaction so that the reaction can more easily occur, even though the starting and ending energies will be the same as without the enzyme.

QUIZ 1. What is the origin of the oxygen that humans breathe? a. Glucose metabolism b. Fatty acid metabolism c. Photosynthesis d. It always existed on the earth as O2 gas 2. What is the specific heat of water in calories per gram per degree Celsius? a. 0.5 b. 1 c. 2 d. 4 3. What is true of the lattice energy of an ion compared to its charge and size? e. The lattice energy decreases with increased size and increases with increased charge on the ion f. The lattice energy decreases with both the size and charge on the ion g. The lattice energy increases with both the size and charge on the ion h. The lattice energy increases with increased size and decreases with increased charge on the ion 4. What is not a suffix used to describe an anion in written form? a. ide b. ous c. ate d. ite 5. What type of bond is considered the weakest bond? a. Van der Waals forces b. Hydrogen bonding c. Ionic bonding d. Covalent bonding

6. What is the most common element seen in human life by weight? a. Carbon b. Oxygen c. Hydrogen d. Nitrogen 7. Which of the following is not a polysaccharide but is a disaccharide? a. Lactose b. Glycogen c. Chitin d. Cellulose 8. How many rings make up the cholesterol molecule? a. Zero b. Two c. Four d. Six 9. What type of reaction happens alongside an oxidation reaction? a. Reduction reaction b. Hydrolysis reaction c. Dehydration reaction d. Acid-base reaction 10. What type of reaction is the same thing as a condensation reaction? a. Reduction reaction b. Dehydration reaction c. Hydrolysis reaction d. Oxidation reaction

CHAPTER TWO: CELL STRUCTURES In this chapter, the discussion moves from biochemistry to the biology of cells and cell structures. There are two major types of cells: prokaryotic cells and eukaryotic cells. These are quite different from one another in structure and function, which will be covered in the chapter. Cells inside multicellular organisms must communicate with one another through different mechanisms. Animals that are complex and multicellular (such as are seen in the human body) have different cell types that form tissues. The tissues together form organ systems. The different types of tissues are covered in this chapter.

PROKARYOTIC CELL STRUCTURES In molecular biology, there are two kinds of cells: prokaryotic cells and eukaryotic cells. Of these, prokaryotic cells are the simplest. All cells have these things in common: 1) they all have a plasma membrane made from a phospholipid bilayer, 2) they all have a cytoplasm or jelly-like liquid that suspends the cellular structures, 3) they all contain DNA, and 4) they contain ribosomes that synthesize proteins. Prokaryotes are single-celled organisms lacking membrane-bound organelles and nuclei. Rather than a nucleus, the prokaryotic DNA is found centrally in the cytoplasm, being located in the nucleoid rather than a true nucleus. There is a peptidoglycan cell wall in most of these; many of these cells have a polysaccharide capsule on the outside of the cell. Some prokaryotes have appendages, such as fimbriae, pili, or flagella. Pili are used in conjugation (reproduction), while flagella are used for cellular movement. Fimbriae are used for bacterial attachment. Figure 11 shows a bacterial cell and its structures:

Figure 11.

Prokaryotes are much smaller than eukaryotes. They can be as large as 5 micrometers in diameter, while eukaryotic cells are about 10 to 100 micrometers in diameter. Because they are small, prokaryotic cells can easily diffuse nutrients and waste products into and out of the cells. The small size increases the surface to volume ratio so there is room to diffuse things into and out of the cell at its surface. There are different cell wall types of these organisms. Archaea and Bacteria have different cell walls. The cell wall gives the cell its shape. The capsule can allow some species to attach to specific surfaces. Inside the cell, plasmids with DNA inside them call also be seen. The plasma membrane is a lipid bilayer that separates the inside of the cell from the outside of the cell. It consists of a phospholipid bilayer that is selectively permeable, allowing some things to stay within the cell, some things to stay outside of the cell, and some things to be allowed in or out of the cell, depending on the circumstances. Archaea organisms have isoprene chains in place of the fatty acids found in bacterial cell membranes. In other cases, the lipid layer is a monolayer and not a bilayer. 26

The cell of prokaryotes has a high osmotic pressure within it. This necessitates something that will give the cell some shape and rigidity, leading to the presence of a cell wall, which will prevent cell bursting from influx of water into the cell. The chemical composition of the cell wall will be different, depending on the species. Most bacterial cell walls consist of peptidoglycan, which are polysaccharides that are crosslinked by peptides. Some antibiotics are active because of their activity against bacterial cell walls. There are hundreds of different kinds of peptidoglycans that are possible, depending on the species. Most bacteria also have an S-layer, which stands for surface layer; this is made from proteins. Gram staining, giving rise to gram-positive and gram-negative bacteria, depends on the amount of peptidoglycan contained around the organism. Gram-positive organisms have a thick peptidoglycan layer, while gram-negative bacteria have a thin peptidoglycan layer plus a liposaccharide outer envelope. Gram staining is different between the organisms because of the differences in cell wall structure. Prokaryotic cells reproduce asexually through binary fission. Their DNA is a single, circular chromosome rather than separate chromosomes seen in eukaryotic cells. Their division process does not involve mitosis; instead, the chromosome is simply replicated, with the two copies separating from one another. One cell pinches off from one another, resulting in two separate cloned cells. There is no genetic diversity involved with this process. There is genetic diversity that can happen through transformation. In this case, DNA from the environment is shed from another prokaryote and shared with the organism. This is how cells can share pathogenicity and ability to fight off antibiotics. Transduction can also happen, when bacteriophages, which are viruses that pass infection to bacteria, inject their DNA into a bacterium, the bacterium can take up the DNA. In conjugation, DNA is injected via a pilus from one bacterium to another. This reproduction can be very fast so that, coupled with mutation, the population can change dramatically in a short period of time.

EUKARYOTIC CELL STRUCTURES Eukaryotic cells have each of the things found in a prokaryotic cell plus a membranebound nucleus containing DNA, multiple membrane-bound organelles, and several chromosomes. The organelles include Golgi-apparatus, chloroplasts, endoplasmic reticulum, vacuoles, and mitochondria. Each organelle has a specialized role with the membranes allowing for compartmentalizing of the different cellular functions. Figure 12 shows the interior of a eukaryotic cell:

Figure 12.

The nucleus is the largest and most prominent organelle in the cell. The DNA is completely surrounded by the nuclear envelope. The DNA within the cell’s nucleus

directs the synthesis of proteins and ribosomes, which are responsible for protein synthesis. The envelope is a double membrane—each consisting of phospholipid bilayers. There are pores within the envelope that control the passage of molecules, RNA, and ions through the membranes. The nucleoplasm is the fluid within the nucleus. It is semisolid in structure and contains the chromosomes made from DNA. Figure 13 shows the human cell nucleus:

Figure 13.

Surrounding the nuclear envelope is the endoplasmic reticulum, which is continuous with the nuclear envelope. This configuration allows for RNA to exit the nucleus and take part in the synthesis of proteins in the rough endoplasmic reticulum, which is itself studded with protein-producing ribosomes. The smooth endoplasmic reticulum, on the other hand, does not contain ribosomes and is responsible for lipid synthesis. Mitochondria in the eukaryotic cells are oval in shape and double-membrane bound. They have their own DNA and protein-producing ribosomes. They make the ATP that is necessary for cellular energy by engaging in cellular respiration. The Golgi apparatus is the “post office” of the cell. It sorts, labels, packages, and distributes the substances made by the cell. Peroxisomes are single-membrane bound organelles that participate in redox reactions that break down amino acids and fatty acids, detoxifying cellular toxins. There are many vesicles and vacuoles inside the cell. These are single-layer membranous sacs that transport and store substance within the cell. Some will take up extracellular substances, while others will relieve the cell of waste products by combining with the cell membrane, allowing the waste products to leave the cell. All living things have a plasma membrane, which is part of what defines a living thing. It separates the inside of the cell from the extracellular space. While containing a phospholipid bilayer, as mentioned, it also consists of cholesterol and multiple plasma membrane proteins that have many functions. Everything that enters and leaves the cells comes through the plasma membrane. Figure 14 shows what the cell membrane looks like:

Figure 14.

The cell membrane is not static but is fluidic. The phospholipid molecule is extremely important in making the cell membrane because it has a polar end and a nonpolar end. The integral proteins that exist within the membrane have hydrophobic and hydrophilic components that allow them to imbed within the cell membrane. Some of these proteins form pores that allow certain ions, nutrients, and amino acids to enter or leave the cell, depending on the circumstances. The water-soluble substances, such as electrolytes, amino acids, and glucose, cannot pass through by themselves so they need an ion channel or other hydrophilic condition in order to pass through. There are substances that pass through actively (requiring energy) or passively (not requiring energy). Passive transport involves simple diffusion or facilitated diffusion. Water passes through via osmosis, which only works for water. Water passes down through its concentration gradient. Those things that require energy are transported through active transport, which involves substances like ATP to provide energy.

Endocytosis and exocytosis involve the movement of substances via vesicles that fuse with the membrane rather than being passed through membrane itself. The purpose of the nucleus of the cell is to store DNA plus the proteins that together form chromatin. In eukaryotes, the chromatin is not in a circular format but is linear and found in several separate chromosomes. In humans, there are 46 chromosomes. Other organisms have more or fewer chromosomes than this. They are generally invisible unless they are in the process of dividing. DNA is wrapped around histone proteins, which together make chromatin. The nucleolus resides within the nucleus. It is an area of condensed chromatin that is responsible for the synthesis of ribosomes. Ribosomes are complexes of RNA and protein that make proteins for the cell. They are made in the nucleolus and travel to the rough endoplasmic reticulum. Their job is to read the messenger RNA message, which has been transcribed from the DNA of the cell, and use transfer RNA to add one amino acid at a time to a growing peptide chain. Figure 15 shows what a ribosome looks like:

Figure 15.

The mitochondria are double-membrane structures, with an inner membrane that has many infoldings called cristae. This inner membrane contains many proteins and enzymes that are responsible for aerobic respiration. This is where ATP is synthesized. Figure 16 is what the structure of mitochondria looks like:

Figure 16.

As you can see by the figure, mitochondria have their own DNA, which is usually circular. They also have their own protein-making ribosomes. Because of the shape and structure of mitochondria, it is believed that mitochondria were evolutionarily once prokaryotic cells that have been incorporated into the structure and function of eukaryotic cells. They are essential to the life of the cell. Mitochondria, as you will learn more about later, make ATP energy as part of cellular respiration. There is a series of chemical reactions that start with simple sugars, fatty

acids, and amino acids, making carbon dioxide and water, plus many molecules of ATP, which are later used as cellular fuel. Oxygen is necessary for this process to occur. Carbon dioxide and water are the waste products after these reactions have completed. Cells that require a great deal of ATP energy, such as muscle cells, have a great many mitochondria in order to do this job. Cells that do not require a lot of ATP energy do not have many mitochondria. Red blood cells, for example, do not have mitochondria and do not participate in aerobic respiration. Instead, they participate in anaerobic metabolism, sometimes giving off lactic acid as a byproduct. The centrosome is something found in animal cells but not in plant cells. Each centrosome contains one pair of centrioles, which are perpendicular to one another. The centriole consists of a cylinder of microtubules. The centrosome is where all the microtubules of the cell come from; it divides when the cell divides in order to pull chromosomes to opposite ends of the dividing cell during cell division. Animal cells also have lysosomes, which are not found in plant cells. Lysosomes are where waste products accumulate and are taken care of by the body. This process in plant cells happens in the vacuoles of the cell instead. There are enzymes in the lysosomes that break down worn-out organelles, proteins, carbohydrates, lipids, and nucleic acids no longer needed by the cells. The environment inside lysosomes is highly acidic, allowing for their breakdown. There are some differences between plant cells and animal cells. Plant cells have microtubule organizing centers, just like animal cells, but they do not have centrosomes. Plant cells also do not have lysosomes but have vacuoles instead. Plant cells have cell walls and chloroplasts, which are not seen in animal cells. Figure 17 describes what a plant cell looks like:

Figure 17.

Plant cells contain chloroplasts, which are the structures of the cells that participate in photosynthesis. Chloroplasts also have their own DNA and ribosomes, similar to mitochondria. The act of photosynthesis involves using carbon dioxide, water, and the energy of the sunlight in order to make sugar or glucose plus oxygen as a byproduct. Plant cells are autotrophs because they make their own food, while animal cells are heterotrophs that must ingest food in order to survive. There is an inner and outer membrane in a chloroplast, similar to mitochondria. The biggest difference is that within the space inside the chloroplast are stacked membranous sacs called thylakoids. Each stack is called a granum. The stroma is the fluid around the thylakoids. The chloroplasts contain chlorophyll, which captures the light necessary for photosynthetic reactions. Figure 18 describes what a chloroplast looks like:

Figure 18.

The central vacuole is also present in plant cells but not animal cells. It allows for the regulation of the concentration of water inside the cell with differences in environmental conditions. The central vacuole will shrink under dry conditions in order to support the cell. It also supports the cell in conditions of increased water in the environment by holding more water under these circumstances. The cell wall covers and protects the cell. It is present in protists and fungal organisms. In plants, the cell wall consists of cellulose, which is nothing more than repeating units of glucose. It allows for the crunchy sensation you notice when biting into a fresh fruit or vegetable.

CELL TO CELL COMMUNICATION Cells do not operate in a void and must be able to communicate with cells beyond their borders. Cells can both send out and receive different signals that get unified in order to react in a certain way. Most of the signals a cell receives are purely chemical. Prokaryotes can detect nutrients and toxins. Multicellular organisms can detect hormones, neurotransmitters, growth factors, and components of the extracellular matrix. Cells can also respond to certain mechanical stimuli, such as with sound waves and sensory receptor cells in the skin. Most cells have receptors on them, which are proteins that respond to signals. We will talk about signaling systems in a later chapter. There are different receptors for the different molecules. Cells have hundreds of receptors on their surface that respond to different things. There are three different receptor types: G-protein-coupled receptors, enzyme-linked receptors, and ion channel receptors. As you will see in later chapters, they respond in different ways. They are important because they allow larger molecules to have access to the cell without actually entering the cell. There are also some receptors within the cell itself, such as those that respond to steroid hormones. Receptors act by undergoing conformational changes that change the interior of the cell biochemically. There are signaling pathways called signal transduction cascades that amplify the chemical message, leading to secondary messengers that act within the cell. An example of this is cyclic AMP, which is involved as a secondary messenger in several situations. It acts until it gets acted on by phosphodiesterase, which degrades it. Cells respond to numerous signals all at the same time. There are multiple signal transduction pathways operating within the cell. A single secondary messenger or protein kinase can be functional in several different pathways, leading to more than one cellular activity happening at one time. As you will find out later, there are three major stages of cellular communication. The first is reception. This happens outside of the cell that binds to a ligand or signaling molecule. Many of these receptor proteins span the membrane so they can act on the

cell internally, usually by changing their conformation or permitting a molecule to enter a channel that is part of the receptor. The next part is transduction. This is the process by which there are relay molecules that often involves the addition or subtraction of phosphate groups from larger molecules in what involves multiple steps. The last part is called the “response phase”. It can involve any possible cellular activity that is present in the body, triggered by the transduction phase. The response phase can involve the turning on or turning off of specific genes. Cellular communication can happen locally or from a distance. Locally, there can be communication via gap junctions between local cells. Plants themselves are connected through plasmodesmata. These kinds of communications are seen in embryonic development. Cell communication happens locally through paracrine signaling, which is signaling that happens over short distances. Autocrine signaling happens when cells act on identical cells. Endocrine signaling happens over large distances within the organism. All of these types of signaling mechanisms can happen in both plants and animals.

TISSUE DIFFERENTIATION Cells that are of the same type form tissues, which together form a specific function. In this case, we are talking about multicellular animal organisms. There are four types of tissues in the human body, each of which forms a different function. These are connective tissue, epithelial tissue, nervous tissue, and muscle tissue. In general, connective tissue is supportive to many other tissue types, while epithelial tissue creates protective barriers and is involved in ion and molecule diffusion. Nervous tissue will both transmit and integrate information and muscle tissue initiates movement. Epithelial tissue is the tissue that forms glands. It forms the coverings over body surfaces and lines body cavities. The tissues that form the receptors for the special senses (like smell and taste) is also epithelial tissue. These cells are closely connected to one another and have junctions that connect each other. These are cells that have an 38

apical surface or outer surface and a basal surface or inner surface. The apical surface is the lining of ducts, tubes, and the outer surface of the body. This is tissue that is innervated but not vascularized. Figure 19 shows what the different epithelial tissues look like:

Figure 19.

In fact, there are three sides to epithelial tissue: a basal side, an apical side, and a lateral side. The basal surface is closest to the basement membrane. The basement membrane is a thin substance that acts as a barrier between connective tissue and the basal layer of the epithelial tissue. There are hemidesmosomes, which will be discusses, which are specialized junctions that connect the basal surface to the basement membrane. The apical surface is nearest the free space or ductal lumen. There may be extensions into the lumen, called microvilli. Microvilli are intended to increase the surface area of the apical surface. These are found, for example, in the small intestinal lumen and in the kidneys, where absorption is important. Cilia are found in the female reproductive

system and the respiratory tract of humans. Cilia cause movement of things like mucus across the apical surface. Stereocilia are similar to cilia but are not motile. Stereocilia are found in the male reproductive system. The lateral surfaces are the surfaces between adjacent epithelial cells. This is where epithelial cells have most of their junctions. Desmosomes are connectors between neighboring cells, forming spots where the cells are connected to one another. These desmosomes use the cytoskeleton of the cell to interconnect the cells. On the other hand, tight junctions between the cells will form a solid barrier that does not allow substances to cross the epithelium. Gap junctions between cells allow molecules to pass between adjacent cells. These allow for coordinated movement of heart muscle cells, for example. As you can see by figure 19, there are different shapes of epithelial cells, which can be layered or non-layered. Squamous cells are flattened and can be either keratinized or nonkeratinized. These are protective cells that sometimes are used for diffusion. Cuboidal cells are cube-shaped, involved in absorption and secretion. Columnar cells are rectangular and sometimes have cilia. They have multiple functions. The epithelial cells can be simple (with one layer), stratified (or layered), or pseudostratified (which have one layer that looks stratified under the microscope). Connective tissue is the most common tissue type in the body. It consists of connective tissue cells and extracellular matrix, made from protein fibers and ground substance. The connective tissue is also what makes up blood and lymph cells, which do not have ground substance or fibers. All connective tissue arises from embryonic mesenchyme cells. Connective tissue has several possible functions. It can be structural, as is seen in chondroblasts, osteoblasts, and fibroblasts. It can be immunological, such as is seen in leukocytes and plasma cells. It can be related to defense, as is seen in macrophages and mast cells. It can be an energy reservoir, as is seen in fat cells. There are three major types of connective tissue fibers that make up the ground substance in connective tissue. The most abundant is collagen fibers. These are flexible but have a high tensile strength. There are several types of collagen fibers, that vary

according to their function. Reticular fibers are similar to collagen fibers but are thinner. They form a structural framework in connective tissue, usually invisible when connective tissue is stained. Elastic fibers are also thin. These are highly stretchable, able to stretch without breaking. They are found in the lungs, in blood vessels, and in skin tissue. Connective tissue can be described as proper, specialized, or embryonic. Proper connective tissue is loose connective tissue or dense connective tissue. Loose connective tissue is also called areolar tissue and has loosely-arranged collagen fibers in it. Dense connective tissue can be regular or irregular. Regular dense connective tissue is what makes ligaments or tendons. Irregular dense connective tissue is linked to things like the hollow intestinal organs. Embryonic connective tissue is the precursor tissue to other types of connective tissue. It is divided into mucous connective tissue and mesenchyme. Mesenchyme is embryonic tissue. Mucous connective tissue is found in the umbilical cord and is associated with the Wharton’s jelly that surrounds the cord. Specialized connective tissue is that which is seen in adipose tissue, cartilage, blood, and bone. Adipose tissue stores fat energy and makes certain molecules, like hormones and growth factors. These cells are mixed with loose connective tissue individually or in clusters. Bone has mineralized extracellular matrix, making it very strong. Blood is specialized connective tissue that has plasma as its extracellular matrix. Muscle tissue is distensible and elastic, able to be stretched and contracted. These cells are capable of being contractile because of the action of actin and myosin filaments within the cells. The cells are highly organized into bundles. While there are three types of muscle fibers (cardiac, smooth, and skeletal), all are arranged parallel to one another to some degree. Figure 20 shows the three different muscle types:

Figure 20.

Skeletal muscle is the type of muscle fiber that is voluntary. The cells are long and cylindrical. They are multinucleated from embryonic myoblasts that fuse together in the embryo. The muscles appear striated because of the arrangement of actin and myosin. Cardiac muscle is found in the heart and also appears striated. The movement is involuntary. Gap junctions coordinate these cellular functions. The cardiac muscle cells have just one nucleus. Smooth muscle tissue is that found in the GI tract and arterial walls. The action of these muscle cells is involuntary and relatively weak compared to other muscle types. They are shaped like spindles and have a single central nucleus. The cells do not appear striated because the cells are irregularly arranged. The main cells of the nervous system are the neurons and the glial cells. Neurons transmit electrical signals and have a large soma or body, with long projections called axons or dendrites that send information from one neuron to another. In most cases, it is the axon that sends signals away from the soma and dendrites that receive information for the cell. A group of neurons is called a nucleus in the central nervous system or a ganglion in the peripheral nervous system. Glial cells are the supportive cells of the nervous system. There are astrocytes, oligodendrocytes, and Schwann cells, for example. The oligodendrocytes and Schwann cells make myelin, forming the myelin sheath around white matter in the nervous system. Microglia, on the other hand, are the main macrophages of the nervous tissue. It is microglia that destroy pathogens and cellular debris in the nervous system.

KEY TAKEAWAYS •

There are fundamental differences between prokaryotic cells and eukaryotic cells, with eukaryotic cells having membrane-bound organelles.

•

Organelles in the eukaryote can be double-membrane bound or single-membrane bound. The nucleus, mitochondria, and chloroplasts have two membranes.

•

There are differences between plant cells and animal cells, including the presence of cell walls, chloroplasts, and central vacuoles in plant cells.

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Cells communicate through short or long distances, setting up signaling pathways that change the activity of the cell.

•

The main tissue types in humans are epithelial tissue, connective tissue, nervous tissue, and muscle tissue.

QUIZ 1. What aspect of a cell is not shared by all cells—both prokaryotic and eukaryotic? a. Nucleus b. DNA c. Cytoplasm d. Ribosomes 11. What is the innermost layer of the outer layers of the bacterial cell? a. Pili b. Capsule c. Cell wall d. Cell membrane 12. What part of the eukaryotic cell is responsible for making lipids? a. Smooth endoplasmic reticulum b. Rough endoplasmic reticulum c. Peroxisome d. Lysosome 13. What part of the eukaryotic cell packages and sorts substances made by the cell? a. Smooth endoplasmic reticulum b. Centriole c. Lysosome d. Golgi apparatus 14. What part of the eukaryotic animal cell will make microtubules? a. Golgi apparatus b. Lysosome c. Peroxisome d. Centrosome

15. What is seen in animal cells and not in plant cells? a. Centrosome b. Chloroplast c. Central vacuole d. Cell wall 16. What tissue type is most supportive to other tissues? a. Connective tissue b. Epithelial tissue c. Muscle tissue d. Nervous tissue 17. What tissue type generally lines body cavities? a. Connective tissue b. Epithelial tissue c. Muscle tissue d. Nervous tissue 18. What type of extracellular matrix protein in connective tissue is highly distensible, making it useful in skin and lung tissue? a. Collagen fibers b. Mesenchymal fibers c. Reticular fibers d. Elastic fibers 19. Which type of junction coordinates the movements of myocardial cells? a. Desmosomes b. Hemidesmosomes c. Gap junctions d. Tight junctions

CHAPTER THREE: INTEGRATING CELLS INTO TISSUES The focus of this chapter is the integration of cells into tissues. This chapter looks specifically into intercellular connections and how some of these connections create cellto-cell communication. In epithelial cell tissues, there is the basal lamina, the structure and function of which will be covered in the chapter. In addition, the structure and function of connective tissue structures are discussed as are the adhesions seen in plant cells.

CELL-CELL CONNECTIONS As we talked about in Chapter 2, there are connections between adjacent cells of different types. This chapter explores these connections in more detail. There are several types of junctions between the different cells.

TIGHT JUNCTIONS Tight junctions are also called zonula occludens. These are typically found in epithelial cells and endothelial cells. They act mainly to prevent diffusion across the cells. There are several molecules that together make tight junctions, such as claudins, occludins, tricellulin, and junctional adhesion molecules or JAMS. These are proteins that help make the anastomosis or connection between the cells that becomes impermeable to many things. The tight junction between cells marks the demarcation between the apical part of the cell (the apex) from the basolateral part of the cell. This junction marks the cell as being polar—with an apical and basal or basolateral part. The tight junction allows for the selective diffusion of ions and solutes between the cells. This process of diffusion between the cells is known as paracellular transport.

Tight junctions are formed because of connections between claudin proteins and other transmembrane proteins, like occludin, tricellulin, and JAMS (junctional adhesion molecules). Figure 21 shows the appearance of tight junctions between two epithelial cells:

Figure 21.

After the claudin strands polymerize or connect with one another. There are strengthening molecules and proteins that help to form the tight junction. These are scaffolding proteins such as cingulin, MUPP1, and ZO proteins. These proteins help seal the tight junction. The main protein involved in tight junctions is claudin, of which there are many types. Some claudin proteins are relatively porous, while others are barrier proteins. These proteins allow for the selective permeability seen in tight junctions of the GI tract and other epithelial tissues. The intestines and kidneys both have epithelia with tight

junctions that specifically allow for the influx and efflux of specific ions and molecules within these systems. The tight junctions are considered extremely tight in situations like the blood-brain barrier, which separates the central nervous system or CNS from the rest of the circulation. There are similar proteins in the retina, which allow for a strong barrier in the eye. Other impermeable states exist in the bladder and skin. When the tight junctions become dysregulated by inflammation or disease, this can lead to neuroinflammation, diarrhea, leaky gut syndrome, gastritis, irritable bowel syndrome, dermatitis, kidney disease, and even metastatic cancer.

DESMOSOMES Desmosomes are also referred to as maculae adherens. This means “adhering spot” in Latin. It is a cell to cell adhesion that are seen on the sides of cells. They are relatively strong and are found in tissues that are under certain kinds of mechanical stress, such as bladder tissue, GI tissues, cardiac muscle, and other types of epithelia. These are made from cadherin proteins, keratin intermediate filaments and linker proteins, which are collectively referred to as desmosome-intermediate filament complexes. Figure 22 shows what a desmosome looks like:

Figure 22.

The goal of desmosomes is to link intermediate filaments in the cell to the plasma membrane and other intermediate filaments in nearby cells. Again, resistance to mechanical stress is the purpose of these adhesions. There are specific proteins that facilitate the connection between the intermediate filaments. These include plakophilin, desmoplakin, plakoglobin, desmoglein, and desmocollin. These linkage proteins connect the intermediate filaments. Desmoglein and desmocollin are in the intracellular space, while plakophilin, desmoplakin, and plakoglobin are in the cell itself—all use to connect intermediate filaments.

ADHERENS JUNCTIONS These are cell to cell adhesion complexes that respond to forces within the tissues. They are similar to desmosomes because they use cadherins proteins but are band-like rather than spot-like in appearance. They also are necessary for resistance to mechanical tension on the tissues and are seen connecting cardiac muscle cells. Adherens junctions can assemble and disassemble, depending on the circumstances. They are seen during development when cells must migrate in order to form a particular tissue or when a change in the tissue is necessary. They can change in shape or move whenever there is a biochemical or mechanical stimulus to the tissue. These junctions help maintain cellular shape and the integrity of the tissues. In cardiac muscle, it is the adherens junction that helps connect the actin filaments in the cardiac cells.

GAP JUNCTIONS Gap junctions are also intercellular connections seen in animal cells. Unlike the other connections, these actually connect the cytoplasm of cells that are next to one another. They allow ions, electrical impulses, and small molecules to pass through a regulated gate that exists between the two cells. There are two hemichannels or connexons—one from each cell—that connect between the cells. As you will see, these are the “animal equivalent” of the plasmodesmata that exist between plant cells. All tissues of the body have gap junctions except for developed skeletal muscle and motile cells. When found in neural tissue, these are the same thing as the electrical synapse.

The pair of connexons together allow for the transmission of small molecules like second messengers, ions, and some nutrients to pass from one cell to another. Electricity can also pass from one cell to another through these gap junctions.

CELL-MATRIX CONNECTIONS Cells have the ability to anchor or adhere to the extracellular matrix through the use of anchoring junctions. Anchoring junctions are made from many different proteins that connect the cell to matrix, stabilizing the position of the cell within the tissue. They can also seal away cells so that ions and molecules cannot flow out of the tissue. Anchoring junctions regulate the motility of certain cells as they pass from one place to another. Like other adhering proteins, they can assemble and disassemble so that the cell can move under stress. Many link actin filaments to substrate outside of the cell. A hemidesmosome is basically the same thing as a desmosome except that it binds a cell to the basement membrane of the epithelium. They are focal adhesions that use integrin proteins instead of the desmoglein and desmocollin proteins seen in desmosomes. They connect the lamina lucida of skin cells to the skin’s epithelial basement membrane. They connect intermediate filaments to the extracellular matrix.

BASEMENT MEMBRANE The basement membrane is very important to epithelial tissues. They surround many animal tissues and are thin, dense connective tissue-like structures. They contain two protein networks: one made from laminin and another from type VII collagen. Basement membranes are biochemically-distinct structures, made from proteins, such as proteoglycans, glycoproteins, and others that connect to form the basement membrane structure. The foundation of the basement membrane is laminin, which has three subunits that form a sheet-like lattice connected to the epithelial cell surface. The laminin is what connects the basal portion of the cell to the collagen VII fibers through receptors on the cell.

The basement membrane is part of the barrier necessary in the epithelium. This becomes important in tissues like the kidneys and brain, where barriers are necessary. The laminin and collagen networks in the kidneys allow for selective permeability of the epithelial lining. The same thing happens in the brain with the blood brain barrier and in the capillaries. In these cases, the basement membrane assists in controlling the intermembranous passage of molecules. Laminin is also important in the structure of hemidesmosomes. It interacts with the integrin on the cell surface and type VII collagen anchors the basement membrane to the underlying connective tissue, protecting the tissue from shear forces.

CONNECTIVE TISSUE AND CONNECTIVE TISSUE PROTEINS We’ve talked about connective tissue as being one of the four major types of tissues. It is an abundant tissue, acting as a framework for the other tissues of the body. It is important for communication between tissues, mechanical support, and transport within the body. It also has the possibility for inflammation because immune cells can be found within connective tissue. The key component of connective tissue is that it consists of individual cells that are not directly connected directly but are connected via the extracellular matrix. Connective tissue comes from mesoderm or mesenchyme within the embryonic body. Common cells of connective tissue include adipocytes, fibroblasts, and the immune cells, such as lymphocytes, macrophages, and mast cells. A main feature of connective tissue is the presence of ground substance (made of minerals, plasma, proteoglycans, glycosaminoglycans, and glycoproteins). Minerals are found in bone, while plasma is found in the blood fluid because both bone and blood are considered connective tissue. The main fiber is collagen, with elastin and reticular fibers found in lesser amounts. Fibroblasts make the collagen in connective tissue. As mentioned, there is ordinary connective tissue—adipose and fibrous tissue—and specialized connective tissue—lymphoid tissue, elastic tissue, bone, cartilage, and blood. These will differ in the cell types seen as well as in the type of protein seen in the tissue.

Collectively, connective tissue’s three main roles include immunological protection, nutritional support, and mechanical support in the body. The most common resident cell in ordinary connective tissue is the fibroblast. These will secrete collagen and other aspects of the extracellular matrix. Fibroblasts are not immature cells as the name implies but are mature connective tissue cells. These are the cells that form scars after an injury. Chondroblasts in cartilage and osteoblasts in bone are related types of cells. The extracellular matrix in connective tissue is made from ground substance or fibers. Ground substance is mainly water, although there are other proteins and carbohydrates in the substance. The effect of glycosaminoglycans, glycoproteins, and proteoglycans is to make ground substance similar to gelatin. The fibers, collagen and elastin, are commonly seen as well. Reticular fibers are the same thing as collagen but are more delicate fibers in connective tissue. As mentioned, there are many different types of collagen but just a few types are commonly seen. Type I collagen is seen in ordinary fibrous connective tissue. Type II collagen is seen in cartilage. Type III collagen is in reticular fibers. Type IV collagen is found in smooth and skeletal muscle. Type VII is seen in basement membranes. There are different disorders that affect different types of collagen. The functions of connective tissue include the transportation of metabolites and nutrients, mechanical support, and immunological defense. It is extremely important in tissue repair, as is seen when scar forms. Specialized connective tissue can engage in hematopoiesis, heat generation, and energy storage. Collagen is the main protein in connective tissue. It is the most abundant protein in the entire animal kingdom. Most collagen is types I, II, and III, although there are 16 different types. They form collagen fibrils. Not all collagen is made by fibroblasts; some is made by epithelial cells. Collagen is not stretchy so it keeps connective tissue mechanically stable. Collagen is made as a triple helix. Figure 23 shows what the collagen fibril looks like molecularly:

Figure 23.

The three-stranded collagen molecule packs side-by-side. Collagen fibrils have significant tensile strength so that it can be stretched a great deal without being broken. Altogether, the collagen molecules form a fiber, as is seen in tendons. Type 1 collagen is so strong that it is stronger than steel. Collagen starts out as procollagens, made typically in the rough endoplasmic reticulum. It gets processed in the Golgi apparatus and is secreted into the extracellular space through exocytosis. The protein becomes tropocollagen and is a triple helix. The molecule gets completed in its construction outside of the cell. As mentioned, there are different structures that are made from collagen. Type I is the major collagen in connective tissue, while type II is seen in collagen. Type II collagen has smaller fibrils that are oriented more randomly than in type I collagen. It forms a rigid substance as is typical of cartilaginous tissues. Type II collagen is linked with type 9 collagen to make the cartilaginous matrix.

Elastin is named for its high elasticity in connective tissue. It allows for the stretching or contracting of tissues, including the skin. It is encoded by the ELN gene in humans. If the gene is defective, there can be a genetic disorder, such as is seen in cutis laxa, which is an autosomal dominant disorder of elastin synthesis. Elastic fibers are made from elastin, which is more amorphous in shape, and fibrillin, which is more fibrous. Elastin is particularly important in arteries, in the lungs, in the skin, and in the bladder, where elasticity is necessary. Elastin is made by the linkage of many soluble tropoelastin molecules in order to make the durable elastin protein. The tropoelastin is cross-linked in order to make the whole elastin molecule. As mentioned, fibrillin is necessary to make elastic fibers; fibrillin is a glycoprotein secreted by the fibroblasts in the connective tissue. Fibrillin is made by the FBN genes. There are three types of fibrillin. Fibrillin-1 is made into microfibrils. Mutations in the gene FBN1 leads to conditions like Marfan syndrome, which involves increased elasticity of some tissues in the body. There are more than 1500 mutations that are possible in the FBN1 gene. Fibrillin-2, fibrillin-3, and fibrillin-4 have been more recently isolated and are less commonly linked to known disease states.

PLANT CELL ADHESIONS Plant cells have unique structures called plasmodesmata. These are also seen in some algae. The purpose of these structures is to allow transport of molecules and communication between the different cells. Almost all plant cells have a cell wall around the cell, keeping it effectively separate from other cells. Cell walls can be somewhat impermeable to certain substances so plasmodesmata are necessary to have transport between the cells. There are two types of plasmodesmata: primary plasmodesmata, which are made during cell division, and secondary plasmodesmata, which happen between already mature cells. Primary plasmodesmata are made from endoplasmic reticulum, which can become trapped outside the cell at the time of cell division. These lead to cytoplasmic connections between the two sister cells. The cell wall is not made where the 56

plasmodesmata are formed, allowing for connection to happen between the cell membranes of the plant cells. Figure 24 shows what the plasmodesmata look like:

Figure 24..

There are thousands of plasmodesmata seen in each plant cell. There are three main layers: the plasma membrane, the cytoplasmic sleeve, and the desmotubule. They can get through very thick cell walls, up to 90 nanometers thick. The purpose of the plasmodesmata is to allow sugars, amino acids, water, and ions to pass from one cell to another. There is no need for chemical energy to pass these things from cell to cell; they pass through via simple diffusion. Larger molecules can also sometimes get from cell to cell but the mechanism by which it does this is unknown. Signaling molecules, RNA, and transcription factors seem to be able to get from one cell to another but it isn’t known how this occurs.

KEY TAKEAWAYS •

There are different connections between cells, including tight junctions, gap junctions, desmosomes, and plasmodesmata.

•

Hemidesmosomes connect one cell to the basement membrane and not a cell to another cell directly.

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Collagen and elastin are major connective tissue membranes that give connective tissue its durability.

•

Plasmodesmata are specifically found in plant and algal cells; it provides a direct connection between the different cells of the organism.

QUIZ 1. What type of tissue mainly has tight junctions or zonula occludens? a. Epithelial tissue b. Connective tissue c. Nervous tissue d. Muscle tissue 2. Which intercellular junction is most associated with impermeability? a. Gap junctions b. Desmosomes c. Tight junctions d. Hemidesmosomes 3. Where in the human body are tight junctions between epithelial cells relatively permeable to certain ions but not to others? a. Kidneys b. Brain c. Retina d. Bladder 4. Where can you least find desmosomes between epithelial cells? a. Cardiac muscle b. GI tract c. Brain d. Bladder 5. Which cell connector makes use of integrin proteins in order to connect the cell to the basement membrane of an epithelial tissue? a. Gap junctions b. Adherens junctions c. Hemidesmosomes d. Desmosomes

6. Which type of collagen is most associated with the formation of the basement membrane? a. Type I b. Type II c. Type III d. Type VII 7. What is the main structure of collagen when seen with an electron microscope? a. Globular b. Linear sheets c. Single helix d. Triple helix 8. What is the main function of collagen in connective tissue? a. To provide elasticity b. For tensile strength c. For molecular transport d. For immune support 9. Which animal cell connection system is most similar to plasmodesmata seen in plant cells? a. Adherens junctions b. Gap junctions c. Desmosomes d. Tight junctions 10. How to molecules get from cell to cell through the plasmodesmata between neighboring plant cells? a. Simple diffusion b. Facilitated diffusion c. Active transport d. Exocytosis

CHAPTER FOUR: BIOMEMBRANES This chapter talks about the synthesis and structure of biomembranes. It covers fatty acid synthesis, which is how the basic molecules of biomembranes get created and incorporated into things like cell membranes and the membranes seen in organelles. The composition of membranes is also introduced, including the phospholipids and membrane proteins that together make up the cell membrane structure.

FATTY ACID SYNTHESIS The best way to understand biomembranes is to first learn how fatty acids are synthesized. Fatty acids make phospholipids, which ultimately make up the bulk of the cell membrane. There are enzymes called fatty acid synthases that take acetyl-CoA and NADPH, making fatty acids as a result. This process happens in the cell cytoplasm. Most of the acetyl-CoA comes from glycolysis, which as you will see comes from the initial breakdown of glucose using glycolytic enzymes. Glycolysis also provides glycerol, which is necessary to make triglycerides. Triglycerides are nothing more than three fatty acids that are connected to a glycerol molecule via an ester bond. Figure 25 shows what a triglyceride molecule looks like:

Figure 25.

Phospholipids, which are the substances that make up cell membranes, are actually made from glycerol, two fatty acids, and a phosphate group on the third alcohol moiety. These are polar on one end and nonpolar on the other end, making them good molecules for the lipid bilayer that makes up the cell membrane and other biomembranes in the cell. Saturated fatty acids have no double bonds in the molecule; in that sense, they are “saturated” with hydrogen atoms. The resultant fatty acid is relatively straight in its structure. There are six reactions that occur in the synthesis of saturated fatty acids, which occur repeatedly to get a long-chain fatty acid. The prokaryotes have fatty acid synthase II, while animals and some fungi have fatty acid synthase I as the molecule that creates the fatty acid. The reaction occurs to make a sixteen-carbon saturated fatty acid, which is palmitic acid. Palmitic acid is the most common fatty acid seen in animal cells. After palmitic acid is made, it can be desaturated to make an unsaturated fatty acid or it can be elongated to make longer fatty acids. This is done in the smooth endoplasmic reticulum. The reaction necessary to make a fatty acid is a redox reaction, involving a reducing agent NADPH or nicotinamide adenine dinucleotide phosphate. The opposite reaction to turn fatty acids back into acetyl CoA in the breakdown of fatty acids is NAD or nicotinamide adenine dinucleotide. This NADPH is made in the mitochondria through several different oxidative pathways. The acetyl CoA necessary to make fatty acids comes directly from glucose breakdown and the glycolysis pathway, which will be discussed in a later chapter. The three areas of the body that make fatty acids in humans are the liver, adipose tissue, and mammary glands during lactation. The acetyl CoA is made in the mitochondria but it needs to be transported to the cytoplasm, where cholesterol and fatty acids are made. In order to do this, citrate is made in the citric acid cycle, removed from the cycle, gets transported across the mitochondrial membrane, and becomes acetyl CoA. Most branched-chain fatty acids are saturated. These are made using alpha-keto acids rather than acetyl CoA. Valine, leucine, and isoleucine are amino acids that are 62

transformed into branched chain fatty acids. There are many steps necessary in order to make branched-chain fatty acids that can be between 12 and 17 carbons in total length. The reaction involves branched-chain fatty acid synthase.

COMPOSITION OF MEMBRANES Fatty acids can be made into phospholipids in order to create the plasma membrane. In total, the plasma membrane is made from lipids and proteins. The phospholipid bilayer forms a stable barrier between the two aqueous compartments (inside and outside the cell). There are several different types of proteins that perform different functions in and out of the cell, including the all-important functions of selective molecular transport and cell-to-cell recognition. There are four major phospholipids in the plasma membrane of animal cells: sphingomyelin, phosphatidyl serine, phosphatidylethanolamine, and phosphatidylcholine. These together make up more than half of the total lipids in the membranes. Interestingly, the makeup of the outer layer is slightly different than the makeup of the inner layer. The outer layer consists of sphingomyelin, phosphatidylcholine, and glycolipids. The inner layer consists of phosphatidylserine and phosphatidylethanolamine. Phosphatidylinositol is also a major part of the inner layer but is not seen much in the outer layer. The head groups of the inner layer are more negatively charged so the inner part of the cell is more negatively charged when compared to the outer layer. Glycolipids and cholesterol are also seen as part of the cell membrane. The glycolipids are found only on the outer layer, with their carbohydrate moieties sticking out of the cell. They represent just about 2 percent of the lipids in the plasma membrane. Cholesterol is a major part of the cell membrane—it makes up about half of the total lipids seen in animal cells. The membrane is relatively impermeable to water-soluble molecules, including ions and most small and large biological molecules. Some fatty acids in the phospholipid molecule are unsaturated and have double bonds that make them hard to pack together. 63

The structure of these membranes makes lateral movement possible of proteins and lipids. Cholesterol can move freely within the membrane but cannot form a membrane by itself. Most plasma membranes of animal cells have 50 percent lipids and 50 percent protein by weight. Carbohydrates make up about 5 to 10 percent of the mass of the membrane. Because proteins are heavier, there is only about 1 protein molecule per 50 to 100 molecules of lipids in the membrane. The fluidity of the membrane creates a fluid mosaic model—a raft of sorts where things can move relatively freely throughout the membrane. Figure 26 shows these free-floating proteins in the cell membrane:

Figure 26.

There are peripheral proteins and integral membrane proteins that are identified in the laboratory by their ability or lack of ability to be dissociated from the membrane after being treated with polar reagents. Peripheral proteins lie on the surface of the membrane, while integral proteins are within the membrane itself. Integral proteins cannot be isolated unless the lipid bilayer is disrupted. Most integral proteins are transmembrane proteins that span the entirety of the lipid bilayer with parts of the protein exposed on both sides of this membrane. Electron microscopy will show these proteins as they stick out on either side of the membrane

with hydrophilic parts on the outside of the membrane and hydrophilic parts on the inner aspect of the membrane. The carbohydrate groups sticking out of the membrane are made in the Golgi apparatus. Membrane proteins are not able to move in and out of the lipid bilayer but they can diffuse laterally because of the fluid mosaic model. This has been proven by fusing two cells together and observing the hybrid cell that will contain aspects of both pre-hybrid cells covering the entire surface of the hybrid cell. Some proteins, however, are restricted because they are associated with the cytoskeleton, which is attached to the cell membrane in order to form the structure of the cell. This is especially true in cells that are polar, such as epithelial cells that have an apical portion and a basolateral portion. There are proteins that exist just on the apical side of the cell and not on the basolateral part of the cell, and vice versa. Tight junctions are part of the mechanism that make sure the proteins stay where they are supposed to. As mentioned, the outer portions of the plasma membranes usually have sugar or carbohydrates attached, making the proteins called glycolipids. This leads to an outer surface of the cell membrane being called a glycocalyx. It is made from oligosaccharides attached to various proteins in and on the surface of the cell. The glycocalyx protects the cell surface and participate in cell to cell interactions.

MEMBRANE PROTEINS There are several different kinds of membrane proteins. There are membrane receptor proteins that send signals from the outside of a cell to the inside of the cell and vice versa. There are transport proteins that move ions and small molecules across the membrane. There are several membrane enzymes. Finally, there are cell adhesion proteins that allow cells to identify one another. Integral membrane proteins are specific types of membrane proteins that can be transmembrane proteins. There are two types of integral membrane proteins. These are integral polytopic proteins (also called transmembrane proteins) and integral monotopic proteins.

Most integral membrane proteins are transmembrane proteins, which exists throughout the membrane. They can pass through the membrane just once or can weave in and out of the membrane, being multi-pass membrane proteins. Integral monotopic proteins, on the other hand do not span the entirety of the lipid bilayer. Many transmembrane proteins attach to the cell membrane and cannot move out of the membrane. Most are transport proteins that act as ion or small molecule channels. They require detergents to be extracted from the cell in most cases. The two main types of transmembrane proteins are alpha-helical and beta-barrel proteins. The alpha-helical proteins are found in prokaryotes and eukaryotes; they can be found in the inner or outer membrane leaflets. Beta-barrels are only seen in prokaryotes or in the outer membranes of chloroplasts and mitochondria. Types I through IV are single-pass molecules, while other types are transmembrane proteins are multi-pass molecules. Peripheral membrane proteins only adhere temporarily to the biomembranes. They are attached to integral proteins or penetrate the outer lipid layer to a slight degree. These molecules include regulatory subunits of other transmembrane proteins. They are largely water soluble. Those that are called amphitropic proteins have hydrophobic parts that can slightly penetrate the lipid bilayer. Others can do both—can penetrate the lipid bilayer and can attach to transmembrane proteins. The connection between the lipid bilayer and a protein may involve changes in the structure or shape of the protein so that it can bind to the bilayer. The protein may need to rearrange itself into a specific shape in order to connect to the lipid bilayer. The different functions of these proteins include membrane anchoring, enzymatic activities of lipids, and the transfer of small nonpolar substances across the membrane.

KEY TAKEAWAYS •

Biomembranes are synthesized in the cytosol by fatty acid synthases that take acetyl CoA and add to it to make long-chain fatty acids.

•

Palmitic acid is a sixteen-carbon chain fatty acid that is the most common one found in biomembranes in animals.

•

Membranes are made of phospholipids, cholesterol, and proteins.

•

The proteins in the cell membrane can be peripheral or transmembrane proteins. They serve several different functions for the biomembranes.

QUIZ 1. What is not a part of a triglyceride molecule? a. Glycerol e. Carboxylic acid f. Ester bond g. Fatty acid 2. What is part of the phospholipid that is not a part of the triglyceride molecule? a. Fatty acids b. Ester bonding c. Glycerol d. Phosphate group 3. Fatty acid synthesis happens in the human body through the breakdown of glucose and the making of acetyl CoA. What area of the body is not associated with this fatty acid synthesis process? a. Liver b. Adipose tissue c. Muscle cells d. Mammary glands 4. Which fatty acid is made in fatty acid synthesis the most, becoming the most common fatty acid in animal cells? a. Arachidonic acid b. Palmitic acid c. Stearic acid d. Linoleic acid

5. What type of lipid is only found on the outside of the cell membrane and not on the inside? a. Glycolipids b. Cholesterol c. Phosphatidylinositol d. Phosphatidylserine 6. What is the major difference between integral proteins and peripheral proteins? a. Peripheral proteins are hydrophobic and integral proteins are hydrophilic b. Peripheral proteins are only on the inside of the cell membrane c. Peripheral proteins lie on the outer surface of the cell d. Peripheral proteins cannot be isolated unless the cell membrane is disrupted 7. What makes up the outer portion of a cell for the most part? a. Phosphate molecules b. Lipid layer c. Hydrophobic proteins d. Carbohydrates 8. What is the main purpose of a transporter protein in a cell membrane? a. To transport ions or small molecules across the membrane b. To aid in endocytosis for the cell c. To aid in exocytosis for the cell d. To attach the cell’s exoskeleton to the cell membrane 9. Which membrane protein in animals is most responsible for chemical signaling in and out of the cell? a. Transporter protein b. Cell adhesion protein c. Membrane receptor protein d. Protein enzymes

10. What is the main difference between transmembrane proteins and integral monotopic proteins? a. Integral monotopic proteins are more lipophilic than transmembrane proteins b. Integral monotopic proteins do not pass all the way through the membrane and transmembrane proteins do c. Integral monotopic proteins are larger than transmembrane proteins d. Integral monotopic proteins have a glycocalyx, which is not true of transmembrane proteins

CHAPTER FIVE: TRANSMEMBRANE TRANSPORT The main focus of this chapter is the different things that happen in transmembrane support. Water, for example, can pass through the membrane by osmosis—from a high concentration of water to a low concentration of water. Other types of membrane transport include simple and facilitated diffusion, as well as active transport. The sodium-potassium ATPase pump is particularly important in cell membrane transport. Symporters and antiporters also aid in the transport of certain molecules across the membrane. Ion transport helps account for a difference in electric potential between the inside and outside of the cell.

OSMOSIS Osmosis involves the net movement of a solvent through a selectively permeable membrane. In biological systems, this applies only to water because this is the solvent used. The water goes from an area of low solute concentration (such as a dilute solution) to an area of high solute concentration (such as a concentrated solution). In a sense, it goes from a high water concentration to a low water concentration in order to balance out the solute concentrations. In such cases, the membrane is permeable to water but not to the solutes. The osmotic pressure in a system is the pressure applied to an aqueous system so that there is no net movement of the solvent across the semi-permeable membrane. It is usually also defined as the concentration of the solvent; it is a concentration that depends on the number of moles of the solute that are present but does not depend on the identity of the solute in the solution. The cell membrane in biological systems is generally impermeable to ions because the ions are polar; it is also impermeable to larger molecules, such as sugars and peptides (because of their size). Molecules that are hydrophobic, such as lipids, and gaseous molecules, like oxygen, nitrogen, and carbon dioxide do not contribute to osmotic pressure because these are permeable across the membrane. Water passes through

aquaporins, which are small transmembrane proteins that allow water to get from one side of the membrane to the other. Aquaporins are also called “water channels”. These are integral membrane proteins that facilitate the passage of water across the membrane more rapidly that through passive diffusion. There are different aquaporins, depending on the organism, each of which span the membrane several times. Aquaporins allow water to pass through the cell but do not allow ions and other small molecules get through. Aquaporin molecules are particularly important for plants that rely on the rapid transport of water from cell to cell. During osmosis, water enters and leaves the cell in both directions with no net change of water as long as the concentration of solute is the same on both sides. Cells that placed in plain water will burst because water will be driven into the cell. On the other hand, cells that are placed in a hypertonic (concentrated) salt solution will shrink because water will leave the low concentrated solution in the cell for the highly-concentrated solution outside of the cell. Figure 27 shows red blood cells in different solutions:

Figure 27.

Plant cells in hypertonic solution become “plasmolyzed” in that it draws away from its cell wall or becomes flaccid; plant cells in hypotonic solution (such as plain water when flowers are put in a watered vase) become turgid. In the same way, plants will 72

concentrate their root cells with solute through active transport mechanisms, allowing for osmosis to drive the water in from the soil. Evaporation of water from the leaves draws more water up the stem; this evaporation of water is called transpiration. As mentioned, the osmotic pressure is determined by the concentration of solutes in the solution. A substance that dissolves in water to make sodium and chloride will have twice the osmotic pressure as the same number of moles of dissolved sugar—because sodium chloride dissolves into two solutes. The osmotic gradient is the difference in the concentration of two solutions on either side of the membrane.

DIFFUSION Diffusion can be passive or “facilitated”. Passive transport involves the movement of a substance across the cell membrane without the addition of energy. The rate of transport, depends on how permeable the membrane is to the substance. The different types of passive transport include filtration, facilitated diffusion, diffusion, and osmosis. Simple diffusion involves the net transport of a substance from an area of high concentration to an area of low concentration. It does not necessarily involve a membrane as substances can diffuse across open areas of a solvent. The driving force is the concentration gradient. Solutes travel down their concentration gradient until it no longer exists. Simple diffusion and osmosis are similar; the main difference is that in diffusion, the substance moving is the solute, while in osmosis, the substance moving is the solvent. Facilitated diffusion or facilitated transport is movement across a membrane through transmembrane integral proteins that does not require ATP energy. Molecules will still pass from their highest concentration to their lowest concentration. Figure 28 shows facilitated diffusion across a membrane:

Figure 28.

The main differences between simple diffusion and facilitated diffusion are that facilitated diffusion depends on binding to the membrane-embedded channel protein. This is saturable, which is not true of simple diffusion. Finally, facilitated diffusion is more dependent on temperature, which is not the case with simple diffusion. Polar molecules and large ions cannot diffuse freely across the plasma membrane because the membrane is hydrophobic. Only small and nonpolar substances can diffuse

across the membrane. Simple diffusion happens with CO2, oxygen, and other gases that are nonpolar and small. Glucose, sodium, and chloride are passed through facilitated diffusion. Filtration involves the movement of water plus solute because of the differences in hydrostatic pressure and oncotic pressure. This happens in the kidneys. The hydrostatic pressure is generated by the heart, which raises the pressure in the capillaries of the kidneys. Depending on the size of the holes in the glomerulus of the kidneys (which are the filtration components of the kidneys), small substances, including albumin, are passed through the pores. It happens to a degree in the liver as well; however, the pores are larger in the liver.

ACTIVE TRANSPORT There are two types of active transport. Primary active transport makes use of ATP energy in order to allow for the transport of substances against their concentration gradient across a membrane. The ATP energy comes from the cytoplasm and will not be on the outside of the cell. The system requires a pump that has at least one binding site for ATP. There are four different classes of ATP-dependent ion pumps related to the cell membrane. These include the following: •

P-class pumps

•

F-class pumps

•

V-class pumps

•

ABC pumps

Of these, the F, P, and V-class pumps only transport ions, while the ABC pumps can transport small molecules. These each take a great deal of ATP energy so that about a quarter of the ATP produced by the cell is used in ion transport among kidney cells. In electrically active cells, like nerve cells, about two-thirds of the ATP energy is used to pump just sodium and potassium through the cell membrane.

P class pumps will use the phosphorylating activity of ATP to change the conformation of the alpha subunit of the pump. This changes its conformation so that transport is possible. The sodium-potassium ATPase pump to be discussed soon is one of these pumps. Figure 29 shows what this type of pump looks like:

Figure 29.

Other pumps that are of the P class include the calcium-ATPase pump. This pump is seen in the sarcoplasmic reticulum inside muscle cells and in the plasma membrane of some animal cells. The pump uses ATP to send calcium out of the cytoplasm—either out of the cell or into the sarcoplasmic reticulum lumen of the muscle cell. The sarcoplasmic reticulum is the same as the endoplasmic reticulum in other cells but it pumps calcium as a major function. With the calcium-ATPase pump, calcium is bound to the pump proteins while they are unphosphorylated. ATP binds and releases phosphate that binds to the protein, resulting in a large conformational change. This change allows for calcium to pass through the membrane so it can be released on the other side. Another related pump is the hydrogen-potassium ATPase pump. This is seen in the stomach, in the distal renal tubules, and in the renal collecting ducts. It is directly involved in acid secretion by the stomach, exchanging potassium for hydrogen ions. The same thing happens in the kidneys. V-class pumps will only pump protons across the membrane. These pumps do not involve phosphorylation and dephosphorylation. The V-class pump is seen in plant vacuoles and in certain lysosomal membranes in animals. It keeps the pH level low inside lysosomes and endosomes of animal cells, which is necessary for the activity of the enzymes within these organelles. F-class pumps only pump hydrogen ions and does not involve phosphorylation. These are found in certain bacterial plasma membranes and in both chloroplasts and mitochondria. These pumps are also known as ATP synthases because they act in the synthesis of ATP. The pumps use the electron transport chain as an energy source to cause oxidative phosphorylation, which makes ATP. ABC pumps are a family of pumps that are also referred to as the ATP-binding cassette. There are specific ABC pumps that work for different substrates or related substrates. There are more than a hundred of these transport proteins in all types of cells. These will transport amino acids, sugars, ions, and even drugs. The CFTR protein is a protein of this family that is defective in patients who have cystic fibrosis; this is a chloride channel pump.

Secondary active transport is the transportation of molecules across the cell membrane, making use of energy that is not from ATP. It is instead energy that comes from the pumping of ions out of the cell and the electrochemical gradient that comes from this process. This type of energy is referred to as symport or antiport transfer. The mechanism of action of these types of transport processes happens through the primary active transport of sodium. Sodium is pumped out of the cell, creating a high extracellular sodium concentration versus the concentration on the inside. This gradient produces energy because sodium is constantly trying to diffuse back into the cell. The antiport system involves two separate molecules getting transported in opposite directions. Sodium is allowed to flow from a high concentration to a low concentration, while the other species get transported against their concentration gradient. Figure 30 shows both the symporter and antiporter mechanisms across the membrane. Examples of antiport systems include the sodium-calcium counter-transport system, which has sodium bound on the outside of the membrane and calcium bound on the inside of the membrane. After both our respectively bound, there is a conformational change that allows both to cross over. Sodium ends up on the inside and calcium ends up on the outside. All cell membranes have this function. An antiporter system occurs with the transport of hydrogen and sodium in the proximal renal tubules. This is not as powerful as the primary active transport of hydrogen ions but participates greatly in hydrogen atom homeostasis because it can transport a great many hydrogen atoms at a time. Symport mechanisms involve the co-transport of a molecule from high to low concentrations, while pulling another molecule along in the same direction from a low concentration to a higher concentration. An example of this is the co-transport of sodium and glucose. In this system, there are two binding sites outside the cell membrane—one for glucose and one for sodium. They bind and create a conformational change that allows both to enter the cell. The same thing happens with amino acid entry into the cell. These symporter mechanisms are particularly active in the intestinal tract and kidneys.

SODIUM-POTASSIUM ATPASE PUMP The sodium-potassium ATPase pump is an important transport pump. It is specifically responsible for transporting sodium and potassium across the cell membrane from areas of low concentration to areas of high concentration. These actions require ATP energy. There are three sodium ions bound to the inner surface of the membrane with phosphorylation of the ATP molecule, providing energy allow for a conformational change. The sodium ions exit the cell with two potassium ions entering the cell. The transport protein is phosphorylated and dephosphorylated in the process. One ATP molecule is used up for every 3 sodium ions and every 2 potassium ions that are transported. Both of these ions get pumped against their concentration gradients. Because this involves a difference in the charges that enter and leave the cell, there is a net positive charge leaving the cell from the extra sodium ion exiting the membrane. Besides setting the resting membrane potential, this pump is important in other ways. It is what provides the energy for the secondary transport of glucose, amino acids, and several other nutrients. Sodium leaks back into the cell and helps transport the other molecules. It also provides control over the cell volume. Without the pump, the cell can unnecessarily swell. The pump maintains the ion transport, triggered by swelling of the cell.

RESTING MEMBRANE POTENTIAL There is electronegativity—that is, a net negative charge—in all cells. This becomes most important for nerve cells and muscle cells that rely on this electronegativity to pass electrical signals down the cells. This resting membrane potential is the electrical difference across the membrane, between the inside of the cell and the outside of the cell. The resting membrane potential for a given cell is about negative 70 millivolts, with a range between minus thirty to minus ninety millivolts. This will lead to the definition of “polarized” in defining the cell. All cells have a resting membrane potential, even if they are not nerve cells or muscle cells.

When the membrane potential is less electronegative, it is said to be depolarized. If the membrane potential is more electronegative than the baseline, it is said to be hyperpolarized. When electrical signals are passed along a neuron, it always involves depolarization or hyperpolarization of the resting membrane potential. The resting membrane potential comes from differences in the sodium and potassium concentration across the membrane. In neurons, depolarization happens when voltage-gated sodium channels lead to an influx of sodium into the cell, making the cell less polar or more positive. The influx of sodium through the voltage-gated channels allow the cell to become less negative. This leads to a brief period of electropositivity in the cell, where there is a net positive charge within the nerve cell. At maximum depolarization, the voltage-gated sodium ion channels close again and potassium channels within the cell open. This causes potassium to leave the cell toward a less concentrated outer cellular area. This causes repolarization to occur and the cell becomes more electronegative again. The sodium-potassium ATPase pump acts the same throughout this process and is not particularly involved. Hyperpolarization involves an overshooting of the negative potential within the cell. All voltage-gated ion channels close and the sodium-potassium ATPase pump reestablishes the resting potential. In nerve cells, the process starts all over again, with depolarization of the cell.

KEY TAKEAWAYS •

Osmosis involves the transfer of water across a semipermeable membrane.

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Simple diffusion involves the transfer of a solute from an area of high concentration to an area of low concentration, not necessarily across a membrane.

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Aquaporins allow water to pass through a membrane more easily than would happen through osmosis.

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Facilitated diffusion does not require energy, while active transport usually requires ATP energy.

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The presence of an electrochemical gradient will drive the secondary active transport of certain molecules but the primary active transport happens with the sodium-potassium ATPase pump and other pumps.

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The resting membrane potential of a cell is maintained by the sodium-potassium ATPase pump but, in certain cells, there are voltage-gated channels that allow for depolarization and repolarization.

QUIZ 1. In biological systems, which molecule is most able to undergo osmosis? a. Sodium b. Glucose c. CO2 d. Water 2. What is most likely to be permeable across the cell membrane of the animal cell? a. Lipids b. Glucose c. Sodium d. Amino acids 3. What is the driving force behind simple diffusion? a. The permeability of the membrane b. The concentration gradient c. The energy substrate used to drive diffusion d. The type of solute involved 4. What molecule passes through the cell membrane via simple diffusion rather than facilitated diffusion? a. Oxygen b. Glucose c. Sodium d. Chloride

5. Which category of pump involved in active transport belongs to the class of sodium-potassium ATPase pumps? a. V-pump b. ABC pump c. P-pump d. F-pump 6. Which category of membrane pump will pump protons in lysosomes of animals and in the central vacuoles of plants? a. V-pump b. ABC pump c. P-pump d. F-pump 7. In the sodium/calcium antiporter system of membrane transport, what happens to the sodium and calcium? a. Calcium and sodium end up on the outside of the cell together b. Calcium and sodium end up on the inside of the cell together c. Calcium ends up on the outside of the cell and sodium ends up on the inside of the cell d. Calcium ends up on the inside of the cell and sodium ends up on the outside of the cell 8. Which symporter system involves the co-transport of a molecule and sodium in the same direction into the cell? a. Glucose-sodium transport b. Hydrogen-sodium transport c. Hydroxyl-sodium transport d. Calcium-sodium transport

9. What causes a nerve cell to depolarize or to become less electronegative on the inside? a. The sodium-potassium ATPase pump is turned off for a brief period b. Sodium passes through voltage-gated sodium channels into the cell c. Potassium leaves through voltage-gated potassium channels out of the cell d. Calcium enters the cell through calcium-ion channels 10. What causes the nerve cell to repolarize after it has depolarized initially? a. The sodium-potassium ATPase pump is turned off for a brief period b. Sodium passes through voltage-gated sodium channels into the cell c. Potassium leaves through voltage-gated potassium channels out of the cell d. Calcium enters the cell through calcium-ion channels

CHAPTER SIX: PROTEINS AND PROTEIN CHEMISTRY This chapter mainly covers proteins and their biochemistry. Proteins have several different characteristics, based on how they are made and on post-translational modification of the protein structures. The different factors that play a role into making proteins from amino acids is introduced in this chapter. Some proteins are functional enzymes; how these behave is covered in the chapter as are the different methods of detecting and characterizing proteins in molecular biology.

STRUCTURES OF PROTEINS As we have already discussed, proteins are polymers found ubiquitously in biological systems that are ultimately made from amino acids held together by numerous peptide bonds. They form complicated shapes, from globular to linear pleats with complex folding patterns that happen spontaneously. Proteins can be soluble or insoluble in water, depending on their structure. There are generally four types of proteins structures you should know about. All proteins have these simultaneous types of structures associated with them. These include the following: •

Primary structure—this basically involves the specific order of amino acids, of which there are twenty basic types in animal systems. Figure 30 shows the basic amino acid structure:

Figure 30.

The alpha carbon of the amino acid has a carboxyl group, a hydrogen ion, an amino group, and an R-side chain, which is variable, depending on the amino acid. The primary structure is determined by the cell’s genetic code. A single genetic mutation will throw off one amino acid or can result in many amino acids being abnormal.

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Secondary structure—this is the structure component related to the protein’s three-dimensional shape. There are two major protein structures. The alpha helix is a coiled string structure mad by hydrogen bonding in the protein’s polypeptide chain. The beta pleated sheet is a folded or pleated structure made by hydrogen bonding lined up so that there are parts of the chain lying side-byside with one another.

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The tertiary structure of the protein molecule is also three-dimensional but it is determined by specific interactions of the R side chains. The R group can be hydrophobic or hydrophilic, which determines how the peptide is folded. Hydrophobic groups will fold themselves to keep these groups away from water. There can be hydrogen bonding, ionic bonding, and disulfide bridges between R groups that specifically determine the peptide’s shape. Van der Waals forces also help the polypeptide have a particular shape.

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The quaternary structure is the structure made of the protein by the interaction of more than one peptide unit. It is the type of structure formed by molecules like hemoglobin, which actually consists of two pairs of globular subunit chains.

PROTEIN SYNTHESIS Protein synthesis is actually a drawn-out process that starts with the DNA blueprint in the nucleus of the cell. The basic function of DNA is to encode for proteins that are made in the ribosomes of the cell. DNA in the cell only codes for proteins; it does not code for other cellular structures. The genome of the cell is the full complement of DNA for the cell, while the proteome is the entirety of the proteins made by the cell. Genes are discrete sections of DNA that encode for specific proteins. There are about 20,000 genes in the human genome. Most of the DNA, however, is not made into genes and is considered noncoding DNA. Proteins are made from amino acids and are made by “reading” the DNA in the genome. Remember that, for DNA, there are four different bases (adenine, thymine, guanine, and cytosine). In order for there to be enough sections of DNA to encode for all the possible twenty amino acids plus sections for starting and stopping protein synthesis, the DNA 87

segments must be read in “triplets” or groups of three bases. An example is the DNA code for valine, which is CAC for cytosine, adenine, and cytosine). One of the important things in reading these sequences is not to be off by even one base pair. Because they are read in triplets, a missing or added base pair will throw off the entire sequence read from the point onward after the mutation is found. Sometimes, the base will be replaced by another base, leading to misreading of the triplet but with less of an impact than if a base was added or subtracted. Transcription involves the reading of a segment of DNA in a gene in order to make messenger RNA or mRNA. This happens through the action of an enzyme called RNA polymerase. The DNA, which is normally tightly wound, gets unwound and read frame by frame in triplet code by this enzyme, leading to a single strand of messenger RNA that goes on to make proteins. There are different types of RNA that have different functions. Most RNA is singlestranded, while DNA is almost always double-stranded. The different types of RNA include ribosomal RNA, which makes up the structure of ribosomes, messenger RNA, which is what gets transcribed into the RNA message in the nucleus, and transfer RNA, which adds the amino acids to the growing peptide chain one amino acid at a time. Transcription occurs in the nucleus. Messenger RNA gets transcribed from the DNA template, making the single strand of RNA that ultimately exits the nucleus to go to the ribosomes in order to make protein. The RNA molecule is organized into codons, which are the triplet sequences that “code” for amino acids. There are three stages to the transcription process: initiation, elongation, and termination. Figure 31 shows the process of transcription and subsequent translation:

Figure 31.

There is a promotor region that is associated with the initiation process. This is the part of the gene that gets read first. Elongation happens when RNA polymerase unwinds the segments of DNA, reading fragments of the gene from one end to the other, creating a length of messenger RNA. Termination happens with a “stop” signal. This involves the reading of one of three specific triplets that indicate the release of the completed messenger RNA transcript. In actuality, messenger RNA is not what comes off the transcription process. Instead, it is called pre-mRNA, which needs splicing in order to get rid of noncoding regions of RNA, leaving behind mature messenger RNA. There is a complex called a “spliceosome” that helps this process happen. The intron is the removed section of messenger RNA, while the exon is the section of RNA that remains to be translated into protein. Translation is the process of making protein out of messenger RNA and transfer RNA. It requires the messenger RNA molecule that comes from the nucleus after being transcribed from DNA. Transfer RNA is necessary to add one amino acid at a time to the growing polypeptide chain. This takes place in the ribosomes. The ribosomes are what makes rough endoplasmic reticulum “rough” in appearance. The ribosome is made out of ribosomal RNA and proteins. There are two components to the ribosome: a small subunit and a large subunit. The two subunits come together in order to attach to the messenger RNA. This aligns the messenger RNA so that it can

interact with transfer RNA. It is the transfer RNA that contains a specific amino acid on each molecule in order to add to the polypeptide. Figure 32 shows what ribosomes look like:

Figure 32.

The transfer RNA molecule is made up of an anticodon that matches with the triplet codon on the messenger RNA. As in the case of transcription, there is initiation, elongation, and termination. The polypeptide chain gets added on one amino acid at a time until there is a stop codon read. This stops the process so that the protein synthesis stops.

POST-TRANSLATIONAL MODIFICATION When a protein gets translated, this isn’t the end of the process. There are many different things that happen to a peptide chain so that a different functional protein can result from this. These changes involve the addition of functional groups, partial protein degradation, or proteolytic cleavage of parts of the protein. As mentioned, the genome in humans involves about 20,000 genes, while the proteome (the numbers of different protein molecules) is about a million. This means that a single gene can encode for multiple proteins. It is believed that about 5 percent of the human proteome is made from enzymes that participate in more than 200 different types of post-translational modifications. There are phosphatases, kinases, ligases, and transferases that add and subtract things from the pre-proteins. Many proteins also have the capability of acting on themselves to create a unique protein under specific circumstances. The post-translational modification of proteins can be permanent or reversible, depending on the type of modification that occurs. For example, phosphate groups can be added or subtracted as needed, while degradation is usually irreversible. In the next few paragraphs, we will look at some changes that can happen to a protein as part of these processes. Proteins and peptides can be phosphorylated, which is the addition of a phosphate group on some of the amino acids that make up part of the peptide. This is a reversible process. Glycosylation is also a common modification—adding sugars to the peptide in certain places. This is also somewhat reversible. There is a process too called ubiquitination, which is the addition of 76 amino acids to the lysine amino acid on the peptide. Nitric oxide can be used in a reversible S-nitrosylation of the peptide chain. The process is used to stabilize proteins and to provide nitric oxide donors in the cell. S-adenosyl methionine or SAM is commonly used to at a methyl or CH3 group to proteins. In the same way, an acetyl group can be added to nitrogen in reversible and irreversible reactions. It is used to add acetyl groups to histone proteins, which are the proteins used to condense DNA that is not being used for transcription. When lipids are

added in lipidation, these proteins go into the membranes found in vesicles, mitochondria, endoplasmic reticulum, Golgi apparatus, and the plasma membrane. Proteolysis tends to be irreversible. Proteases are enzymes that cleave peptide bonds in post-translational protein modification. There are regulatory processes that make sure that proteolysis doesn’t become uncontrolled.

ENZYMOLOGY Enzymes are all catalysts for chemical reaction but not all catalysts are enzymes. The catalyst in any reaction will lower the activation energy of a reaction, allowing the reaction to proceed faster. In biological systems, the enzymes are almost always proteins; however, some ribosomal RNA molecules can be enzymes as well. As we have discussed in a previous chapter, enzymes will bind to reactants or substrates in a reaction, holding them in a way such that the chemical process can become the endproduct much more efficiently. Figure 33 shows what enzymes do in order to facilitate a reaction:

Figure 33.

As you remember from the previous chapters, enzymes only change the activation energy. They do not lower the beginning energy level or ending energy level. The reaction must be favorable with a negative free energy level change in order for the reaction to occur. The activation energy or the energy of the transition state is lowered. The transition state is the unstable state that the substrates must go through in order to have the final end-product.

As you can see by figure 33, the enzyme will bind to the reactants or “substrates” in such a way that they are in close proximity to one another. These binding sites are specific to the substrates. While attached to the enzyme, the reaction occurs efficiently, leading to the transition state and finally the products or “end-products” are made and released by the enzymatic binding sites. This binding site is also referred to as the “active site”. The active site is made from specific amino acids that are designed to attract and bind the substrates. There can be hydrophobic, hydrophilic, acidic, basic, or ionic amino acids that fit specifically to the amino acids of the reaction substrates. Enzymes are very sensitive molecules and only function under certain conditions. Temperature is perhaps the most important thing to keep in mind with regard to enzymatic function. These enzymes are highly temperature-dependent and will work only with a certain temperature range. High temperatures can denature proteins. This includes enzymes, which denature or “break down” in higher temperatures. The pH of a system can also affect the enzyme function. There are certain amino acids that have basic or acidic properties. This means that a pH change will affect how the enzyme is able to bind to the substrate. In addition, the concentration of the enzyme and substrate affect how much work the enzyme is able to do. The fit between an enzyme and substrate isn’t exactly a lock and key model. Instead, researchers refer to the fit of an enzyme and substrate as an “induced fit model”. What this means is that the enzyme will slightly change its conformation as a result of binding to the substrate. This results in a tighter fit with the substrate. It is similar to the sodium-potassium ATPase pump, which is an enzyme system. Binding of sodium onto the pump induces a conformational change that cleaves the ATP molecule and opens the pump so that sodium can pass through. You should think of the enzymatic process as being temporary. The enzyme changes it conformation, allows for the reaction to occur, releases the end-products and then returns to its original state. This means that enzymes are not consumed in the enzymatic process so that it can participate in another enzymatic reaction.

PROTEIN DETECTION AND CHARACTERIZATION In molecular biology, it is important to study proteomics, which is the study of proteins and the characteristics of proteins. There are two major ways to identify proteins in biological systems. The first is antibody testing, which is referred to as immunoassays, or mass spectrometry. With immunoassays, it is necessary to have a specific antibody to the protein in order to tag it and identify it. With antibody detection or immunoassays, antibodies are developed against a specific protein. What this means is that the antibody has specific binding properties affiliated with the protein so that it can bind and tag the protein if it is present in the sample. This is the most common method of detecting proteins. Examples of these types of tests include the ELISA test or enzyme-linked immunoassay test. This test measures the protein levels in the sample. Another is the Western blot test, which requires separation of the protein before detection. In the ELISA test, specific antibodies bind to the protein. This complex gets acted upon by an enzyme, yielding a product that can be identified chemically by a change in color. The antibodies are fixed to a plastic plate and the serum with the possible protein on it will stick to the plate. If the protein is present, the test will show positivity and a color change. You should know that, in cases like HIV disease, the antigen is fixed to the plate and the HIV antibody is washed over it in order to detect the presence of the antibody, which is itself a protein. The Western blot test also uses an immunoassay but is more difficult to do. The same principles apply as is seen in the ELISA test; however, the protein is first separated from other antibodies using gel electrophoresis. For HIV disease, this is used as a confirmatory test for HIV disease after the ELISA becomes positive. The HIV testing starts with the ELISA test and is confirmed with the Western Blot test. There are also protein detection systems that do not require antibodies. They can be used to determine the sequence of a peptide or protein and can detect proteins that do not have a matching antibody available. There is an older technique called the Edman

degradation technique, where the protein is selectively degraded in order to define its sequence. Mass spectrometry techniques are used after the protein is separated. Proteins are separated using liquid chromatography or gel electrophoresis, which separates proteins out according to their size and electrical charge. The mass spectrometer can analyze the components of the compound. This technique works for non-protein substances as well.

KEY TAKEAWAYS •

Proteins are based on amino acids and have several different structures: primary, secondary, tertiary, and quaternary.

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Protein synthesis starts with transcription of DNA into messenger RNA. It then proceeds to the ribosome with translation into proteins.

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There are many post-translational modifications that can happen to the preprotein that is originally made, resulting in a proteome that is many times greater than the genome.

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Enzyme speed molecular reactions by lowering the activation energy or the energy of the transition molecules.

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There are several protein detection techniques, some of which use immunochemistry, while others use separation and detection techniques that are not based on immunology.

QUIZ 1. What protein structure is specifically determined by the protein’s genetic code? a. Primary structure b. Secondary structure c. Tertiary structure d. Quaternary structure 2. Which aspect of a protein is considered the smallest molecule? a. Amino acid b. Oligopeptide c. Polypeptide d. Protein 3. What does DNA traditionally encode for within the cell? a. Proteins or peptides b. Lipids c. Carbohydrates d. Ether peptides or lipids or carbohydrates 4. About how many genes are there in the human genome? a. 5000 genes b. 20000 genes c. 100,000 genes d. 1 million genes 5. What is the segment of messenger RNA called that ultimately doesn’t get spliced out of the pre-mRNA molecule and so gets translated into protein? a. Intron b. Exon c. Transfer RNA d. Spliceosome

6. What is the process of making a polypeptide chain in the ribosomes using messenger RNA and transfer RNA called? a. Replication b. Transcription c. Translation d. Post-translational modification 7. What do enzymes do in order to facilitate a reaction to occur in biological systems? a. They lower the free energy level of the substrate b. They lower the free energy level of the end-product c. They change the delta G or total energy level between the substrate and the end-product d. They change the activation energy of the reaction 8. Which energy level is changed during enzymatic reactions? a. The substrate energy level b. The transition state energy level c. The end-product energy level d. The difference between the substrate energy level and the end-product energy level 9. What is true of the Western blot test for HIV disease? a. It does not require separation of the antibody b. It is an immunoassay c. It is the first test used for the detection of HIV antibodies d. It is technically easier than the ELISA test

10. In gel electrophoresis, what happens in the separation of proteins in this type of system? a. Proteins cannot be separated using this technique b. Proteins are separated based on size c. Proteins are separated based on charge d. Proteins are separated based on charge and size

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CHAPTER SEVEN: MOLECULAR GENETICS The structure and molecular processes of DNA and RNA are the topics of this chapter. DNA and RNA have similar structures, although DNA is usually double-stranded and RNA is usually single-stranded. There are different types of RNA that vary according to their function. The chapter also talks about DNA replication, DNA repair, and the process of recombination.

STRUCTURE OF DNA The primary structure of DNA relates specifically to the bases used to make the molecule and its covalent backbone. A nucleoside is the deoxyribose sugar plus the nitrogenous base. A nucleotide is the same as a nucleoside plus a phosphate sugar. The nucleotide in DNA is called a deoxyribonucleotide, while a nucleotide in RNA is called a ribonucleotide. The sugar in DNA is called deoxyribose, which has a hydrogen atom where a hydroxyl group should be on the second carbon atom. Figure 34 shows the structure of deoxyribose and ribose:

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Figure 34.

In DNA, the purine nitrogenous groups are adenine and guanine, while the pyrimidine nitrogenous groups are cytosine and thymine. In RNA, the thymine group is replaced by uracil. Adenine hydrogen-bonds with thymine and cytosine hydrogen-bonds with guanine in the DNA molecule. Figure 35 shows the different nitrogenous bases:

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Figure 35.

When nucleotides are connected together in the DNA molecule, they form a corkscrew right-handed double helix. The two strands are considered antiparallel to one another. What this means is that the five-prime end to three-prime end on one strand is reversed on the other strand. Figure 36 describes the shape of a typical DNA molecule:

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Figure 36.

One helical turn consists of ten base pairs. The hydrophobic bases are attached to one another on the inside of the helix through hydrogen bonding between the nitrogenous bases. A purine on one strand will connect with a pyrimidine on the other strand. There are two hydrogen bonds between adenine and thymine, and three hydrogen bonds between guanine and cytosine. Because of this strict bonding pattern, the two strands of DNA are always complementary to one another.

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The DNA double helix is rather rigid and can be remarkably long, with a very thin diameter. There is a major groove seen and a minor groove seen. Proteins bind through hydrogen bonding and van der Waals bonding so that rarely is there naked DNA. The two strands are known as plus strands and minus strands; alternatively, they can be called direct strands and reverse strands. The direct strand contains the coding sequences, while the reverse strand does not usually have coding sequences (although it is possible). DNA is not found as naked DNA but is surrounded by histone proteins and non-histone proteins. Histones are basically a family of alkaline proteins that help condense DNA into chromatin. Chromatin is highly condensed strands of DNA. The DNA strands are highly condensed around the histone proteins so that they will fit within the nucleus. DNA is negatively charged; it relies on the positive charges on the histone proteins to bind so that the DNA can be wrapped around the histones. Chromosomes look like beads on a string under the microscope. Each of these beads are referred to as nucleosomes. There are eight histone proteins, called a histone octamer, that collectively make up the nucleosome. There is a chain of nucleosomes that spiral together in order to form a solenoid, which is a thirty-nanometer spiral. There are five basic types of histones. These are H1, H2A, H2B, H3, and H4. Of these, H1 is a linker histone, while the others form an octet that the DNA is wrapped around. Figure 37 describes the histone proteins attached to the DNA molecule:

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Figure 37.

Chromatin is described as the combination of histone proteins and DNA. Each cell in humans contains about 1.8 meters of DNA. Wound on the histones, it is only ninety millimeters long. When chromatin is condensed during the process of mitosis, only about a hundred twenty micrometers is the total length of the molecule. Histones play an important role in the regulation of chromosomes and in the expression of genes. DNA that is tightly wrapped with histones will not be able to transcribe or interact with other proteins. When unwound, it can do these things. A single nucleosome is made from eight histone proteins and a section of DNA. One nucleosome has a diameter of eleven nanometers. Each nucleosome is considered the fundamental subunit of the total chromatin molecule. While DNA is mainly found in the nucleus of the cell, it is also found in the mitochondrion. Consider that mitochondria probably once were ancient bacteria, it makes sense that DNA would be found in these structures as well. Chloroplasts also have DNA within them. The genetic code in these structures is different than in the 106

DNA of the nucleus. This DNA is circular, which is what is seen in bacteria as well. There are also no introns in this DNA. The DNA in mitochondria is transcribed and code for proteins that are involved in electron transport within the mitochondrion. The DNA double helix can unwind under certain circumstances. Heat, extremes of pH, and certain chemicals will cause denaturation of the DNA molecule. Low salt concentrations, dimethyl sulfoxide, and formamide will all help to denature DNA. DNA can be denatured and will reanneal or come together, coming together to bind in the same way that existed before the molecules became denatured.

TYPES AND FUNCTION OF RNA RNA or ribonucleic acid is extremely similar to DNA. Two major differences are that RNA strands are shorter and are typically single-stranded molecules. RNA is mainly involved in the synthesis of proteins and in the regulation of the translation process. RNA is made from ribonucleotides linked together through many phosphodiester bonds, which is similar to DNA. The four bases are adenine, guanine, cytosine, and uracil. These different aspects of RNA make it less stable than DNA. Even though RNA is single-stranded, it can fold on itself and make bonds with itself; this tends to stabilize the molecule. There are three main types of RNA—each of which has different structures and functions. All of them participate in the translation process. The three main types are messenger RNA or mRNA, ribosomal RNA or rRNA, and transfer RNA or tRNA. Messenger RNA is what gets transcribed as the chemical messenger between DNA and protein synthesis. DNA is quite large and cannot leave the nucleus. For this reason, messenger RNA is made by “reading” genes on the DNA molecule, making an exactly opposite match to the gene, only the structure made is messenger RNA instead of another DNA strand. The entirety of the transcription process happens through the activity of RNA polymerase, which takes the DNA strand and turns it into a complementary strand of RNA. The strand is read from the five-prime end to the threeprime end.

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There are three stages of transcription: initiation, elongation, and termination. In prokaryotes, the process is relatively simple. RNA binds to the promotor region near the gene’s beginning. Each gene has its own promotor sequence. At this level, the RNA polymerase separates the DNA strands so that there is a strand to read in the transcription process. Next comes elongation. There is a template strand on the DNA molecule that is read by RNA polymerase one base at a time. The process ends up building a messenger RNA molecule out of nucleotides that are complementary to the DNA strand. The RNA strand starts at the five-prime end and adds on at the three-prime end. The messenger RNA strand is the same as the noncoding DNA strand with the exception that it has uracil instead of thymine. The RNA strand only hangs onto the DNA it is reading for a short period of time. Most of it dangles freely so that the DNA molecule gets reconnected almost as soon as it is read. There are also sequences on the DNA molecule called terminators. These sequences signal that the transcription process is finally completed. The reading of this sequence means that the transcripted messenger RNA will be released from the RNA polymerase molecule. The terminator sequence encodes for a portion of the RNA molecule that forms a hairpin, which is when RNA folds back upon itself to make a hairpin structure. This is followed by a number of U-nucleotides that cause stalling of the RNA polymerase molecule. The uracil nucleotides cause the transcript to separate from the template DNA molecule. In eukaryotes, the initially coded messenger RNA is called pre-mRNA because it is not completely ready to be translated. As mentioned previously, there are introns and exons that need to be separated to make the whole mRNA molecule. There is also the addition of a five-prime cap and a three-prime poly-A tail. Remember, it is the introns that are chopped out and the exons remain in. Figure 38 shows the splicing and addition of the cap and tail:

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Figure 38.

These end modifications serve to increase the stability of the messenger RNA molecule, while the splicing out of introns will give the RNA the proper sequence. The mRNA molecule will not read properly if the introns remain in the sequence. Not all genes are transcribed at the same time. Each gene is opened up for transcription individually when needed so that only necessary genes are transcribed at any given

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period of time. In some cases, many RNA transcripts are made over a short period of time, while others are not made at all. In the process of transcription, the histone proteins unwind and DNA polymerase opens up a transcription bubble, in which the strands separate so that the template strand can be transcribed. The coding strand is the strand of RNA that is made from the template strand. It is the mRNA transcript that gets made into the protein molecule. The coding strand is also referred to as the non-template strand. In eukaryotes like humans, there are general transcription factors that help RNA polymerase to bind to the DNA molecule. There is a promotor sequence known as the TATA box. It is recognized by the transcription factors, allowing RNA polymerase to bind to the molecule. This TATA sequence allows the DNA strand to pull apart more easily. The DNA template always gets read from the three-prime end to the five-prime end. The RNA nucleotides get added at the three-prime end, one nucleotide at a time with the tail hanging off the DNA template as the nucleotides are added. There are three phosphates on each RNA nucleotide, with two phosphates dropping off to provide the energy to make the phosphodiester linkage between the bases. Termination happens differently in bacteria compared to eukaryotes. In bacteria, termination can be Rho-dependent or Rho-independent. There is a Rho-factor binding site in rho-dependent termination. The Rho-factor attaches to the RNA transcript and gradually works its way toward the transcription bubble. When it reaches the transcription bubble, the RNA transcript falls off the DNA template strand. In Rho-independent termination, there are specific sequences of the DNA template strand that have a great deal of cytosine and guanine nucleotides. The RNA transcribed from this region will fold back on itself, making a hairpin that is stable enough to fall off. The hairpin also has a long stretch of Uracil nucleotides that have a weak connection to the template. This also encourages the falling off of the transcript. In bacteria, the messenger RNA doesn’t need to be spliced. Instead, translation happens at the same time as translation. Transcription also happens at the same time throughout the DNA molecule. This means that DNA transcription and translation 110

happen all throughout, leading to polyribosomes that look like beads on a string connected to the mRNA transcript, which are themselves connected to a long stretch of DNA. There are no organelles to separate these processes. This isn’t the case with eukaryotes, where there is splicing as well as separation of the translation process from the transcription process. The five-prime cap and poly-A tail (which stands for poly-adenosine) are used to protect the messenger RNA from becoming damaged. These will protect the messenger RNA so that it can get exported from the nucleus. The five-prime cap gets added during the transcription process. It is a modified guanine molecule that prevents breakdown of the transcript and helps in the translation process. There is another enzyme that adds the poly-A tail, which is also to add stability to the molecule. There is a process known as alternative splicing, in which different introns get spliced out, depending on the circumstances. When some introns get spliced out, certain proteins are made; when other introns get spliced out, other proteins are made. It is a way to make two different proteins from the same piece of DNA. Transfer RNA or tRNA and ribosomal RNA or rRNA are more stable. Transfer RNA transfers the amino acid to the growing polypeptide chain. Ribosomal RNA is seen in eukaryotes. It goes into the making of ribosomes as part of the translation process. Ribosomal RNA gets made and assembled in the nucleolus of the cell. These do not carry a DNA message but are important in the translation process. Ribosomal RNA has enzymatic properties. It ensures the adequate alignment of the messenger RNA and transfer RNA in order to facilitate the process of translation. This part of ribosomal RNA is called peptidyl transferase. Transfer RNA is very small. It is only about 80 nucleotides long. There is different transfer RNA for each of the amino acids that get connected to the growing polypeptide chain. The transfer RNA is a hairpin molecule that has an amino acid attached to the three-prime end. There are multiple hairpins in the transfer RNA molecule so that it has a three-dimensional shape.

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RNA generally does not participate in being an aspect of the genome. It is only a genome when virus particles are concerned. Viruses have a wide variety of genomes that can include double stranded RNA or even single-stranded RNA.

DNA REPLICATION There is a completely separate process that goes on with regard to the replication of DNA. Replication happens when the cell needs to divide itself. The enzyme that does most of the replication process is called DNA helicase. Figure 39 shows what DNA replication looks like:

Figure 39.

There are other enzymes involved in the replication process, including topoisomerase and DNA primase. DNA helicase disrupts the hydrogen bonding between the two DNA strands, creating a replication fork. Remember that the DNA strands run in opposite directions from one another. The five-prime end have a phosphate group attached,

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while the three-prime end has a hydroxyl group attached. One strand is called the leading strand, while the other strand is called the lagging strand. The leading strand is easier to replicate than the lagging strand. There is a primer piece of RNA on the three-prime strand that gets made by DNA primase. DNA polymerases then engage in the process of elongation of the new strand. There are DNA polymerases that do most of the actual replication and DNA polymerases that participate in error checking and in DNA repair during the replication process. Replication proceeds in eukaryotes in the five-prime to three-prime direction. The lagging strand is harder to replicate. There are multiple primers that participate in this process. Each primer is just a few bases long. There are pieces of DNA that get added between the primer strands called Okazaki fragments. These fragments then get joined together. After the strands are completely made in the replication process, there is an enzyme called an exonuclease that gets rid of the RNA primers. These get replaced with the proper DNA fragments. There is another exonuclease that properly proofreads the DNA in order to replace errors. DNA ligase is important in joining the Okazaki fragments so there is a unified strand. Telomeres are the protective end of the DNA strands. These telomere sections prevent DNA molecules from attaching to one another. After the telomeres are added by an enzyme called telomerase, the DNA forms its typical double-helical shape. Topoisomerase is also referred to as DNA gyrase. This is the molecule that unwinds and rewinds the DNA strands in the process of DNA replication. The purpose of this enzyme is to keep the DNA from becoming supercoiled or tangled in the replication process.

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DNA REPAIR The structure of DNA must be preserved because of its importance to the genetic process. Mutations can occur when the wrong base is added in the replication process; in the same way, chemicals can result in DNA mutations, which need to be repaired. There are mechanisms in place that repair the damaged DNA. There are two mechanisms in place that can do this. There is the direct reversal of whatever reaction caused the DNA damage in the first place as well as removal of damaged bases and replacement with the correct base. If this fails, there are other mechanisms in place that help the cell deal with the results of the mutation. Spontaneous damage to DNA can happen with deamination of cytosine, guanine, and adenine. There can also be loss of purine bases—called depurination. Spontaneous damage can occur from radiation and certain mutagenic chemicals. UV light can form pyrimidine dimers. This is when two side-by-side pyrimidines form a connected structure. Alkylation can occur, in which methyl groups get added to the base pairs. Most of the DNA damage gets repaired by removing the damaged bases, making new DNA where the damaged bases were once located. Pyrimidine dimers, however, can be repaired directly as can alkylated guanine fragments. UV light mostly causes pyrimidine dimers but can cause other DNA changes. These dimers can block the transcription and replication processes. In some species, UV light can also repair pyrimidine dimers but this is not the case in humans. Another DNA damage that can be seen is the addition of methyl or ethyl group to guanine. Methylation of guanine will lead to a hydrogen bond with thymine rather than cytosine. There is an enzyme that can reverse this process. It is seen in many organisms, including humans. If direct repair cannot happen, excision repair can take place. This is the most important type of repair in most prokaryotic and eukaryotic cells. Damaged DNA is recognized by the cell, leaving behind a space where new bases are added based on the preexisting template. There is base-excision repair, mismatch repair, and nucleotide excision repair. Uracil is cut out and replaced in DNA using base-excision repair. There

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is an enzyme called DNA glycosylase that frees up uracil so it can be replaced by another base. An enzyme called AP endonuclease removes the deoxyribose molecule so that DNA polymerase and ligase can be used to fill in the single-base gap.

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KEY TAKEAWAYS •

Nucleic acids consist of DNA and RNA. These are made of nucleotides that are linked together.

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RNA polymerase is the main enzyme that participates in the transcription process of DNA going to messenger RNA.

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There are several types of RNA, which include messenger RNA, ribosomal RNA, and transfer RNA.

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DNA is usually double-stranded as a double helix, while RNA can be singlestranded or double-stranded, when is used for the viral genome.

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DNA replication consists of multiple enzymes that unwind DNA, fill in the opposite strands of the template strands, and connect the newly-constructed strands together.

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DNA repair is of many different types. Repair is necessary when different bases of DNA are mutated.

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QUIZ 1. What is added to a nucleoside in order to make a nucleotide? a. Phosphate b. Nitrogenous base c. Deoxyribose d. Hydrogen bonding 2. In DNA, the adenine molecule forms a hydrogen bond with what other nitrogenous base? a. Cytosine b. Guanine c. Uracil d. Thymine 3. Which DNA structure is considered the smallest? a. Histone b. Nucleosome c. Solenoid d. Chromosome 4. How many histone proteins are necessary to make a nucleosome? a. 2 b. 4 c. 6 d. 8 5. What does not happen to pre-mRNA in order to have the total mRNA molecule? a. Exons are spliced out of the molecule b. Introns are spliced out of the molecule c. A 5-prime cap is added d. A 3-prime poly-A tail is added

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6. In the transcription of DNA to RNA, what is the transcript made up of? a. Transfer RNA b. Ribosomal RNA c. Messenger RNA d. DNA 7. Where does ribosomal RNA get made and assembled in the eukaryotic cell? a. Nucleus b. Cytosol c. Nucleolus d. Ribosomes 8. Which type of nucleic acid is covalently linked to an amino acid? a. DNA b. rRNA c. mRNA d. tRNA 9. Which enzyme in the DNA replication process separates the hydrogen bonds between the two DNA strands? a. DNA helicase b. DNA primase c. Topoisomerase d. DNA polymerase 10. What enzyme joins the Okazaki fragments after the lagging strand is properly made during DNA replication? a. Exonuclease b. DNA ligase c. Topoisomerase d. DNA primase

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CHAPTER EIGHT: GENES AND CHROMOSOMES There is a difference between prokaryotic genes and eukaryotic genes, which is part of the discussion of this chapter. Genetic material is divided up into genes, which are the readable segments of DNA in the organism. Transposons or transposable DNA are also covered, which is DNA that does not stay in the same place throughout the lifespan of the cell. Also included is a discussion of genomics, which is the collection of all the genes that exist as part of a given organism’s genetic material.

PROKARYOTIC GENES Studies of prokaryotic genes have mainly been done on Escherichia coli bacterial species. These studies have shown that the main genes of E. coli are located in a nucleoid that is circular in nature. There is no nucleus. The nucleoid is not membrane bound but is just the area where the nucleus is located. The DNA is supercoiled in E. coli but it does not include histone proteins seen in Eukaryotes. The circle of genetic material twists around and around until it forms tiny coils. This is how the genome becomes compacted—similar to twisting a rubber band. They can be negatively supercoiled or twisted in the opposite way as the double helix or positively supercoiled, in the same direction of the double helix. Most of these genomes are negatively supercoiled. There are proteins that contribute to the supercoiling of prokaryotic DNA. One protein called HU is extremely prevalent in the nucleoid, along with topoisomerase I, which binds to DNA so that it can bend properly in the supercoiling genome. There are other proteins that add to this process. Figure 40 shows this supercoiling of the DNA using topoisomerase I:

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Figure 40.

There are tetramers of the HU protein that act similar to histones that wrap around DNA to cause this supercoiling. The enzymes DNA gyrase and topoisomerase help to maintain the supercoiling of the DNA. The protein called H-NS helps modulate the expression of the bacterial genes, depending on the external environment around the bacterium. The main gene that controls or regulates gene expression in bacterial DNA is called “factor for inversion stimulation” or FIS. It regulates over 200 different bacterial genes. 120

How do bacterial genes replicate if they are so tightly packed? Replication actually happens at 1000 nucleotides per second. It does this by projecting DNA into the cytoplasm from the nucleoid, where it unwinds. It associates itself with ribosomes to allow for transcription and translation at roughly the same time. This allows for the fast growth of the organisms while it is still growing and dividing. While most prokaryotes have a single circular piece of DNA, other prokaryotes will have up to four pieces of circular or linear DNA, but these are less common than a single circular piece of DNA. Borrelia burgdorferi, which causes Lyme disease, has 11 copies of a linear chromosome that are identical to another. The strands do not fit within a nucleoid but are spread out throughout the chromosome. Archaea are unique prokaryotes distinct from bacteria. The biggest differences between bacteria and archaea are that the DNA in archaea can be negatively, positively, or not supercoiled at all. They also have histone proteins like eukaryotes. Bacteria respond to their rapidly changing environment by changing the pattern of their gene expression—expressing certain enzymes depending on the circumstances. An example is the synthesis of lactose when there isn’t enough lactose to live on. If there is only lactose available, however, there will be lactose-metabolizing enzymes expressed. The regulation happens along with the transcription process. Bacterial genes occur in clusters called operons. They are regulated together at the same time. This allows for rapid induction of a group of proteins or enzymes at the same time. The best-known operons in bacteria are those for lactose and tryptophan, called the lac operon and the trp operon, respectively. In the lac operon, the RNA polymerase binds to a promotor site. There is a regulator and operator site next to the promotor, which are involved in regulation. Lactose can bind to the inhibitor, which binds to the regulator sites. This blocks the transcription of the lac operon, which normally translates enzymatic proteins important in importing lactose from the environment. It does this because, when lactose is present, these enzymes are no longer necessary. A terminator sequence finishes up the lac operon, which is separated into three genes that code for three different enzymes.

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All of the bacterial operons are contiguous and located downstream from a single promotor sequence. The promotor sequence binds selectively to RNA polymerase, making things “ready” for transcription when the circumstances are right. There is a single messenger RNA molecule that gets translated into more than one individual protein. The terminator allows for stoppage of transcription of the genes. The operator is what the regulating substances bind to. Mutations in the different operons can be serious for the cell. There can be mutations of the promotor site, regulator sites, the operon itself, or the terminator sites. Some mutations of the genes themselves will affect just the downstream enzymes, which can still be serious. The trp operon is another major operon that has been studied in E. coli. They need tryptophan and use the trp operon in order to make this amino acid. If tryptophan is already available in the environment, E. coli will take it up and use it rather than make it from scratch. There are, however, five genes in an operon that make the tryptophan molecule. Tryptophan synthesis is turned off when it is not necessary and turned on when necessary. In the trp operon, there is a promotor sequence, which binds the RNA polymerase molecule and an operator sequence, which binds a repressor protein. The genes themselves make just one mRNA molecule for all five genes. The regulatory protein is called the trp repressor. The trp repressor binds to the operator and will stop the transcription of the gene sequence. The trp repressor does not just bind by itself. It can only bind to the operator when there is tryptophan also bound to it. Tryptophan plus the repressor protein will cause the blockage of the trp operon. In such a situation, tryptophan is called the corepressor. The trp repressor itself is not active without tryptophan present. In such a case, the trp operon is allowed to be transcribed. There is also a process that occurs with the trp operon called attenuation. This only happens when tryptophan levels are high. With attenuation, the transcription process starts but finishes prematurely. There is a piece of mRNA made but it is shorter than normal and it does not code for any specific tryptophan-making enzyme.

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EUKARYOTIC GENES Remember that eukaryotic genes are linear rather than circular. These are imbedded into nucleosomes, which pack the DNA together. The genome size does not relate to the actual size of the organism; small organisms can have much larger genomes than humans, for example. In humans, thee are about 20,000 different transcribing genes in the genome. Eukaryotic cells also have mitochondrial genomes and plants have chloroplast genomes. These two other genomes are much smaller so that, in humans, the number of base pairs in mitochondrial DNA is just about 16,500 base pairs. Gene regulation in eukaryotes is more complex than it is in bacteria. The main expression occurs at the level of transcription—particularly at the start of transcription. There are proteins in eukaryotic genes that will modulate the activity of RNA polymerase. These proteins and the regulation of transcription is, of course, different in each type of cell in a multicellular organism. This is a necessity because different cell types need to make different proteins and enzymes. There are different regulatory proteins in the different types of cells. Methylation of DNA also adds to cellular complexity. With bacteria and eukaryotes, there are cis-acting genes or sequences, which are genes that are located together or adjacent to one another. Genes are transcribed by RNA polymerase II; each gene has two promotor elements. The first is called the TATA box and the second is called the INR sequence. These bind general transcription factors. There are also sequences called enhancers, which can be located far upstream from the actual genes that get transcribed. These enhancer sequences allow for the more efficient transcription of the genes. Enhancers can also be located downstream from transcribed gene sites. Without an enhancer, the gene will only be transcribed at a low level. Enhancers bind to proteins that change the activity of RNA polymerase. Because of looping of the DNA molecule, the enhancer does not have to be near the promotor site. This allows transcription factors bound to a specific enhancer to act in similar ways to the promotor sites. This basically means that enhancers are really no different from promotor sites and other regulatory sequences on cis-acting genes.

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Interestingly, these enhancers have since been discovered in bacterial cells as well as eukaryotic cells. Certain hormones and growth factors act directly to control gene expression. These act as proteins that turn on some genes and turn off other genes. This is also why mammalian cells act differently depending on the cell type involved. Enhancers themselves can be big so that they bind many different regulator proteins. What this means is that, if there is a mutation of part of the enhancer sequence, the enhancer will work partly but does not fail to work completely. It may be that there is redundancy in these enhancer sequences. In addition, enhancers can promote gene expression in some cells while simultaneously blocking gene expression in other cell types. There are many different protein-based transcription factors that bind to DNA in order to allow for the regulation of gene expression in eukaryotic genes. Transcription factors can be different for different cells in a multicellular organism. It is hard to study these transcription factors because they represent a tiny fraction of the total cell protein in a given cell. Researchers use what’s called “DNA-affinity chromatography”, which can isolate these specific transcription factors. Some transcription factors are known as transcriptional activators, which bind to regulatory sequences on DNA and activate the transcription process. They can bind to either promotor sequences or enhancer sequences on the DNA molecule. There are two parts to a transcription activator. One part binds to the DNA sequence specifically, while another part binds to the transcription machinery in order to start the transcription process. As mentioned, hormones can act as transcription factors. The hormones that specifically do this are the steroid hormones. Steroid hormones are lipophilic so they can get into the cell and into the nucleus, binding to DNA and turning on or turning off transcription. In eukaryotes, gene expression can be turned off with eukaryotic repressor proteins. These will bind to specific DNA sequences and block the transcription process. These can block the interaction of the RNA polymerase with the DNA sequence at the promotor site. Repressors will compete with activators for specific regulator sites. They

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can bind to the regulator sites so that activators cannot bind. Other repressor proteins will interact with general transcription factors so that transcription cannot happen. Repressors can cause a lack of transcription in cells for which the transcription of DNA in the cell would be inappropriate. Remember, though, that DNA in the cell is never naked but is bound with histones in order to form chromatin. Nucleosomes are wrapped up and together are looped into larger loops so the DNA can be highly condensed. This DNA cannot easily be transcribed. Repressors and activators can function by changing the looping and configuration of this chromatin. The chromatin gets decondensed in order for it to be transcribed. You should know, though, that it takes more than decondensed DNA to be able to transcribe. Nucleosomes are still present in decondensed DNA, making it difficult to transcribe this. Nucleosome formation can be inhibitory to transcription. It is relieved by the acetylation of histones and by binding to two nonhistone proteins that alter the nucleosome structure so that transcription can take place. Acetylation will weaken the attachment of histone proteins to DNA and will affect the shape of the nucleosome. This facilitates the binding of transcription factors to DNA. On the other hand, deacetylation will activate transcriptional repressor proteins. There are also nucleosome remodeling factors that will change the accessibility of nucleosomal DNA to the transcription process. The mechanism by which these do this is not known but it can be done without removing histone proteins or dismantling the nucleosome. DNA methylation is another way to control the transcription process. Cytosine in the DNA of vertebrates can be modified through methylation. This will reduce the ability to transcribe these areas of DNA. It occurs primarily where cytosines and guanines are together on the same DNA chain. There is a protein that binds to these areas so that transcription is repressed. The same protein will also form a complex with histone deacetylase, which further suppresses transcription by acting on the nucleosome. This methylation particularly affects gene expression in mammalian embryos and

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participates in the ability to distinguish between maternal and paternal DNA fragments. This phenomenon is known as “genomic imprinting”.

TRANSPOSABLE DNA Transposable DNA or “jumping genes” represent genes that can jump from one place on the genome to another. Both prokaryotes and eukaryotes have transposable DNA; they make up about half of all the human genome and as much as 90 percent of the genome of the corn plant. There are many different types of transposable DNA, which are also called transposons. Some of them require what’s called reverse transcription, which is the transcription of RNA into DNA in order to be transposable, while others do not require this. Those that require reverse transcription are called retrotransposons or class 1 transposons, while those that don’t are called class 2 transposons. Class 2 transposons code for the protein known as protein transposase, which is necessary for insertion and excision of DNA. These always move on their own using cutting and pasting; they do not require RNA to be able to move. Class 2 transposons have terminal inverted repeats that are up to 40 base pairs in length on both ends of the sequence. These terminal inverted repeats are recognized by transposase. There are also direct repeats that aren’t a part of the transposable element but are important in the insertion of the transposon. The repeats are actually left behind after excision of the element. About 2 percent of human genes is made from class 2 transposons. The rest of the transposable elements are class 1 transposons. As mentioned, class 1 transposons need an RNA intermediary. They do not code for transposase but make RNA transcripts, using reverse transcriptase to turn this RNA into DNA that gets inserted into a different part of the genome. Either type of transposable DNA can be autonomous or nonautonomous. The autonomous transposable elements can move on their own, while nonautonomous transposable elements require other transposable elements in order to move. The

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nonautonomous elements do not have transposase or reverse transcriptase and need it from other elements. If a transposable element or transposon jumps to the inside of another gene, this can result in a mutation. Others will cause cancer from mutations. It is surmised that transposable elements are partly responsible for human diseases. Most transposons are, however, silent and do not cause any particular disease state. Things like DNA methylation and chromatin remodeling will sometimes render the transposon unable to actually transcribe or be active. There is a type of RNA called small interfering RNA or siRNA. It is a type of RNA that can be made by transposons and can prevent transposition. This means that transposons can mediate their own silencing. It is not completely clear how it does this but it can form a piece of double-stranded RNA; if this process is blocked, there is more movement of the transposon. Transposons are not completely destructive. They can drive the evolutionary process by moving exons around and by inserting into certain genes on the organism’s DNA. In essence, they can allow for certain genetic traits to be uncovered through the inbreeding of some species of plants or animals.

GENOMICS We have already been discussing genomics, which is the study of DNA; however, we have not yet talked about the branch of DNA concerned with gene sequencing, which is also a part of genomics. In gene sequencing, DNA polymerase is used to generate a brand-new strand of DNA after splitting up an existing strand. The new DNA strand is tagged with fluorescence so that a sequence of up to 125 genes can be read at one time. Overlapping segments are read so that the entire gene can be read over a period of time. Researchers do this in order to map genes and look for gene variations or mutations in a genome. Mutations can involve a substitution, deletion, or addition of one or a couple of base pairs; they can also involve deletions of many thousands of bases at a time.

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GENE MUTATIONS Mutations can happen during DNA replication or recombination; these are permanent. Most genes are completely harmless. Some will lead to cell death, cancer formation, or the production of an abnormal protein. Most of the dangerous complications come when DNA cannot be normally repaired as is the case with certain diseases. There are three major types of DNA mutations that can be seen. Point mutations involve base substitutions. Sickle cell disease stems from a single point mutation in which glutamine is substituted by valine in the making of a hemoglobin molecule. These types of mutations are the most common. There are two types of point mutations. One is called a transition mutation, in which a purine is substituted for another purine base or a pyrimidine is substituted for another pyrimidine base. The other is called a transversion mutation, in which pyrimidines are substituted for purines, or vice versa. Point mutations can also be silent, missense, or nonsense mutations. Silent mutations result in the same amino acid being created. Missense mutations happen when a different amino acid gets made so there is a different protein sequence. The different sequence can be conservative and will have the same basic properties or can be nonconservative, with different properties. Nonsense mutations results in a stop codon being transcribed so there is a shorter protein that isn’t functional. Deletions can result in a frameshift mutation, which is more severe than a point mutation. Frameshift mutations happen when one or two bases are deleted so that the codons after it are completely garbled. The end-product message is completely garbled and nonfunctional. If three bases are deleted, just one amino acid is missing, which is actually better than if one or two bases are deleted. Insertions behave the same way so that, if it occurs in clusters of three base pairs, it isn’t as serious as will be seen if one or two base pairs are inserted. Sometimes, there can be a noncomplementary base incorporated into a daughter strand. This leads to a mutation after the next round of replication. This is very rare because there are enzymes acting in the proofreading process will correct the problem before it

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leads to a mutation. Other times, there can be errors in DNA recombination that will lead to a mutation. Chemicals can also damage DNA. Radiation will also damage DNA.

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KEY TAKEAWAYS •

Prokaryotic DNA is usually circular with few exons and introns.

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In prokaryotes, the transcription and translation occur at the same time.

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Eukaryotic DNA is linear and located in the nucleus.

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Gene expression in prokaryotes happens when entire operons are expressed or not expressed.

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Gene expression in eukaryotes is similar to prokaryotes but involves different activators and repressors.

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Gene mutations are of different types that can be serious or not very serious.

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Many serious mutations become dangerous because of an inability to correct the mutation, as is seen in certain diseases.

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QUIZ 1. What is the main arrangement of the prokaryotic DNA? a. Circular within a nucleus b. Circular without a nucleus c. Linear within a nucleus d. Linear without a nucleus 2. How does the prokaryotic genome get compacted? a. It is negatively supercoiled, against the grain of the double helix. b. It is positively supercoiled, with the grain of the double helix. c. It is wrapped around histone proteins throughout its length. d. It is wrapped around unique, glycoproteins throughout its length. 3. What sequence on an operon will selectively bind to RNA polymerase in order to set the operon up for activity? a. Promotor b. Regulator c. Terminator d. Operator 4. Which part of a eukaryotic cell does not normally contain DNA? a. Nucleus b. Nucleoid c. Chloroplast d. Mitochondria 5. Which hormone is least likely to bind to DNA and regulate gene expression? a. Estrogen b. Testosterone c. Progesterone d. Luteinizing hormone

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6. Where on the trp gene sequence or the trp operon does an inhibitory protein bind? a. Operator b. Repressor c. Promotor d. Terminator 7. What is the major effect of histone acetylation in the eukaryotic nucleosome? a. It decreases transcription of the DNA b. It increases the binding of DNA repressors c. It increases the binding activity of histone proteins to DNA d. It decreases the binding activity of histone proteins to DNA 8. What does not happen as part of genomic imprinting in the mammalian embryo? a. The embryo fails to develop properly b. Some DNA segments are methylated c. The DNA is distinguished as being of maternal or paternal origin d. Some genes get expressed and some genes do not 9. What is the most common sequela of a gene mutation? a. There is no effect on the cell b. A protein is missing or absent, resulting in disease c. The cell becomes cancerous d. The cell dies 10. What type of mutation is also referred to as a point mutation? a. Addition of some bases to the gene b. Deletion of some bases in the gene c. Substitution of one base for another d. Deletion of the entire gene

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CHAPTER NINE: CELLULAR ENERGETICS Cellular energetics is the subject of this chapter. There are hundreds of enzymes and reactions that take place as a result of cellular metabolism. Amino acids, fatty acids, and carbohydrates all get metabolized by the cell to varying degrees, usually with a common final pathway. Prokaryotic cells and eukaryotic cells have both similarities and differences in the way nutrients are metabolized. In addition, photosynthesis is covered as a metabolic process that plants and other photosynthetic organisms participate in.

OVERVIEW OF CHEMOORGANOTROPHY Chemoorganotrophy is the word used to describe the oxidation of organic chemicals in order to yield some type of energy. The organic chemical becomes an electron donor. This does not necessarily involve the input of oxygen but, as you’ll see, oxygen is a big part of most animal cells, turning the organic chemical into CO2 and water. In aerobic respiration, the final oxygen acceptor is oxygen, with the citric acid cycle or tricarboxylic acid cycle used to make CO2. This generates the most ATP for the cell because there are a lot of electrons that glucose itself has to donate. There are many organic substances that can be used but the major ones are polysaccharides (sugars), lipids (fatty acids), and amino acids. These ultimately go into glucose to be funneled into specific pathways. Glycolysis is universal for all organisms. It turns glucose into pyruvate. There are two parts. The first part modifies the glucose six-carbon molecule and the second part deals with this molecule split into two three-carbon molecules. Part one requires energy, while part two conserves or creates energy. Four molecules of ATP energy are created through what’s called “substrate level phosphorylation” in which ADP becomes ATP. The net yield (because energy is needed in the beginning) is 2 ATP molecules per glucose molecule. In addition, two molecules of NADH are made from NAD+ in a process called “reduction”. These electrons go to the electron transport chain in some organisms to get more energy.

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The next part is the citric acid cycle, also referred to as the tricarboxylic acid cycle or the Krebs cycle. It takes the pyruvate generated by glycolysis to make 3 molecules of CO2 and more ATP energy. It also makes one molecule of NADH per molecule of pyruvate. At this point, four molecules of NADH total have been made through reduction for use in the electron transport chain. FADH2 is produced along with GTP, which is an equivalent molecule to ATP. The net yield from the tricarboxylic acid cycle is 2 molecules of GTP, eight molecules of NADH, and two molecules of FADH2. As you might notice, there is no ATP generated. This is where the electron transport chain comes in so that these reduced molecules of FADH2 and NADH can be used to make ATP. The electron transport chain involves oxidative phosphorylation. The electrons get donated to make ATP energy, but what happens to the protons? This is the process known as the proton motive force. The free protons migrate to the outer mitochondrial membrane or cell membrane in bacteria and archaea. This creates a proton gradient. It is used to do work for the cell, such as the rotation of flagella in bacteria. The proton motive force uses ATP synthase in order to synthesize ATP. The enzyme spans the membrane, with the intra-cytoplasmic part making ATP. Protons generate torque in order to drive the rotation of the enzyme necessary for it to do work. When it returns to its normal position, a molecule of ATP is generated. There is some inefficiency in this entire process so that the total possible number of ATP molecules cannot be made. In total, about 2.5 molecules of ATP are generated per molecule of NADH, while 1.5 molecules of ATP are generated per molecule of FADH2. This means that about 32 molecules of ATP are made for every glucose molecule starting this process. This takes into account the GTP molecules made. If the process is entirely anaerobic, fewer ATP molecules are made. There is a different electron receptor in the absence of oxygen. The two main processes are anaerobic respiration and fermentation. In anaerobic respiration, glycolysis starts the process and pyruvate goes to the tricarboxylic acid cycle. The major difference is that oxygen is not the final electron acceptor. Some common electron acceptors in anaerobic respiration include nitrate, 134

ferric ion, sulfate, carbonate, and fumarate or other organic compounds. The final yield of ATP will be less than seen in aerobic respiration. Fermentation is not the same thing as anaerobic respiration. It does involve an anerobic situation and does involve the catabolism of glucose. Oxygen is also not the final electron acceptor. It starts with glycolysis and ends with pyruvate, yielding two molecules of ATP and two molecules of NADH. Fermenting organisms, however, do not have an electron transport chain and do not use the Krebs cycle or tricarboxylic acid cycle. The re-oxidize NADH with pyruvate as the final electron acceptor to make ethanol and CO2, as well as acids like lactic acid. Fermentation is used by humans because we eat fermented things like cheese, tofu, bread, and alcohol.

GLYCOLYSIS Glycolysis is the beginning point of all metabolism of glucose by most living cells. It is completely anaerobic and takes place in the cytoplasm of all cells. Glucose can enter through secondary active transport processes against a glucose gradient or can enter through GLUT proteins, which are specialized glucose transporter proteins in the cell membrane. The GLUT proteins involve facilitated diffusion of glucose rather than active transport. Glycolysis starts with the typical six carbon ring and ends up with a three-carbon sugar, called pyruvate. As mentioned, there are two distinct phases, phase 1 and phase 2. Phase 1 requires energy and phase 2 creates energy. The first enzyme is hexokinase, which causes the phosphorylation of all six-carbon sugars. Any enzyme that is a kinase will phosphorylate something. It uses ATP to provide the phosphate, making glucose-6-phosphate. Figure 41 shows the glycolysis pathway, beginning with this step:

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Figure 41.

When glucose-6-phosphate is made, it can no longer leave the cell through the GLUT protein because it is too negatively charged to pass through its hydrophobic center. Instead, it gets treated with an isomerase to make fructose-6-phosphate. This helps the process of eventually making a three-carbon molecule. In step 3, phosphofructokinase gets phosphorylated again with a second ATP molecule to make fructose-1,6-bisphosphate. This is called a rate limiting step because, when ADP

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levels are high and ATP levels are low, the enzyme works. If ADP levels are low, the enzyme is not active. This glucose-1,6-bisphosphate molecule is highly unstable, so that fructose bisphosphate aldose easily cleaves it into two three-carbon molecules. One is called dihydroxyacetonephosphate, while the other is glycraldehyde-3-phosphate. In the next step, an isomerase (which is a rearrangement enzyme) turns the first molecule into glyceralde-3phosphate, ending the first phase of glycolysis. In the second half of glycolysis, two small three-carbon sugar molecules start the process and energy is created in order to pay back the two ATP molecules used. This leads to a profit of 2 more ATP molecules plus NADH, which has even more energy than ATP. Glyceraldehyde-3-phosphate gets oxidized, giving up two electrons to make NADH from NAD+. A second phosphorus molecule gets added to the glyceraldehyde-3-phosphate but this does not require ATP. This is a rate limiting step because it depends on the availability of NAD+. In the seventh step, phosphoglycerate kinase donates the extra phosphate in order to form ATP from ADP. This is referred to as substrate-level phosphorylation. The end result is 3-phosphoglycerate and an ATP molecule. Then the phosphate group gets moved around to make 2-phosphoglycerate. Enolase is the ninth step. It is a dehydration reaction that forms PEP, also called phosphoenolpyruvate plus water. Finally, PEP is acted on by pyruvate kinase to make another molecule of ATP plus the end-product of glycolysis, which is pyruvate. The pyruvate kinase step is another ratelimiting step.

MITOCHONDRIAL RESPIRATION In glycolysis, ATP is made through substrate-level phosphorylation. As you can see, however, it doesn’t make much ATP and leaves behind pyruvate as an end-product. Most ATP is made in the mitochondria using oxidative phosphorylation. There is a series of reactions that occur after that, through the Krebs cycle, which has oxygen or a non-oxygen inorganic final electron acceptor, depending on the organism. There is a 137

transfer of electrons that takes place on the inner part of the cell membrane of prokaryotic cells or in the inner membrane of the mitochondria in eukaryotic cells. This leads to an electron gradient that drives the making of ATP. The final component of mitochondrial respiration is the electron transport system. There is a series of membrane-associated protein complexes and mobile electron carriers that take FADH2 and NADH in a type of bucket brigade that performs redox reactions to create energy. There are four types of electron carriers: flavoproteins, cytochromes, quinones, and iron-sulfur proteins. The electron transport chain is described in figure 42:

Figure 42.

Oxygen is the final electron acceptor in this electron transport chain in aerobic respiration. It involves cytochrome oxidase, which is the last electron carrier. Each type of bacterium has a different cytochrome oxidase, which helps to define them by

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molecular biologists. This process is not possible if cytochrome oxidase is not present, if the cell cannot tolerate the oxygen-free radicals made in this process, or if oxygen is not available. Remember that it does not have to be oxygen as the final electron acceptor. De-nitrifiers are soil bacteria that use nitrate and nitrite as final electron acceptors, making nitrogen gas. Some aerobic bacteria, like E. coli, have the ability to change the acceptor to nitrate instead of oxygen when oxygen is depleted (making nitrite). The microbial organisms that have anaerobic respiration still have a Krebs cycle so they use the energy held within the NADH and FADH2 molecules. They have a unique electron transport system that generates smaller electrochemical gradients. This means that less ATP is made in the process. In the electron transport system, some energy is used to pump hydrogen ions across some type of membrane. In prokaryotic cells, hydrogen leaves the cytoplasmic membrane. In eukaryotic cells, it is pumped from the inner mitochondrial matrix into the intermembrane space. Hydrogen ions is positively charged so that there is a difference in electric charge across the membrane. This is called the proton motive force. This also creates a pH gradient. It can do more than just produce energy. It can transport nutrients and can rotate flagella. This is all tied to ATP synthase, which is how ATP gets made. The hydrogen ions leak back into the cytoplasm in prokaryotes and into the mitochondrial matrix in eukaryotes, changing the configuration of ATP synthase so that ATP can be made from ADP and phosphate. Figure 43 describes how ATP synthase works:

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Figure 43.

The ten NADH molecules made per glucose molecule during glycolysis, the transition phase, and the Krebs cycle carry enough energy to make 30 ATP molecules, while the 2 FADH2 molecules made in the process make an extra four ATP molecules. This is a theoretical yield of 34 molecules of ATP, except that there is leakage of electrons so the actual yield is less.

CITRIC ACID CYCLE There is a transition phase that occurs before glycolysis enters the Krebs cycle or the citric acid cycle. Pyruvate gets transported into the mitochondria in eukaryotes, where it gets turned into acetyl-CoA by removing carbon dioxide from it and adding coenzyme A. It delivers the acetyl group to the Krebs cycle. This “transition phase” makes a molecule of NADH in the process.

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The next part is the Krebs cycle or citric acid cycle. It takes place in the mitochondrial matrix and is a closed loop system. There are eight steps to the cycle, which makes 2 carbon dioxide molecules, one ATP molecule, NADH, and FADH2. Part of this is oxygen-requiring because NADH and NADH2 need to transfer their electrons to the next part of the system—which does require oxygen. It will not work if oxygen is not present. There are two carbon atoms entering the citric acid cycle. Two CO2 molecules are released by the cycle but these are not the same carbon atoms coming from the acetyl group. It takes two turns of the cycle in order to process one glucose molecule. Each turn makes three NADH molecules, one ATP molecule, and one FADH2 molecule. Figure 44 shows the Krebs cycle:

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Figure 44.

So far, not many high energy molecules are made. It takes oxidative phosphorylation in order to make most of the necessary ATP molecules. Oxidative phosphorylation can happen in prokaryotes and eukaryotes. 142

FATTY ACID OXIDATION Not all cellular energy comes from glucose. Fats are important in providing necessary energy for the cell. Triglycerides first get broken down into fatty acids plus glycerol. Fatty acids ultimately get broken down into two carbon units in the making of what’s called acyl-CoA. In order to be oxidized, the fatty acids must be attached to coenzyme A and moved into the mitochondria. The coenzyme A must detach at the mitochondrial membrane so the fatty acid can attach to carnitine. This carnitine complex gets transported across the inner mitochondrial membrane, where it can then be reattached to coenzyme A inside the matrix of the mitochondrion. Carnitine just keeps getting recycled. So, how does fatty acid oxidation work? The fatty acid is attached to coenzyme A. It looks like a long chain attached to this coenzyme A molecule. There is dehydrogenation between carbons 2 and 3, with number one being attached to coenzyme A. There will be a double bond between the two carbon atoms. Then, a hydroxyl group gets added to the third carbon atom and there is oxidation to make a ketone. There is a cleavage at this point to release an acetyl CoA molecule plus the rest of the fatty acid. The fatty acid left over can get oxidized again. These reactions that cause beta oxidation are very similar to the last half of the Krebs cycle. One molecule of FADH2 is made as is one molecule of NADH. The process goes on in a cycle with two carbon atoms knocked off at a time until only two carbon atoms are left. These last two carbon atoms make acetyl CoA and the process ends. As you can imagine, this process works well for fatty acids that have an even number of carbon atoms but is not as helpful for those few fatty acids that have an odd number of carbon atoms. In these cases, the end result is a three-carbon molecule called propionyl-CoA. It can’t be oxidized any further. Instead, it gets turned into methyl malonyl-CoA and gets rearranged to make succinyl-CoA. This can go into the citric acid cycle. Alpha oxidation may also need to happen if there are branches in the fatty acid chain. This is a minor metabolic pathway that only becomes significant if it does not work. In

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such cases, the person with an inability to do this develops a disease called Refsum disease. In the disease, a metabolite called phytanic acid builds up, leading to neurologic disease.

PHOTOSYNTHESIS Photosynthesis is a necessary part of life on this planet. It is necessary for the plants and animals alike because it can capture sunlight energy in order to make food energy in the form of carbohydrates. Energized electrons are stored in covalent bonds inside sugar molecules. This energy can ultimately last many millions of years on earth. Photosynthesis can occur in plants, algae, and in cyanobacteria. These organisms are known as photoautotrophs. Those that feed on other organisms are called heterotrophs. There are organisms known as chemoautotrophs, that extract energy from inorganic compounds. Photosynthesis helps to power 99 percent of the ecosystems on Earth. Photosynthesis requires sunlight, water, and carbon dioxide. Carbon dioxide is low itself in energy and gets “raised” in energy by the sunlight. The end result is glyceraldehyde3-phosphate, which can get further converted into sucrose, glucose, or other sugar molecules. It takes six CO2 molecules and six water molecules in order to make a sixcarbon sugar and six oxygen molecules. Photosynthesis takes place in the leaves of the plant. Leaves have several layers of cells with photosynthesis occurring in the mesophyll or middle layer. Gas exchange occurs through stomata, which are regulated openings in the leaves. The stomata are located on the underside of the leaf. Swelling and shrinking in response to osmotic changes will affect the size of the stomata. The chloroplast is the place where photosynthesis takes place. These are doublemembraned structures that have an outer and inner membrane. Inside the chloroplast are flat stacks of discs called thylakoids. The thylakoid membrane has chlorophyll, which absorbs light. Inside the thylakoid membrane is the thylakoid lumen. One stack of thylakoids is called a granum. Figure 45 shows the structure of a chloroplast:

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Figure 45.

There are two parts to photosynthesis: there is a light-dependent series of reactions and light-independent reactions. The light-dependent reactions take sunlight energy and convert it to stored chemical energy. In the light-independent reactions, there is assembly of the energy into sugars. These are interdependent reactions that depend on one another. The light energy, of course, happens from the sun, which emits a great deal of electromagnetic radiation. Humans see part of this in the form of visible light. Light travels as waves and particles at the same time. One particle of light is called a photon. The electromagnetic spectrum is the range of all of the radiation emitted by the sun. Each type of electromagnetic radiation has a specific wavelength, with shorter wavelengths having the most energy. High-energy waves can damage living systems. There is a narrow range of energy or wavelength that participates in photosynthesis. Retinal pigments can see between 400 and 700 nanometers of light, which is visible light. Plants absorb light in the range of 700 nanometers to 400 nanometers as well. 145

Pigments can absorb certain wavelengths of light and transmit the wavelengths that cannot be absorbed. Chlorophylls and carotenoids are the two major classifications of pigments in algae and plants. There are five major chlorophyll types and dozens of carotenoids. Green is reflected from chlorophyll a, leading to its green color. Light-dependent reactions work by converting the sun’s energy into NADPH and ATP. This is the energy that supports the light-independent reactions. This occurs in a photosystem, of which there are two types in the thylakoid membrane. They differ in the redox reactions that occur within them. These photosystems have antenna proteins that bind the chlorophyll molecules. Each photosystem has a light-harvesting complex in the thylakoids that contain chlorophyll a and b molecules, as well as carotenoids. One photon of light gets absorbed, pushing chlorophyll to its excited state. It gets transported to the reaction center. There is an electron transport chain that moves protons into the thylakoid lumen, lowering its pH. ATP synthase is tied to this in order to make ATP similar to that seen in mitochondria. The protons come from the splitting of water. So, the light-dependent reactions make ATP and NADPH as fuel, which go on to the light-independent reactions in the stroma of the chloroplast, which make sugars that can survive for hundreds of millions of years. These sugars come from carbon dioxide, which is also a waste product of glucose metabolism. Carbon dioxide enters the stomata and participates in the light-independent reactions. The light-independent reactions are also referred to as the Calvin cycle. Each turn of the cycle uses two ATP molecules and one NADPH molecule to make glyceraldehyde-3phosphate, which then goes on to make glucose outside of the cycle. Figure 46 depicts the Calvin cycle:

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Figure 46.

There are three stages to the Calvin cycle. The first stage is “fixation” and involves a five-carbon structure called ribulose bisphosphate and the fixation of CO2. The second stage is called “reduction” in which the molecule gets reduced. The third stage involves “regeneration”, in which ribulose bisphosphate is regenerated to continue the cycle. It takes three cycles to make the three-carbon glyceraldehyde-6-phosphate and six cycles to make a molecule of glucose.

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KEY TAKEAWAYS •

Almost all cells will make use of glycolysis in order to start the breakdown process of glucose.

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There is a transition phase between glycolysis and the Krebs cycle.

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There is a difference between fermentation and anaerobic metabolism, with fermentation having specific end-products, such as lactic acid.

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The Krebs cycle can be done by anaerobes and aerobes.

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Most of the ATP is gotten through oxidative phosphorylation and the electron transport chain.

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Photosynthesis is not the opposite of glucose catabolism. It makes use of lightdependent reactions and light-independent reactions in order to make glucose.

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The Calvin cycle is a light-independent reaction cycle that makes glyceraldehyde3-phosphate.

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QUIZ 1. What chemical process happens during chemoorganotrophy in animal and plant cells? a. Photosynthesis b. Oxidation c. Reduction d. Hydrolysis 2. In aerobic respiration, what becomes the final electron acceptor in the making of energy? a. Oxygen b. Carbon dioxide c. NADP d. ATP 3. What is the major difference between fermentation and anaerobic metabolism? a. Glycolysis is not a part of fermentation. b. Pyruvate is not a part of glycolysis but is a part of fermentation. c. ATP is not generated in fermentation. d. There is no Krebs cycle used in fermentation. 4. Where does glycolysis take place in the cell? a. Ribosomes b. Nucleus c. Cytoplasm d. Mitochondria

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5. What molecule is the end-product of the first phase of glycolysis? a. Glyceraldehyde-3-phosphate b. Citric acid c. Pyruvate d. Acetyl-CoA 6. Which is the function of an isomerase enzyme? a. It cleaves a molecule into two parts. b. It adds a hydrogen ion to a molecule. c. It dephosphorylates a molecule. d. It rearranges atoms on a molecule. 7. Why might a given cell perform anaerobic respiration instead of aerobic respiration? a. It does not have enough glucose to metabolize. b. It cannot perform the transition to make acetyl CoA from pyruvate c. It does not have enough Krebs cycle enzymes to turn acetyl-CoA into CO2. d. It does not have cytochrome oxidase to pass electrons to oxygen. 8. In prokaryotic enzymes, how does the electron transport system get used? a. Electrons get transferred through an electron transport system, so hydrogen ions get pumped out of the cell. b. Electrons get transferred through an electron transport system, so hydrogen ions get pumped into the cell. c. As protons get transported through the electron transport system, electrons get pumped out of the cell. d. Protons get transported through the electron transport system, so electrons get pumped into the cell.

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9. What is the end product of the light-dependent reactions in photosynthetic cells? a. NADH b. ATP and NADPH c. Carbon dioxide d. Oxygen 10. What is made in the Calvin cycle as its end-product? a. Glyceraldehyde-3-phosphate b. Carbon dioxide c. ATP d. NADH

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CHAPTER TEN: VESICULAR TRAFFIC, SECRETION, AND ENDOCYTOSIS The focus of this chapter is the function of vesicles in exocytosis and endocytosis. Vesicular budding and fusion is a process where by small vesicles break off or fuse with the cell membrane or other membranes in order to dump or take up contents within the vesicles. This process can happen either to rid the cell of substances or take on substances by the cell. The process of receptor-mediated endocytosis is covered as part of this chapter as is the complex process of neurotransmitter secretion by nerve cells, which also involves vesicles.

VESICULAR BUDDING AND FUSION The endoplasmic reticulum and Golgi apparatus participate in protein transport through vesicles. Other membranous organelles will participate in vesicular budding. These vesicles do not randomly travel through the cell but get to their location by attaching to kinesin or myosin, which are parts of the cytoskeleton. They then fuse with the target membrane or with the organelle. Vesicles tend to move from the endoplasmic reticulum to the cis Golgi apparatus, then to the medial Golgi apparatus, and then to the trans Golgi apparatus. Finally, they go to the plasma membrane or to other important compartments for storage. There are vesicles that travel in the opposite direction but this is not common. Figure 47 describes the Golgi apparatus:

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Figure 47.

There are transmembrane proteins that will help to make the vesicle into its spherical shape. The three major proteins that do this are the COPII, COPI, and clathrin proteins. COPI coating proteins are used to help the vesicle get through the different types of Golgi apparatuses. COPII coating proteins get vesicles from the endoplasmic reticulum to the Golgi apparatus and back. Clathrin is used to help vesicles go to the plasma membrane for exocytosis. Clathrin is also important in endocytosis. Clathrin is well described. It is made from clathrin triskelions (which means threelegged). There are three heavy chains to each triskelion and several light chains. The heavy chains are responsible for the structure of the vesicle. The light chains prevent accidental discharge of the vesicle while in the cytoplasm.

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There are adaptors that link to the coat proteins and allow for the spontaneous selfassembly of the vesicle into a cage-like spherical structure. Vesicles, then, are not completely spherical but resemble soccer balls because they have coat proteins that make hexagonal and pentagonal sides that only make the vesicle look spherical because there are so many sides to its structure. All three coat protein types will have this ability to self-assemble into the spherical structure. It is the COPI and COPII proteins, though, that help the vesicle pinch off the main membrane. Clathrin does not do this. Clathrin requires dynamin in order to pinch off the vesicle. Figure 48 shows this process:

Figure 48.

As you can see from figure 48, GTP is required to make use of its energy in order to allow dynamin to cinch itself so the vesicle can be pinched off. The dynamin protein contracts so as to seal off the vesicle effectively. The smooth endoplasmic reticulum makes glycerophospholipids. They are also made in peroxisomes and mitochondria. Sphingolipids are made in the cis and medial Golgi apparatus. These lipids will make up the coating membrane of the vesicles. The coat proteins are left off after the vesicle is released. This process requires ATPase and GTPase.

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Vesicles will carry transmembrane proteins and soluble proteins. Some soluble proteins are taken up because they are bound to a receptor. Some proteins are taken up accidentally, such as the PDI protein. It is needed back in the endoplasmic reticulum, from which it originated. This protein and others have a sequence that is recognized by the Golgi apparatus so it is sent back to the endoplasmic reticulum. Because it is sometimes necessary for proteins to be concentrated in the vesicle, the trans Golgi apparatus will do this. It will aggregate certain secretory proteins so they can be more concentrated. The proteins secretogranin II and chromogranin B will help to concentrate proteins. These granins operate under low pH and high calcium concentrations. When they are discharged, the low calcium concentration and higher pH situation will break up these protein aggregates. There is a progressive decrease in pH through the different Golgi types so that the trans Golgi apparatus has the greatest acidity in the lumen. There is a docking mechanism involved in helping the vesicles get to where they are needed. There is a v-SNARE protein outside the vesicle and a t-SNARE protein on the target membrane. These proteins link up and allow for fusion of the vesicle. It only works if the SNARE proteins match. There are tethering proteins on the vesicle that allow it to travel to certain places. The tethering proteins bring the SNARE proteins together so they can be “tested” to see if there is a match. They help the connection take place and help the attachment if there is a match. The cytoplasmic-facing side of the membrane will always face the cytoplasm. Figure 49 shows this process:

Figure 49.

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As you can see, the SNARE proteins have twisting ability so they can fuse the vesicle to the target membrane. The tethering proteins help them to get in contact with each other. RAB-GTP is one of these tethering proteins. There is an additional SNARE protein involved in order to allow for twisting of these proteins together. Interestingly, the tetanus toxin protein called tetanospasmin cleaves a specific SNARE protein so that neurotransmitters cannot fuse with the cell membrane. The same is true of botulinum toxin, which prevents neurotransmitter release. These toxins do basically the same thing but have opposite effects on the muscle cell. One blocks inhibitory neurotransmitters, while others block excitatory neurotransmitters.

SECRETORY PATHWAYS IN NERVE CELLS There is a regulated release of neurotransmitters through exocytosis in the nerve cell. The process by which it does this is similar to all vesicular trafficking. Neurotransmitters are released from small vesicles that take part in many rounds of recycling and fusion at the presynaptic terminals. These are not made in the Golgi apparatus but are made in presynaptic endosomal compartments. The vesicles are filled after being formed, which is different than normal vesicles. Loaded neurotransmitter vesicles are sequestered in a reserve pool in the cytoplasm or cluster at “active zones” near the presynaptic membrane. When calcium levels rise enough in the cell, the vesicles will discharge into the synaptic cleft. In fact, this is the major trigger for neurotransmitter vesicle release. Synaptic vesicles need to find the right acceptor membrane in order to discharge. This relies on SNARE proteins that are specific to the vesicle and synaptic cleft, similar to other vesicles. The SNARE proteins are called synaptobrevin, syntaxin, and SNAP-25. There is also a v-SNARE and a t-SNARE protein involved as in other vesicular attachment. VAMP is another protein linked to this type of vesicular transport and attachment. At rest, neurotransmitters inside vesicles are stored either in the active zone near the synaptic cleft, where the actual neurotransmitters are released. Most neurotransmitters

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are held a distance away, held by calcium-sensitive VAMPS (or vesical membrane proteins). They are bound to the cytoskeleton until they can be released. When calcium rushes into the cell as part of the action potential of the nerve, this triggers the release of the neurotransmitter from the vesicle because the VAMPs are calcium-sensitive. Ultimately, the neurotransmitter leaves the cell to go into the synaptic cleft between nerve cells. The vesicles can leave once calcium is present because the VAMPs let go of them. Once in the active zone, the vesicles are docked, ready for release. Fusion then happens with the presynaptic membrane getting a small pore that connects to the lumen of the neurotransmitter vesicle. The pore gets larger and then the vesicle membrane collapses, letting neurotransmitters out into the synaptic cleft. This is how exocytosis happens in the nerve cell. After this happens, the vesicle forms a pit and pinches off to make a new, vacant vesicle. The vesicle is then recycled, where it is filled again with neurotransmitter. It can also get sent back to the cell body of the nerve cell, where it gets broken down to be made into a new vesicle. Figure 50 shows the synaptic cleft and what happens to the neurotransmitters:

Figure 50.

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There are two types of neurotransmitter vesicles. One is a small type (about 50 nanometers in diameter) and another is a large type (that is up to 200 nanometers in diameter. Neurotransmitter release happens at the active zones. Only a small number are stored at the active zones. Synapsin I and actin hold the rest of the neurotransmitters further away from the active zones. Synapsin I binds to actin in order to hold the vesicle in place. Calcium is crucial to the release of neurotransmitters. There are voltage-dependent calcium channels that open when there is electrical activity in the nerve cell. Calcium rushes in and the process begins to take place. Calcium influx is about ten times greater in the active zone compared to other places in the neuron. During an action potential, the calcium concentration increases by 1000-fold in just a few milliseconds. Synapsin I immobilizes the vesicles until it is time for release of the vesicles into the active zone. It is dephosphorylated at rest and becomes phosphorylated when activated. ATP does the phosphorylation process. There is an enzyme called calcium-calmodulin-dependent protein kinase that does the phosphorylation of the synapsin I. It works when calcium is present. When calcium is bound, the kinase is activated and synapsin I gets phosphorylated. Vesicles get released by the cytoskeleton to go to the active zone. VAMPs include synapsin I and synapsin II, although there are others. Two proteins called Rab3a and Rab3b bind GTP and are believed to guide the vesicles to the active zones, where docking can occur. Synaptobrevin is another VAMP that helps recognize the nerve cell plasma membrane. Two other important proteins linked to this process are called synaptotagmin and synaptophysin. Synaptotagmin binds to phospholipids when calcium is around. Synaptophysin helps to form the pore in the presynaptic membrane. SNAP-25 is a protein that attaches to fatty acids, acting as a SNARE protein when the vesicle docks. Physophilin is a protein on the membrane that also participates in making a fusion pore with the vesicle. Both synaptophysin and physophilin are necessary—they bind together to allow the pore to open.

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After docking, there is a secondary influx of calcium at the active zone, which causes the fusion of the vesicle to the membrane. This forms a temporary ion channel. As mentioned, this pore opens because of the binding of synaptophysin and physophilin. It requires ATP energy in order to do this. If calcium doesn’t influx, no fusion pore can happen. Synaptotagmin binds to calcium; if it does not bind to calcium, it acts like a clamp in order to inhibit the fusion of the vesicle. It activates fusion when calcium is present by pulling the vesicle closer to the presynaptic membrane. After the pore happens, it dilates quickly so that exocytosis can occur. This excess membrane made by fusion does not keep enlarging the membrane. Instead, it forms a pit that is coated with clathrin. This clathrin-coted pit eventually pinches off the vesicle again so that an empty synaptic vesicle is made again.

RECEPTOR-MEDIATED ENDOCYTOSIS Endocytosis involves the essential opposite of exocytosis. Substances are brought into the cell, forming a vesicle. There are two types of endocytosis: pinocytosis, which is also referred to as cell-drinking, and phagocytosis, which is also referred to as cell-eating. There is also receptor-mediated endocytosis, and caveolae, which will be discussed. Clathrin-mediated endocytosis is the same thing as receptor-mediated endocytosis. It makes small vesicles about 100 nanometers across, coated with clathrin. They are formed from clathrin-coated pits that start the entire process of endocytosis. There are different receptors that participate in this type of endocytosis. Caveolae are not related to clathrin. There is a cholesterol-binding protein called caveolin that participates in making small pits in the membrane. They are seen in smooth muscle cells, adipocytes, endothelial cells, type 1 pneumocytes, and fibroblasts in high concentrations. There are receptors in these caveolae that mediate their formation. Caveolae participate in potocytosis, which is the uptake of molecules that are released into the cytosol rather than into other organelles.

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With pinocytosis, there is a pocket that pinches of to make a vesicle that is filled with a lot of extracellular fluid. It fuses with other vesicles like endosomes or with lysosomes. Phagocytosis involves taking in large particles, sometimes as large as parts of apoptotic cells (dead cells). The big difference is that a lot of extracellular debris is taken up by the cell. There is an endocytic pathway that starts at the plasma membrane and ends at the lysosomes. Early endosomes are seen in the cell periphery. They sort the vesicles near the cell membrane. Late endosomes will take material that is on the way to the lysosomes. They are acidic vesicles that help also to sort the contents of that which is endocytosed into the cell. Lysosomes are the end of the endocytic pathway. They break down the products of cellular waste into much simpler compounds. There are forty different hydrolytic enzymes that participate in the process. The pH is extremely low at about 4.8. Clathrin-mediated endocytosis is the best understood and is a major route for cellular endocytosis. Clathrin can form pits on the inside of the plasma membrane in order to form a coated vesicle inside the cell. The coat needs to be shed before the vesicle can continue on to the endosomes down the endocytic pathway. Endocytosis with clathrin usually means that a receptor has been bound by something that triggers clathrin to form the pit on the inside of the cell. There are many ligands that can bind to a receptor. The choices include attacking viruses that bind to the cell membrane, a nutrient molecule that needs to get inside, and any other molecule (such as LDL-cholesterol) that needs to be taken up by the cell. Transferrin is a serum protein that causes iron to be taken up by the cell. Some of the ligands get broken down, while others are exocytosed in order to be recycled. Once these vesicles get taken up by an endosome, the contents get acidified, which can affect the characteristics of the ligand. In the case of LDL, the LDL disconnects from the LDL receptor gets packaged up again so it can be recycled. LDL goes into a different vesicle to be transported elsewhere in the cell. The lysosome is highly acidic and has hydrolytic enzymes that work in the acidic environment but are inactivated in the environment of the cytosol. This means that, if

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the lysosome breaks, it doesn’t allow enzymes to digest any part of the rest of the cell. There are proton pumps on the lysosome that lead to the high acidity of the environment. Lysosomal enzymes are tagged with mannose-6-phosphate, which is added in the cisGolgi apparatus. This is how these enzymes get recognized as being lysosomal enzymes. They get sorted out in the trans-Golgi apparatus, where they are sent to the lysosomes. When some of these acid hydrolases in the lysosome don’t work properly, the end result is an incomplete digestion of lysosomal contents. Inclusions can build up, leading to one of several lysosomal storage diseases. There are genetic diseases like Hurler’s disease and Hunter’s disease that are lysosomal storage diseases because of accumulation of certain things. Hurler’s disease, for example, is a buildup of glycosaminoglycans. Gaucher’s disease is also a lysosomal storage disease that affects the brain. Tay-Sachs and Niemann-Pick diseases are also lysosomal storage diseases. Mucolipidosis type II is the most severe disease of this type because none of the lysosomal enzymes are present. Iron is transported into the cell via receptor-mediated endocytosis. Iron is bound to apo-transferrin, which binds two iron ions. It is then called transferrin, recognized by transferrin receptors on the cell. It starts clathrin to form a pit and a vesicle is made. A lysosome is not involved in this process, however. In the early endosome, iron is released from the transferrin. The iron then leaves the enzyme through the protein called DMT1. The receptor and the apo-transferrin together get recycled back to the cell surface. Apo-transferrin breaks off after this to travel around to bind more iron ions.

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KEY TAKEAWAYS •

Vesicles are small parts of membrane with some component inside of it.

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Vesicles can leave the cell through exocytosis or can enter the cell through endocytosis.

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Clathrin is involved in the making of many vesicles on the cell surface.

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In nerve cells, the neurotransmitter is in vesicles that get released in the active zone of the nerve cell.

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In endocytosis, the vesicles go to early and late endosomes and finally to the highly acidic lysosome, where things are hydrolyzed and broken down.

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QUIZ 1. Which organelle does not participate in vesicular budding? a. Ribosomes b. Golgi apparatus c. Endoplasmic reticulum d. Lysosomes 2. What substance surrounds each vesicle in the cell? a. Proteins b. Carbohydrates c. Triglycerides d. Glycerophospholipids 3. What is not a vesicle coat protein? a. Dynamin b. Clathrin c. COPI d. COPII 4. Where do proteins go that accidentally go into the Golgi apparatus, where they are not needed? a. They are degraded in the Golgi apparatus. b. They leave the cell through exocytosis. c. They are degraded by lysosomes. d. They are sent back to the endoplasmic reticulum. 5. Where are the vesicles made that transport neurotransmitters to the presynaptic cleft? a. Golgi apparatus b. Endoplasmic reticulum c. Cytoplasm d. Endosomal compartments

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6. The increase in concentration of what ion will cause neurotransmitters to be released into the synaptic cleft? a. Calcium b. Sodium c. Potassium d. Phosphate 7. What happens to synapsin I when the nerve cell gets activated by calcium influx into the nerve cell? a. Synapsin I gets a phosphate group attached to it by ATP b. Synapsin I loses a phosphate group c. There is increased binding of synapsin I to actin filaments d. Synapsin I causes release of the neurotransmitter from the vesicle 8. What is the area called where neurotransmitters are released? a. Neurotransmitter release zone b. Active zone c. Presynaptic zone d. Calcium release zone 9. Where do the vesicles first go when endocytosed and when they travel down the endocytic pathway? a. Late endosomes b. Early endosomes c. Peroxisomes d. Lysosomes 10. What protein forms the pits that draw a vesicle into the cell in endocytosis? a. Dynamin b. COPI c. COPII d. Clathrin

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CHAPTER ELEVEN: SIGNAL TRANSDUCTION BY THE CELL This chapter introduces the topic of signal transduction or cell signaling. There are several signaling pathways that involve the ways that cells send and receive signals from other cells in multicellular organisms. There are ligands and receptors involved in signal transduction, of which there are many types. The largest family of membrane receptors is the G-coupled protein receptor family, which involves a specific protein type that many cells make use of in cell signaling. The ways this receptor operates in the cell membrane and within the cell are covered as part of this chapter.

SIGNAL TRANSDUCTION Cells in a multicellular system have the capabilities of reacting in real time with their neighboring cells and to their environment through chemical signaling mechanisms. There are extracellular signals sent and received by cells over both short and long distances. In order to respond to a molecule, the cell must have a receptor for a specific ligand. A nontarget cell is called this because it has no receptor on it. In a cell signaling situation, the molecule is called a ligand that has a receptor associated with it. After binding the ligand, the receptor sets off a chain of events that lead to some type of message getting passed into the cell. There can be gene activation, cell division induction, or other intracellular response. There are several types of signaling. Not all signaling has to happen between neighboring cells; it can happen at a distance. There are four types of chemical signaling mechanisms: paracrine signaling, autocrine signaling, endocrine signaling, and signaling by direct contact. The biggest difference is the distance the signal has to travel. Paracrine signaling happens over short distances. It allows for coordination between neighboring cells. This type of signaling is important in development, where cells tell

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other cells what identity they need to take on. It also happens in synaptic signaling between two nerve cells. As mentioned in the previous chapter, neurotransmitters cross the gap between cells to send signals between the cells. The neurotransmitter is either degraded or taken back up into the sending cell so another signal can be sent. Autocrine signaling involves a cell signaling itself, releasing a ligand that binds to its own receptors. It is important during development as cells take on their identity. It is important in cancer and in cancer metastases. Signals can be both autocrine and paracrine at the same time. Endocrine signaling happens over the longest distances. It makes use of the circulatory system in order to pass a signal from one place to another. The signal goes through the bloodstream in order to get from one place to another in the organism. The target cell can be anywhere in the organism’s body. The cell signals in such cases are referred to as hormones. Signaling can happen through direct cell to cell contact. This happens through connections called plasmodesmata (in plants) and gap junctions (in animals). These allow for intracellular mediators to diffuse between the cells so both cells have the same signal. This especially connects things like ions but will not allow larger molecules to pass between the cells. Plasmodesmata connect practically every plant cell together in the organism. When cell signaling happens, it starts with a ligand and a receptor. A receptor can match just a single or a few ligands to it in a sort of lock-and-key mechanism. When the ligand binds the receptor, it changes the shape or activity of the receptor so that there is an intracellular change.

RECEPTORS There are two types of receptors. There can be intracellular receptors inside the cell (nucleus or cytoplasm) and cell surface receptors (on the plasma membrane). Most intracellular receptors are small hydrophobic molecules that can cross the plasma membrane. These include the different steroid hormones, like sex hormones. These intracellular receptors often induce a change in gene activity, regulating transcription. 166

Cell surface receptors are membrane-bound proteins that bind to specific ligands outside of the cell. The ligand never has to cross the plasma membrane so they can be large, hydrophilic molecules. The cell surface receptor has three different domains. There is an extracellular, ligand-binding domain, a hydrophobic domain (inside the plasma membrane), and an intracellular domain. The hydrophobic part can go in and out of the membrane several times. Ligand-gated ion channels involve ion channels that can open up after binding a ligand. There is a hydrophobic part that is in the membrane with a hydrophilic core. After binding the ligand, the core opens up so that the ions can pass through the membrane opening. In most cases, the ligand binding will open a channel but in other cases, the ligand binding will close the channel. Neurons have ligand-gated channels that connect to neurotransmitters. Figure 51 shows a ligand-gated ion channel in action:

Figure 51.

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G protein-coupled receptors or GPCRs will be discussed in a minute. These are actually a family of cell surface receptors that traverse the membrane seven different times. They transmit signals inside the cell through a G-protein. Many different ligands will bind to these types of receptors. The smell receptors are G protein-coupled receptors. All G proteins will bind to GTP, which breaks down to make GDP. A G protein attached to a GTP molecule is considered “on”, while a G protein that’s bound to a GDP molecule is considered “off”. The G proteins have three subunits called heterotrimeric G proteins. There are enzyme-linked receptors that are cell-surface receptors linked to an enzyme. In some cases, there is a part of the receptor that is actually an enzyme. Others will just interact with an enzyme. Receptor tyrosine kinases are types of enzyme-linked receptors. As you’ll remember, kinases are enzymes that phosphorylate other substances. In this case, tyrosine kinase transfers phosphate groups to tyrosine. Two nearby receptor tyrosine kinases will come together or “dimerize”. The receptors then are able to attach phosphates to each other’s domains. The phosphorylated tyrosine molecules are able to transmit a signal to other molecules within the cell. It takes two receptor tyrosine kinase molecules together in order to cause the phosphorylation of tyrosine. These receptor tyrosine kinases are important to signaling processes. They bind to growth factors that help to promote cell survival and cell division. There are different growth factors, such as nerve growth factor and platelet-derived growth factor, which are related to the tyrosine kinase receptors. Certain cancers are related to overactivity of these receptors. Figure 52 shows the tyrosine kinase activity with respect to these receptors:

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Figure 52.

LIGANDS There are many different types of ligands that can bind to receptors. There can be gaseous ligands, like nitric oxide, and hydrophobic molecules, like steroids. Peptides and proteins can be ligands as well. Ligands that enter the cells include steroid hormones, such as estradiol and testosterone. Vitamin D is another steroid hormone that binds first to carrier proteins, enter the cell, and bind to intracellular receptors. Nitric oxide is a ligand that binds inside the cell because it can pass through the plasma membrane. Ligands that bind outside of the cell are water-soluble, polar, or charged so they cannot readily pass through the plasma membrane. The most common ligands of this type are

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peptides or proteins. Insulin, neurotransmitters, and certain growth factors are considered these types of ligands. Some amino acids are considered these types of ligands.

SIGNALING PROCESSES With intracellular ligands, there is no ongoing signaling because the ligand binds directly to the gene and activates it. When the receptor attaches to the cell membrane, a signaling process needs to happen to send the signal into the cell. There are several intracellular signal transduction pathways that connect the ligand-receptor complex to the interior cell signal. It all starts with the ligand binding to the cell-surface receptor, which has an intracellular domain that changes its configuration in certain ways. Another signaling molecule can become activated as a result of the ligand binding. The reaction goes from upstream to downstream. The ligand itself is the most upstream and the reaction proceeds more downstream. There is amplification of the signal so that one ligand can activate many molecules downstream of it. One thing that can happen is that a protein can by phosphorylated in order to cause it to be activated. This is the addition of a phosphate group to a protein, which can only happen to three amino acids: threonine, serine, and tyrosine. It takes a kinase enzyme in order to cause this phosphorylation to happen. Phosphorylation can either activate, inactivate, or cause the breakdown of a protein molecule. Phosphorylation is not a permanent thing because phosphatases can ultimately remove the phosphate group. Kinases require ATP energy to do their job but the same isn’t true of a phosphatase. Growth factor signaling is an example of the phosphorylation pathway. One example of this is epidermal growth factor. It involves a series of kinases that phosphorylate different proteins. Epidermal growth factor has two receptors next to one another. These receptors act as kinases to each other’s intracellular tails. RAF is a kinase in this system that activates MEK, which in turn phosphorylates and activates ERK proteins. The ERK proteins activate many different target molecules. This three-tiered pathway is called the MAPK pathway, which stands for mitogen170

activated protein kinase pathway. The pathway is involved in promoting cell division. If overactive, it can result in cancer. Many signaling pathways involve second messengers, which are non-protein molecules that are a part of the pathway. Calcium can be a second messenger as can inositol phosphates and cyclic AMP. Calcium is a common second messenger. Its normal concentration in the cell is low but it can be stored in places like the endoplasmic reticulum. Usually, when calcium is a second messenger, there are upstream events that open a ligand-gated calcium ion channel so that calcium ions can be increased in the cell. There are certain proteins that have binding sites for calcium so that they change their shape. When it happens, for example, in pancreatic cells, it signals these cells to release insulin. When it happens in muscle cells, it triggers the contraction of the muscle cells. Cyclic AMP is another common second messenger. It is a small molecule that is ultimately made from ATP. There is an enzyme called adenylyl cyclase that makes ATP into cyclic AMP, which has one phosphate group that is linked to the sugar in a cyclic or ring shape. Cyclic AMP can activate protein kinase A or PKA, which is different in different types of cells. Cyclic AMP can be turned off by phosphodiesterase enzymes, which break the ring so it becomes AMP, which isn’t functional. Certain phospholipids can act as chemical messengers. Phospholipids known as phosphatidyl inositols are phosphorylated and split in two, with both halves acting as second messengers. There is an enzyme called phospholipase C that cleaves phospholipids into two fragments called DAG and IP3, which act as second messengers. The precursor molecule is called PIP2, which stays in the plasma membrane. Phospholipase C is also located in the plasma membrane. DAG can stay in the plasma membrane, where it activates protein kinase C, which can phosphorylate things. PIP3 enters the cytoplasm, where it binds to ligand-gated calcium channels in the endoplasmic reticulum, which continues the cascade of signaling in certain cells. PIP3 causes the endoplasmic reticulum to release calcium ions, which have another effect on the cell.

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Signaling pathways can become really complex. The same signaling molecules can affect cells in different ways, depending on the environment inside the cell. Acetylcholine, for example, is a ligand that can have opposite effects in skeletal muscle and in heart muscle cells. It promotes muscle contraction in skeletal muscle and inhibits muscle contraction in heart muscle. Many signaling pathways result in a cellular response because of a change in gene expression. Genes get expressed in order to make a protein. Regulation can occur at the transcription level or at the translation level. Some of the signaling pathways will induce a metabolic response in the cell, increasing or decreasing the level of metabolic enzymes. Epinephrine is a hormone that does this through a cyclic AMP messenger. It causes the phosphorylation of two metabolic enzymes. Glycogen phosphorylase is activated, while glycogen synthase is inactivated. Glycogen gets broken down into glucose and no new glycogen gets made. The glycogen phosphorylase breaks down glycogen, while glycogen synthase makes glycogen.

G PROTEIN-COUPLED RECEPTORS These have many names, most commonly, seven-pass transmembrane domain receptors, because they pass through the membrane seven times. They are a large family of receptors that activate certain signal transduction pathways, initiating cellular responses in the cell. They are only found in eukaryotic cells and involve odors, pheromones, neurotransmitters, light-sensitive compounds, and hormones. More than a third of medications are based on these receptors. The two main pathways involved with these receptors are the cyclic AMP pathway and the phosphatidylinositol signal pathway. A ligand binds to the receptor and initiates a conformational change in the receptor. It activates a G protein by exchanging GDP attached to the protein for a GTP molecule. No one knows the exact size of this superfamily but at least 810 different genes are involved in coding for them. There are six main classes of these receptors. Class A mainly deals with olfactory sensations. There are others that deal specifically with cyclic AMP and others that deal with pheromones. Some have no known function. Important 172

receptors of this category deal with taste, vision, smell, immune function, and mood regulation. Figure 53 is a depiction of the G protein-coupled receptor:

Figure 53.

The N-terminus of the receptor is on the outside and the C-terminus of the receptor is on the inside of the cell. When activated, a G-protein gets activated. What eventually happens depends on the G protein. GTP replaces GDP after the binding of the receptor takes place. Ligands can activate the protein, can inactivate the protein, or can have a neutral action on the protein. Activated G proteins contain GTP.

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KEY TAKEAWAYS •

Cell signaling can involve cell to cell connections, paracrine, autocrine, or endocrine signaling.

•

Ligands can be extracellular or intracellular, depending on where they bind. The most hydrophobic ligands will be intracellular.

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Signaling pathways can turn on genes, turn off genes, affect cellular metabolism, or affect transcription.

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Calcium, phosphatidyl inositol, and cyclic AMP are common intracellular second messengers.

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G protein-coupled receptors are a large family of receptors that involve many different activities in eukaryotic cells only.

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QUIZ 1. What type of chemical signaling is involved between neurons using neurotransmitters? a. Autocrine b. Direct cell to cell contact c. Paracrine d. Endocrine 2. What type of cell signaling happens over the longest distances? a. Autocrine b. Direct cell to cell contact c. Paracrine d. Endocrine 3. What is the main effect of the binding of an intracellular ligand? a. Induction of transcription of DNA b. Induction of an ion channel c. Change in post-transcriptional modification of proteins d. Binding of two enzymes to make ATP 4. Which type of cell signaling involves plasmodesmata? a. Paracrine signaling b. Autocrine signaling c. Endocrine signaling d. Cell to cell signaling 5. Which is not an amino acid that can be phosphorylated? a. Glutamate b. Tyrosine c. Serine d. Threonine

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6. What is the end result of the MAP kinase signaling pathway? a. The MAP gene gets activated b. Proteins get dephosphorylated c. Phosphatases are activated d. Cell division is promoted 7. What is least likely to be a second messenger in a cell? a. Phosphatidyl inositol b. ATP c. Cyclic AMP d. Calcium ions 8. What happens when a phosphodiesterase enzyme acts on cyclic AMP? a. It becomes AMP b. It becomes ADP c. It becomes ATP d. It becomes adenosine 9. How many times does the G protein-coupled receptor pass through the cell membrane as part of its structure? a. Twice b. Four times c. Seven times d. Twelve times 10. What happens when the G protein-coupled receptor gets bound to the protein by the ligand? a. GDP gets replaced by GTP on the G protein b. An ion channel opens up, allowing calcium to rush in. c. The transmembranous part of the protein gets cleaved into two pieces. d. An enzyme gets activated that draws the ligand into the cell.

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CHAPTER TWELVE: CELL ORGANIZATION AND MOVEMENT This chapter places a focus on cell organization and on how aspects of cell organization control movement within the cell. There are many different types of molecules involved in cellular organization, many of which contribute to the cell cytoskeleton. Organelles and substances move along the cytoskeleton so that the cell can have order and proper placement of intracellular structures. Some of these same fibrous proteins play a role in the cilia and flagella of different types of cells. In addition, cells migrate both as part of cell division and outside of cell division by virtue of the activity of the cell cytoskeleton.

CYTOSKELETON The cell cytoskeleton is very important. It is crucial for organelle placement and as a sort of highway for molecules and organelles to move with purpose through the cytoplasm. All cells will have a cytoskeleton but has different components, depending on the organism. While prokaryotes do have a cytoskeleton, it is less complex because they do not have all the organelles of the eukaryotic cells. They mainly hold ribosomes in place and help molecular transport take place. It is also less well studied than eukaryotic cytoskeletons. In eukaryotes, there are three types of filaments in the cytoskeleton: microfilaments, microtubules, and intermediate filaments. Microfilaments are also called actin filaments because they are made from two strands of actin that have been wound into a spiral shape. These are the thinnest filaments in the cytoskeleton. It is microfilaments that help in the process of cytokinesis, which is the division of a cell into two daughter cells. They also help in cell motility as is seen in amoeba as well as in cytoplasmic streaming, which transports nutrients and cell organelles. These are the filaments, too, that interact with myosin so they can contract in muscle cells.

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Intermediate filaments are between eight and twelve nanometers in diameter. They are made from proteins like keratin, lamin, desmin, and vimentin. Lamins are found in the nucleus but not in the cytoplasm, helping to support the nuclear envelope. These are the structures that give the cell its basic shape. Microtubules are the biggest and thickest of the fibers of the cytoskeleton, being about 23 nanometers thick. These are hollow tubes that consist of both alpha and beta tubulin. It is the microtubules that make the flagella of the cell and the cilia. The centrosome is an organelle that has microtubules sticking out of it. The centrosome is a microtubule organizing center. It separates the sister chromatids during the process of cell division. They also participate in transporting molecules inside the cell. They help to form cell walls in plant cells. In general, the cytoskeleton functions in several ways. Cells get their shape—even those without cell walls. Cells can move because of the cytoskeleton. Cilia and flagella could not exist and participate in movement without the cytoskeleton. Cells are organized because of the organelle placement by the cytoskeleton. Endocytosis, for example, happens because of the pull of microfilaments that take in the vesicle. Chromosomes move because of the cytoskeleton.

MICROFILAMENTS Microfilaments are also called actin filaments because they are mostly made of actin. These filaments extend throughout the cell so as to provide structure for the cell and to keep organelles in place. They participate in organelle movement, cell division, cell movement, and muscle contraction. Figure 54 shows what microfilaments look like:

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Figure 54.

As you can see by the figure in figure 54, the structure is made from wound-up filaments of actin protein fibers. Actin-G is globular and actin-F is filamentous. These are positively-charged polar substances on one end and negatively charged on the other end. The positively-charged end grows faster than the negatively-charged end. The diameter is about 6 to 7 nanometers. The structure starts when three actin-G proteins bind together forming a trimer. More actins add to the positively-charged end. There are autoclampin proteins that help these proteins self-assemble. Eventually a spiral forms, which is made of two strands of actin filaments. A major function of actin filaments is to help contract muscles. They are in a high concentration in muscle cells, forming myofibrils. It is in muscle cells that they are particularly called actin filaments. As you will see, actin interacts with myosin in order to contract a muscle cell. It takes both actin and myosin in order to do this. They cannot do this separately. As already mentioned, cells move because of microfilaments. This occurs in all cells of the body and is functional in single-celled organisms, such as amoeba. The complex of actomyosin also does this type of movement. Myosin is the motor that drives cellular movement. Microfilaments can also attach to an organelle and will contract so that the organelle can be pulled to another site in the cell. Mitosis cannot happen without microfilaments. They aid in the pinching off of two cells in the process of cytokinesis that makes two separate daughter cells. In cytokinesis,

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there is a ring of actin that cinches off the cell in the middle so that physical separation of the cells can take place. After the shortening and cinching off of the two cells, the actin myofilaments break down into separate actin molecules. Actin and Myosin As mentioned, myosin is the motor that drives the contraction of the actin filaments. It uses ATP energy in order to allow the process to energetically happen. Also mentioned is the fact that this actomyosin complex happens in non-muscle cells as well. Figure 55 shows the actin and myosin complex in muscle cells:

Figure 55.

In humans and other vertebrates, there are muscle cells that can be smooth muscle, heart muscle, and skeletal muscle. Skeletal muscle is the only muscle that is voluntary. Skeletal and cardiac muscle have well-organized actinomycin complexes, while smooth muscle is less well-organized.

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Each muscle fiber is a single cell about fifty micrometers in diameter and sometimes several centimeters in total length. The cytoplasm is made from myofibrils, which are thick filaments of myosin and thin filaments of actin. Each myofibril is made up of a contractile unit called a sarcomere. A sarcomere is just 2.3 micrometers in length, having several regions. The ends of a sarcomere are referred to as Z-discs. There are dark bands visible, called A bands, along with light bands, called I bands. I bands have only actin filaments, while A bands have myosin filaments and actin filaments together. In the H zone, there are only myosin components. The positively-charged ends of the actin attach to the Z disc. There are cross-linked proteins on the ends of the sarcomere that are called alpha-actinin. Myosin filaments are anchored in the middle of the sarcomere at the M line. Figure 56 shows a sarcomere:

Figure 56.

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The proteins titin and nebulin add to the structure and stability of the sarcomere. The titin acts like a spring that keeps the myosin filaments centered. Nebulin is associated with actin and regulates the length of the actin filaments as they grow in the sarcomere. Muscles are able to contract through the sliding filament model. The sarcomere actually shortens so the Z-discs come closer together. The A band does not change but the H zone and I bands nearly disappear because all of these sections have come together to make the A band. Myosin II is the type of myosin present in muscle cells. It has two heavy chains and two light chains. It has a globular head region and a narrower twisted molecule as the tail of the muscle. Figure 57 shows the shape of the myosin protein structure:

Figure 57.

The myosin fragments are arranged in a staggered fashion with the polarity of the myosin fragments being reversed at the M line, making the interaction between the actin and myosin symmetric throughout the muscle. The actin slides using the myosin motor toward the M line. Myosin binds to actin as well as to ATP, which is hydrolyzed to provide energy for the filament driving. There is a change in shape of the myosin head that cocks and re-cocks in order to move the myosin head down the actin filament. There is a cycle that starts with myosin bound tightly to actin. ATP binding dissociates this complex. ATP is hydrolyzed so that the myosin head can attach to another myosin segment. ATP hydrolysis provides the power stroke to slide the myosin past the actin. Calcium is also very important in this process. It is released from the sarcoplasmic reticulum in the muscle fiber when the muscle cell is activated. It interacts with 182

proteins bound to actin, called troponin and tropomyosin. When calcium is low, troponin and tropomyosin interfere with actin and myosin interaction. There are three polypeptides associated with the troponin molecule. The first is troponin I, which is inhibitory; the second is troponin T, which binds to tropomyosin; the third is troponin C, which binds to the calcium molecule. It takes the binding of calcium to troponin C specifically to allow the troponin and myosin to interact. In non-muscle cells, actin is still contractile and there are filaments of myosin II associated with this. Tropomyosin is also involved but there are no striations, M lines, or Z discs involved. There are adhesion belts that help to alter the shape of the non-muscle cell. This is what happens in the cytokinesis process so that one cell can pinch off into two cells. Calcium is not involved but there is phosphorylation or the addition of a phosphate group to myosin that assembles myosin and allows it to contract. There is an enzyme called myosin light-chain kinase that performs this reaction. The kinase itself is regulated by calmodulin, which binds to calcium in the cell so that phosphorylation can occur.

CELL MIGRATION Cell locomotion in non-muscle cells is also called cell crawling. It is important in embryonic development, the immune response, and the metastasis of cancerous cells. The actin cytoskeleton is very important to this cell crawling process. Phagocytosis is another type of cell crawling that is mediated by the actin filaments. Cell migration happens because of external physical, mechanical, or chemical triggers. It is necessary in all forms of life, including humans. The gastrulation of embryos takes place because of cell migration. Tissue repair and renewal involves cell migration. Movement of a cell is a cyclic process. There are filopodial or lamellipodial protrusions, adhesion of the cell to the matrix, and the pushing of the cell over the adhesions so that the cell moves. The first part of the process is the polarization of the cell. There are GTPase enzymes that help to determine what is the front of the cell and what is the back of the cell. Microtubules grow at the leading edge and anchor the cell. This facilitates the pulling of the rest of the cell across the adhesions. 183

The lamellipodia formed are branched networks of actin filaments that stretch out from the cell. Filopodia are similar but they have the ability to sense the physical and chemical characteristics of the environment. In order to move, the cell needs to adhere to a point in the matrix. These focal adhesions connect to actin in the cytoskeleton after ligands in the extracellular matrix bind to integrins, which are receptors on the cell surface. This causes the adhesions to occur, which provide traction for the cell. They also sense the environment for the rest of the cell. Actin and myosin at the leading edge will provide the contractile force that causes the cell to move. These adhesions need to disassemble in order to allow the cell to move. There are kinases and phosphatases that help these adhesions turn over as the cell progresses. It is particularly important to have the rear end of the cell to disassemble the adhesions so that the cell can move forward.

MICROTUBULES As mentioned, microtubules are hollow and made from alpha tubulin and beta tubulin proteins. They are important in giving the organelles their proper location. Figure 58 shows the structure of the microtubule:

Figure 58.

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Microtubules are always breaking down and building up. While the structure appears stable in the cell, you need to know that the process is instead quite dynamic. There are alternating alpha and beta tubulin molecules that wrap into a cylindrical shape. Microtubules, like actin, are polar molecules. The positively charged end grows fast, while the negatively charged end grows slowly. The beta end is always exposed on the positive end, while the alpha end is always exposed on the negative end. Microtubules are made at centrosomes in animal cells but not in plant cells or fungi. In plants and fungi, the microtubule organizing center is the nuclear envelope. They give structure to cilia and flagella. Cilia are seen in the female reproductive tract and in the respiratory lining. Flagella are seen in human sperm and certain bacteria. There are three types of microtubules that aid in the process of mitosis. These are astral microtubules, polar microtubules, and kinetochore microtubules. The astral microtubules radiate from the centrosomes to the cell membrane in order to keep the mitotic spindle in place. Polar microtubules help separate the chromosomes. Kinetochore microtubules actually connect to the chromosomes in order to pull them apart.

INTERMEDIATE FILAMENTS Intermittent filaments are just involved in structure and are not involved in cell movement. There are more than fifty different intermediate filament proteins. Some will form from hard keratin and will ultimately become hair, horns, and nails of animals. Soft keratins are also possible parts of intermediate filaments. Vimentin is found in fibroblasts, white blood cells, and smooth muscle cells. Desmin is mainly seen in muscle cells. Other cell types will have their own unique intermediate filaments. There are neurofilament proteins seen in neurons of all types. Lamins are seen in the nucleus. All intermediate filaments form an alpha-helical rod. These are the filaments that attach to desmosomes and hemidesmosomes.

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CILIA, CENTRIOLES AND FLAGELLA Cilia and flagella are made from microtubules covered by plasma membrane extensions. Their goal is to move the cell or move mucus, fluid, or cells over the cell surface. Microtubules and cilia are identical but they are different only in length. Two microtubules form a doublet in cilia and in flagella. There are microtubule associated proteins that also participate in the process of cilia and flagella movement. There is a circle of nine doublets or eighteen total strands of tubulin tubules that form the outside of a flagellum or cilium. There is a central doublet, making twenty total tubules in the cilium or flagellum. There are dynein arms that connect some of these tubules. They have ATPase activity so that, when ATP is around, they can move from one tubulin to another so the cilium or flagellum can bend. Nexin is another protein that links these microtubules in order to allow for the movement of the cilium. Centrioles will control the direction of the flagella or cilia so they can beat in unison.

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KEY TAKEAWAYS •

The cytoskeleton consists of thin microfilaments, intermediate filaments, and microtubules.

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Microfilaments and microtubules are involved in cell movement, while intermediate tubules are involved mainly in cell structure.

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Actin is a microfilament that is involves with myosin in the contraction of muscle cells.

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Actin and myosin interact in non-muscle cells as well.

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Microtubules form cilia and flagella with the help of centrioles, dynein, and nexin proteins that allow the cilia and flagella to go in the proper direction.

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QUIZ 1. What is the main function of the cytoskeleton in prokaryotic cells? a. It holds the cell organelles in place b. It is a highway for molecular transport c. It participates in cell to cell communication d. Prokaryotes do not have a cytoskeleton 2. Which are the thinnest filaments in the cytoskeleton? a. Actin b. Microfilaments c. Microtubules d. Intermediate filaments 3. Which component of the intermediate filaments is found exclusively in the nucleus in order to hold up the nuclear envelope? a. Keratin b. Lamin c. Desmin d. Vimentin 4. What filament is responsible for separating sister chromatids in the dividing cell? a. Microfilaments b. Intermediate filaments c. Microtubules d. Actin filaments 5. What is not an aspect of what microfilaments can do? a. Aid in drawing chromosomes apart in cell division b. Aid in cell movement c. Participate in muscle contraction d. Keep organelles in place

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6. How many actin filaments wind together to make a microfilament? a. Two b. Three c. Four d. Six 7. What are the bands in a muscle cell referred to that contain only actin filaments? a. Z discs b. I bands c. A bands d. H bands 8. What are the ends of the sarcomeres called? a. Z discs b. I bands c. A bands d. Actinomycin complex 9. What molecular structure provides the energy necessary to drive the contraction of the muscle fiber in muscle contractions? a. GTP b. Cyclic AMP c. ATP d. Calcium 10. What molecule is not associated with the actin molecule? a. Troponin b. Tropomyosin c. Nebulin d. Titin

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CHAPTER THIRTEEN: EUKARYOTIC CELL CYCLE This chapter is about the eukaryotic cell cycle. There is a natural progression to the lifespan of a cell. It goes through growing phases, dividing phases, and the phases of death or apoptosis. There are specific controls over the eukaryotic cell cycle. The different phases of mitosis and meiosis are discussed along with the process of cell death, which is also called apoptosis.

CELL CYCLE AND CELL CYCLE CONTROL The cell cycle takes the cell through birth, growth, and cell division. There is a regular series of events that occur as part of this process. There are two separate phases: interphase and the mitotic phase. Interphase involves the cell growth and DNA replication. There is separation of the replicated DNA during the mitotic phase in order to make two daughter cells. Figure 59 shows the cell cycle:

Figure 59.

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It is during the S phase of interphase that DNA polymerase is most reactive. This is when DNA replication occurs. It leads into the G2 phase of interphase, in which there is physical cell growth. What follows is the mitotic phase, which is itself divided into mitosis and cytokinesis. Interphase starts again with the G1 phase, in which there is also cell growth. The G1 phase is the first gap phase. There is little outward change but a great deal of biochemistry is taking place, with the accumulation of nucleic acids in order to make more DNA as well as the buildup of ATP energy necessary for chromosome replication. The S phase or synthesis phase involves increased activity of DNA polymerase. There are identical sister chromosomes made during this phase. The sister chromatids or identical DNA pieces are connected at the centromeric region. The centrosome gets duplicated. The two separate centrosomes become the mitotic spindle. Each centrosome has centrioles in the center of it that help to organize cell division by making microtubules. These are found only in animal cells. In the G2 or second gap phase, the cell replenishes its stores of energy and makes proteins necessary for the replication of chromosomes. Organelles sometimes get replicated and the cytoskeleton breaks down to make things necessary for mitosis. Cell growth can also happen. There is double checking of the duplicated chromosomes in order to help overcome the possibility of errors. Some cells go through a G-zero or G0 phase. This is a quiescent phase of interphase in which no process involved in the division of cells occurs. This phase can be permanent for some cells. When a daughter cell is made, it can go through G0 or to G1, depending on the cell. Nerve cells do not divide and are almost always in the G0 phase. Cells that participate in wound repair go through all phases but are rarely in the G0 phase. Mitosis is just about five percent of the cell cycle in timespan. Interphase makes up the rest and is not considered a resting phase because a great deal happens. The karyotype is most visible in the mitotic phase of the cell cycle. The time for actual cell division can be as short as 90 minutes or as long as many hours, if at all. Embryonic cells have shorter cell cycles.

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Cells have quality assurance techniques, quality control, and internal security. During quality assurance and quality control, there are crucial cell cycle checkpoints where review and decision-making by the cell takes place. The cell decides if a new cell is made and the cell proceeds in a certain order, starting with the G1 phase. As many as half of all cancers are due to some type of quality control issue in the cell cycle regulation. Mitogens will signal cell division. These can continue the cell division process in certain cancers. In a normal cell, only one new copy of a gene is made. As you will see, there are cyclin dependent kinases and other enzymes that operate to allow for the progression of the cell cycle. There are certain checkpoints in cell cycle regulation. A checkpoint consists of some sort of sensor or detector, a signal sender, and a receiver or effector process. At the G1 checkpoint, there is checking for DNA damage. Damaged DNA sends signals, such as proteins from the tumor repressor gene p53. This determines whether or not the S phase should take place. If p53 products are elevated, the cell is considered too damaged and the S phase will not start. It becomes the trigger for cell apoptosis instead. The DNA in the p53 gene can be damaged by sunlight and by mutagenic chemicals, as is seen in aflatoxins and tobacco smoke. The S phase is about a third of the cell cycle. Only one new copy of cellular DNA is created in this part of the cycle but it doesn’t happen if the quality control breaks down. DNA polymerase is very active and new strands of DNA are made. There are three checkpoints in the S phase. One involves having enough nucleotides present to make new DNA. Others involve inhibitory chemicals, while another involves breaks in the newly-made DNA. If all goes well, there are two sets of DNAs made. The gap 2 phase is shorter than gap 1. This time prepares the organelles for division and for being shared between the two daughter cells. Cyclins A and B as well as cyclindependent kinase 1 get the cell through the G2 checkpoint. The cell becomes committed to cellular division after the G2 phase. At the G2 checkpoint, the cell is monitored to make sure there are two identical sets of DNAs in the cell. Proofreading happens and DNA repair takes place. This phase of cell

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division happens only if the repairs can be made. Badly damaged DNA make p53 products, which trigger apoptosis instead of cell division. There are regulators that will be discussed that drive the cell through the process of mitosis. The sister chromatids become separated and move to two ends of the cell. Some organelles get divided as well and cytokinesis takes place in order to completely divide the cell. The main checkpoint in mitosis is called the “metaphase checkpoint”. It checks for misaligned chromosomes and makes sure that microtubules are properly attached. Anaphase does not happen until the metaphase checkpoint occurs.

CELL CYCLE REGULATORS There are specific cell cycle regulators, most commonly the cyclins. There are four types of cyclins in humans: G1 cyclins, G1/S cyclins, S cyclins, and M cyclins. They are active during the named phases of the cell cycle. Most cyclins are at low levels during the cell cycle but rise to a peak at specific parts of the cell cycle. The cyclin needs to activate or deactivate target proteins within the cell. They operate with cyclin-dependent kinases to drive the cell cycle. A typical cyclin-dependent kinase is not active but it takes the binding of a cyclin in order to make the kinase functional. As kinases, these enzymes phosphorylate target proteins. In the case of G1/S cyclins and CDK, the activated proteins are DNA polymerases. Cyclins and CDKs or cyclin-dependent kinases are considered evolutionarily conserved because they are the same across many different organisms. Yeast has just one CDK, while humans have several different CDKs active in the cell cycle. Maturation-promoting factor or MPF is a protein that participates in cell cycle transitions. It triggers a cell to enter the M phase of the cell cycle. M cyclin remains at a low level until mitosis is necessary. It binds to a cyclin-dependent kinase in order to make protein complexes that help to trigger the M phase. The MPF complex adds phosphates to proteins in the nuclear envelope so that it can be broken down and promotes chromosome condensation.

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There is an anaphase-promoting complex/cyclosome factor or APC/C. Its function is to break down M cyclins so the cell can begin to enter the G1 phase again. It destroys the proteins that hold the sister chromatids together so that they can separate. This is an enzyme that attaches ubiquitin to a target protein, making the target recycled by the proteasomes of the cell. This ubiquitin tagging triggers the separation of sister chromatids by destroying cohesin that normally binds chromatids. The cyclin-dependent kinases and the cyclins are direct cell cycle regulators. They respond to cues that can be inside or outside the cell. There are positive cues, such as growth factors, and negative cues, such as DNA damage, that block activity of cell growth and division in the cell cycle. The products of the gene p53 act as regulators of cell cycling. These products will stop the cycle at G1 by producing CDK inhibitor proteins. These will block the activity of CDK-cyclin complexes so that DNA repair can take place. If DNA damage is not fixable, apoptosis will happen so that damaged DNA does not get passed onto the next generation. In this way, p53 prevents the passage of mutations to the next cell generation. If insufficient, cancer can develop.

MITOSIS AND ITS REGULATION Mitosis happens in eukaryotic cells in order to produce two daughter cells that are the same genetically. Chromosomes are copied in order to allow for their separation in the process of mitosis. The process takes about an hour in order to happen. There is a mitotic apparatus that aligns the chromosomes and separates the different sister chromatids. Karyokinesis is the mitotic nuclear division, while cytokinesis is the actual cell division process. Mitosis is continuous but it is typically divided into five separate stages. The five stages of mitosis are prophase, prometaphase, metaphase, anaphase, and telophase. Figure 60 is a depiction of mitosis in the eukaryotic cells:

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Figure 60.

Prophase takes up over half of all mitosis. There is the breakdown of the nuclear envelope and the nucleolus disintegrates. The centrosome duplicates itself to make two daughter centrosomes. These centrosomes form the mitotic spindle. The chromosomes become compacted. Each replicated chromosome can be seen as two separate chromosomes. The chromosomes are held together by a centromere. Prometaphase involves migration of the of the chromosomes to the equatorial plate called the metaphase plate. This forms a kinetochore structure on each side of the centromere. There is a continual condensation of the chromosomes. This leads to metaphase, in which the chromosomes align along the metaphase plate. Anaphase is the shortest phase. It is when the centromeres divide and the sister chromatids are pulled apart. The microtubules pull these sister chromatids to the opposite side of the cell. The sister chromatids are then referred to as daughter chromosomes. Telophase happens when the nuclear envelope is remade and chromosomes become diffuse again. Cytokinesis is the actual separation of the two cells. A cell plate forms in cytokinesis involving plants.

MEIOSIS Meiosis is an aspect of eukaryotic cell division that makes haploid sex cells also called gametes from cells that are diploid or those that contain two copies of each chromosome. There are two parts to meiosis called meiosis I and meiosis II. There is

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DNA replication followed by separation into cells that become haploid cells. Figure 61 shows the process of meiosis:

Figure 61.

Meiosis I will separate the pairs of homologous chromosomes. There are several phases to this, including prophase I, metaphase I, anaphase I, and telophase I, followed by cytokinesis. It is during prophase I that crossing over and recombination of the genes

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occurs so that unique chromosomes can separate. Meiosis I is when the cell turns from being haploid to being diploid. In prophase I, DNA is exchanged and recombinant chromosomes are made. There are five separate phases to prophase I, including leptotene, zygotene, pachytene, diplotene, and diakinesis. During pachytene is when the actual crossing over takes place through the formation of chiasmata between the chromosomes. In metaphase I, the pairs of chromosomes are arranged in rows along the metaphase plate. The arrangement of chromosomes is random so that their can be genetic variation. There are more than 8 million different combinations that can occur because of the random assortment of the 23 pairs of chromosomes. In anaphase I, the chromosomes separate and in telophase I, the chromosomes become diffuse again. Cytokinesis happens with these cells as well, creating two new cells. Meiosis I is considered a reduction division so that the haploid cell is created. This is followed by meiosis II. Meiosis II separates the chromosome into two chromatids. The process is different in males and females. In males, four spermatozoa are created, while, in females, three polar bodies are formed along with one egg cell so that just one egg cell is made in the process. Meiosis II is similar to mitosis.

APOPTOSIS Apoptosis is also referred to as “programmed cell death”. If cells are not necessary, there is a process that takes place in which the cell commits suicide. Apoptosis is extremely common with billions of cells in the healthy human adult dying every hour, particularly in the bone marrow and the intestinal tract. It occurs in embryos and in fetuses in order to sculpt the features of the embryo. In adults, this apoptosis balances cell division so the size of the organism’s organs stays the same over time. Cells die in necrosis by swelling and bursting, spilling contents throughout the extracellular space. Cells die in apoptosis do this differently. They die neatly, without spilling their contents throughout the environment. This can be called shrinkage and condensation rather than swelling and bursting. The cytoskeleton is allowed to collapse and the nuclear DNA is broken up after the envelope disassembles 197

itself. Ultimately, the cell is marked for phagocytosis by the immune system. The organic compounds get recycled. In apoptosis, there are proteases that have a cysteine moiety on their active site. This makes these proteins called caspases. There is a proteolytic cascade that takes place that cleave proteins within the cell. Lamins, which are part of the nuclear cytoskeleton, get cleaved so that the nuclear envelope breaks down. There are also DNA degrading enzymes called DNases that cut up the DNA in the nucleus. As you can see, there is a neat and orderly breakdown of the cell. The process is an all-or-none process. There are procaspases in every cell that can get activated to make caspases as part of the caspase cascade. When cells are under stress or damaged, they can commit suicide by triggering this cascade through signals from within the cell. DNA damage itself can trigger apoptosis through the activity of the p53 gene. There are other activators and inhibitors of the caspase cascade. Apoptosis can get rid of infected or cancerous cells. Their destruction makes the cell unable to do damage to the body, reducing the threat to the organism. DNA damage beyond repair triggers apoptosis from within the cell. Cells that avoid apoptosis when it is necessary can become cancerous cells. Immune cells have specific molecules on their surface that, if not recognized as self-cells, cause the apoptosis of the immune cell.

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KEY TAKEAWAYS •

The cell cycle happens in nearly every cell at all times.

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The cells that divide go through a G1, S, G2, and M phase.

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Cellular DNA divides during the S phase but doesn’t get divided into daughter cells until the M phase.

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There are multiple regulators to the cell cycle that tell the cell whether it should go through to the next phase. There are different regulator cells for each part of the cell cycle.

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Meiosis involves a multi-step process in which the diploid cell makes unique haploid sex cells.

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Apoptosis is different from necrosis. It is an orderly dismantling of a cell that ultimately gets phagocytized by the immune system.

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Failure of apoptosis when it should occur leads to cancer in many cases.

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QUIZ 1. Which phase of the cell cycle involves the most activity of DNA polymerase? a. S b. G0 c. G1 d. M 2. What is not a part of interphase? a. G1 phase b. G2 phase c. S phase d. M phase 3. During which phase of the cell cycle is the cytoskeleton most likely to break down or be dismantled? a. G1 b. S c. G2 d. M 4. In which phase of the life cycle of a cell is a cell considered to be not participating in cell division? a. G1 b. S c. G2 d. G0

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5. When do the protein products of the gene p53 act as a checkpoint during the cell cycle? a. Early G1 phase b. Late G1 phase c. S phase d. G2 phase 6. If a cell is experiencing uncontrolled growth as in cancerous conditions, what phase of the cell cycle happens to a greater degree? a. M phase b. G0 phase c. S phase d. G2 phase 7. Maturation-promoting factor will trigger a cell to enter what phase of the cell cycle? a. G1 phase b. S phase c. G2 phase d. M phase 8. What is the main function of the maturation-promoting factor in the cell cycle? a. It activates DNA polymerase b. It promotes cytokinesis c. It helps break down the nuclear envelope d. It helps separate the chromosomes in the M phase 9. When are the sister chromatids pulled apart in the action of mitosis? a. Metaphase b. Telophase c. Anaphase d. Prophase

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10. During which phase of mitosis does the nuclear envelope get recreated in the daughter cells? a. Cytokinesis b. Telophase c. Anaphase d. Metaphase

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SUMMARY This course involved the study of the molecular structures associated with living things. It combined the related subjects of biophysics, biochemistry, and genetics in order to give a clearer picture of the molecules that interact on a cellular level. The major macromolecules studied in the course included proteins, which make up structural molecules and enzymes, as well as nucleic acids, the underlying biochemical structures seen in ribonucleic acid (or RNA) and deoxyribonucleic acid (or DNA). The course also looked into the molecules used in the making of biomembranes, such as those that comprise the outer cell membrane and organelles. The molecular basis of the functions of prokaryotic and eukaryotic cells, including animal and plant cells, was also covered in this course. Chapter one in the course introduced molecular biology by talking about the basics of biochemistry as it applies to life and living things. All of human life is based on water, which is a polar molecule that acts as a solvent for many biological molecules in living things. The bonds that make up biochemical molecules are also important in the discussion of molecular biology. The types of molecules that make up living organisms were also covered as were the different biochemical reactions that take place inside and outside the cell. In chapter two of the course, the discussion moved from biochemistry to the biology of cells and cell structures. There are two major types of cells: prokaryotic cells and eukaryotic cells. These are quite different from one another in structure and function, which were covered in the chapter. Cells inside multicellular organisms must communicate with one another through different mechanisms. Animals that are complex and multicellular (such as are seen in the human body) have different cell types that form tissues. The tissues together form organ systems. The different types of tissues were covered in this chapter. The focus of chapter three was the integration of cells into tissues. This chapter looked specifically into intercellular connections and how some of these connections create cell-

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to-cell communication. In epithelial cell tissues, there is the basal lamina, the structure and function of which was covered in the chapter. In addition, the structure and function of connective tissue structures were discussed as were the adhesions seen in plant cells. Chapter four in the course talked about the synthesis and structure of biomembranes. It covered fatty acid synthesis, which is how the basic molecules of biomembranes get created and incorporated into things like cell membranes and the membranes seen in organelles. The composition of membranes was also introduced, including the phospholipids and membrane proteins that together make up the cell membrane structure. The main focus of chapter five was the different things that happen in transmembrane support. Water, for example, can pass through the membrane by osmosis—from a high concentration of water to a low concentration of water. Other types of membrane transport include simple and facilitated diffusion, as well as active transport. The sodium-potassium ATPase pump is particularly important in cell membrane transport. Symporters and antiporters also aid in the transport of certain molecules across the membrane. Ion transport helps account for a difference in electric potential between the inside and outside of the cell. Chapter six in the course mainly covered proteins and their biochemistry. Proteins have several different characteristics, based on how they are made and on post-translational modification of the protein structures. The different factors that play a role into making proteins from amino acids was introduced in this chapter. Some proteins are functional enzymes; how these behave was covered in the chapter as were the different methods of detecting and characterizing proteins in molecular biology. The structure and molecular processes of DNA and RNA were the topics of chapter seven. DNA and RNA have similar structures, although DNA is usually double-stranded and RNA is usually single-stranded. There are different types of RNA that vary according to their function. The chapter also talked about DNA replication, DNA repair, and the process of recombination.

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There is a difference between prokaryotic genes and eukaryotic genes, which was part of the discussion of chapter eight in the course. Genetic material is divided up into genes, which are the readable segments of DNA in the organism. Transposons or transposable DNA were also covered, which is DNA that does not stay in the same place throughout the lifespan of the cell. Also included was a discussion of genomics, which is the collection of all the genes that exist as part of a given organism’s genetic material. Cellular energetics was the subject of chapter nine in the course. There are hundreds of enzymes and reactions that take place as a result of cellular metabolism. Amino acids, fatty acids, and carbohydrates all get metabolized by the cell to varying degrees, usually with a common final pathway. Prokaryotic cells and eukaryotic cells have both similarities and differences in the way nutrients are metabolized. In addition, photosynthesis was covered as a metabolic process that plants and other photosynthetic organisms participate in. The focus of chapter ten was the function of vesicles in exocytosis and endocytosis. Vesicular budding and fusion is a process where by small vesicles break off or fuse with the cell membrane or other membranes in order to dump or take up contents within the vesicles. This process can happen either to rid the cell of substances or take on substances by the cell. The process of receptor-mediated endocytosis was covered as part of this chapter as was the complex process of neurotransmitter secretion by nerve cells, which also involves vesicles. Chapter eleven in the course introduced the topic of signal transduction or cell signaling. There are several signaling pathways that involve the ways that cells send and receive signals from other cells in multicellular organisms. There are ligands and receptors involved in signal transduction, of which there are many types. The largest family of membrane receptors is the G-coupled protein receptor family, which involves a specific protein type that many cells make use of in cell signaling. The ways this receptor operates in the cell membrane and within the cell were covered as part of this chapter. Chapter twelve placed a focus on cell organization and on how aspects of cell organization control movement within the cell. There are many different types of

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molecules involved in cellular organization, many of which contribute to the cell cytoskeleton. Organelles and substances move along the cytoskeleton so that the cell can have order and proper placement of intracellular structures. Some of these same fibrous proteins play a role in the cilia and flagella of different types of cells. In addition, cells migrate both as part of cell division and outside of cell division by virtue of the activity of the cell cytoskeleton. Chapter thirteen in the course was about the eukaryotic cell cycle. There is a natural progression to the lifespan of a cell. It goes through growing phases, dividing phases, and the phases of death or apoptosis. There are specific controls over the eukaryotic cell cycle. The different phases of mitosis and meiosis were discussed along with the process of cell death, which is also called apoptosis.

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COURSE QUESTIONS AND ANSWERS 1. What is true of cations and anions? a. Cations are positively charged and anions are negatively charged. e. Cations are negatively charged and anions are positively charged. f. Both anions and cations are positively charged. g. There is no charge on either cations or anions. 2. What is not true of water? a. It has a high heat of vaporization b. It has a high specific heat c. It has a low surface tension d. It is densest in its liquid form 3. What is the best way to describe the lattice energy of a given ionic compound? a. It is the measure of the compound to conduct electricity b. It is another way of describing the surface tension of an ionic compound c. It is a measure of the density of an ionic solid d. It is another way to describe the bond strength of an ionic molecule 4. In what physical state can you find covalent compounds at room temperature and atmospheric pressure? a. Gas b. Liquid c. Solid d. Either gases, liquids, or solids

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5. In what physical state can you find ionic compounds at room temperature and pressure? a. Gas b. Liquid c. Solid d. Either gases, liquids, or solids 6. What is not true of covalent molecules and covalent bonds? a. The bond length is shorter in double and triple bonds b. They do not conduct electricity c. They have low melting points d. They have high boiling points 7. Which of the following is not an atom that makes up a sugar or carbohydrate? a. Carbon b. Oxygen c. Hydrogen d. Nitrogen 8. Which of the following is a five-carbon sugar and not a six-carbon sugar? a. Glucose b. Galactose c. Ribose d. Fructose 9. Which of the following sugars is a monosaccharide rather than a disaccharide? a. Lactose b. Galactose c. Maltose d. Sucrose

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10. What is not a part of a nucleotide or nucleic acids like DNA? a. Nitrogenous base b. Amino acid c. Five-carbon sugar d. Phosphate group 11. What kind of bonding connects the nitrogenous bases together in a doublestranded piece of DNA? a. Covalent b. Ionic c. Polar d. Hydrogen 12. Which of these molecules contains the most energy to drive reactions? a. Guanosine monophosphate b. Adenosine monophosphate c. Adenine triphosphate d. Adenosine diphosphate 13. What is something that an enzyme cannot do as part of helping a reaction occur? a. It can produce physical stress on a bond in order to break the bond b. It can align molecules in a specific orientation in order to facilitate a reaction c. It can change the placement of electrons in order to facilitate the reaction d. It can decrease the final energy level of the products of the reaction, allowing it to move faster 14. What is mainly contained in the plasmids inside a cell? a. Protein b. Carbohydrates c. DNA d. Lipids

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15. What aspect of a prokaryotic or bacterial cell wall makes it stain differently on the gram staining technique used to identify cells under the microscope? a. The cell wall b. The cell membrane c. The cytoplasm d. The nucleic acids 16. What is it called when a piece of DNA from one bacterium is injected into another bacterium through a pilus? a. Sexual reproduction b. Transduction c. Conjugation d. Transformation 17. What part of the eukaryotic cell makes proteins and is continuous with the nuclear envelope? a. Nucleolus b. Rough endoplasmic reticulum c. Lysosome d. Golgi apparatus 18. What part of the cell gets rid of toxins taken up or made by the cell through oxidation reactions? a. Peroxisomes b. Lysosomes c. Centrioles d. Nucleolus

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19. What process involves water that is transported from one side of a membrane to the other side along its concentration gradient? a. Active transport b. Facilitated diffusion c. Osmosis d. Passive diffusion 20. What part of the eukaryotic animal cell makes ribosomes as one of its major functions? a. Nucleolus b. Golgi apparatus c. Rough endoplasmic reticulum d. Centriole 21. What part of the eukaryotic cell is considered an energy-factory because it participates in the making of ATP energy? a. Golgi apparatus b. Mitochondrion c. Centrosome d. Nucleolus 22. What is the main byproduct of the photosynthetic process in the chloroplasts of the cells? a. Carbon dioxide b. Water c. Oxygen d. Amino acids

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23. What structure is seen in the chloroplast of the plant cell but not in the mitochondria? a. Double-layer membrane b. Thylakoids c. DNA d. Ribosomes 24. What is the cell wall of most plants made out of? a. Chitin b. Peptidoglycan c. Lignin d. Cellulose 25. What type of signaling in the organism happens over the longest distances? a. Endocrine signaling b. Neurotransmitter signaling c. Paracrine signaling d. Autocrine signaling 26. What is most true about the nerve supply and vascular supply of epithelial tissue? a. It is innervated and vascular b. It is not innervated and not vascular c. It is innervated but not vascular d. It is vascular but not innervated 27. What side of an epithelial cell has microvilli? a. Basal side b. Medial side c. Lateral side d. Apical side

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28. What connection between cells of a tissue allow for small molecules to pass from cell to cell? a. Desmosomes b. Hemidesmosomes c. Gap junctions d. Tight junctions 29. Which type of connective tissue cell is most considered to have an energy reservoir function? a. Adipose cell b. Plasma cell c. Fibroblast d. Mesenchymal cell 30. What is not something that can be descriptive of smooth muscle cells? a. They are striated b. They have a single nucleus c. They are irregularly arranged d. They are involuntary fibers 31. What cells of nervous tissue act as macrophages to clear out pathogens and cellular debris? a. Astrocytes b. Schwann cells c. Oligodendrocytes d. Microglia 32. What is the type of transport allowed between the cells that are connected by tight junctions known as? a. Intercellular transport b. Diffusion c. Active transport d. Paracellular transport

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33. What protein is not a part of the construction of the tight junction? a. Claudin b. Elastin c. Occludin d. Tricellulin 34. Which type of cell adhesive structure connects the cell to adjacent connective tissue but not directly to another cell? a. Desmosome b. Tight junction c. Hemidesmosome d. Tight junction 35. What protein type is the same for adherens junctions and desmosomes? a. Intermediate filaments b. Plakophilin c. Desmoplakin d. Cadherins 36. What type of cell to cell connection allows for the passage of an electrical signal between the two cells? a. Adherens junctions b. Gap junctions c. Desmosomes d. Tight junctions 37. Which type of cell to cell connector makes use of a pair of connexons that bind together between the cells? a. Gap junctions b. Adherens junctions c. Hemidesmosomes d. Desmosomes

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38. What protein is considered the most prominent aspect of the basement membrane? a. Laminin b. Integrin c. Cadherin d. Plakophilin 39. What tissue is not considered connective tissue? a. Blood b. Bone c. Fatty tissue d. Thymus 40. What are the main cells seen in connective tissue? a. Chondroblasts b. Osteoblasts c. Fibroblasts d. Adipocytes 41. What type of collagen is seen mainly in cartilage? a. Type I b. Type II c. Type III d. Type IV 42. Where is elastin less likely to be seen? a. Cardiac muscle b. Skin c. Bladder d. Arteries

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43. What component of elastic fibers gives the fiber its fibrous nature? a. Elastin b. Tropocollagen c. Fibrillin-1 d. Collagen 44. Where does fatty acid synthesis take place? a. Cytoplasm b. Rough endoplasmic reticulum c. Smooth endoplasmic reticulum d. Mitochondria 45. What seen only in the phospholipid molecule and not a molecule of triglycerides? a. Glycerol b. Phosphate moiety c. Fatty acids d. Ester bond 46. What molecule is most likely to pass through the aquaporin protein spanning the cell membrane? a. Sodium b. Water c. Glucose d. Lipids 47. What happens to plant cells when a plant like a flower is placed into pure water? a. The plant cells become flaccid b. The plant cells undergo transpiration c. The plant cells become turgid d. The plant cells undergo plasmolysis

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48. A solution has 1 mole of different substances dissolved in it. Which solution will have the highest osmotic pressure? a. Glucose b. Sucrose c. Ethanol d. Sodium chloride 49. What is a major organ in the body where filtration of substances occurs? a. GI tract b. Lungs c. Kidneys d. Heart 50. What is least likely to be a factor in primary active transport? a. Binding sites for ATP on the cytosolic surface of the pump b. The presence of a specific ion or molecular pump c. The ability to pass from low concentrations to high concentrations of a solute d. The necessity for a downward concentration gradient 51. What is a main function of the sarcoplasmic reticulum of the muscle cell? e. Pumps and releases calcium ions f. Makes phospholipids g. Participates in protein synthesis h. Packages cellular proteins 52. Which transmembrane pump is also referred to as ATP synthase because it makes ATP from ADP and phosphate on the membranes of bacteria, chloroplasts, and mitochondria? a. V-pump b. ABC pump c. P-pump d. F-pump

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53. Which transmembrane pump will pump both ions and small molecules across the cell membrane rather than just ions? a. V-pump b. ABC pump c. P-pump d. F-pump 54. The primary active transport of what molecule allows for the secondary active transport of other molecules in these secondary active transport processes? a. Sodium ions b. Potassium ions c. Hydrogen ions d. Hydroxyl ions 55. How many ATP molecules are necessary for one pass of the sodiumpotassium ATPase pump? a. Zero b. One c. Two d. Three 56. What happens to sodium and potassium during each pass of the sodiumpotassium ATPase pump? a. Two molecules of sodium enter and two molecules of potassium leave the cell b. Three molecules of sodium leave and three molecules of potassium enter the cell c. Two molecules of sodium leave and three molecules of potassium enter the cell d. Three molecules of sodium leave and two molecules of potassium enter the cell

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57. What is not an activity of the sodium-potassium ATPase pump? a. It raises the pH of the intracellular space b. It contributes to electronegativity of the intracellular space c. It provides symporter mechanisms for the cell d. It prevents swelling of the cell 58. What is the resting membrane potential of a cell under normally polarized conditions? a. + 40 millivolts b. Zero millivolts c. – 30 millivolts d. – 70 millivolts 59. Which cells have a sodium-potassium ATPase pump affecting the cell’s electronegativity? a. Muscle cells only b. Nerve cells only c. Both nerve and muscle cells d. All cells have this pump 60. What protein structural classification comes from hydrogen bonding that forms and alpha helix or a beta pleated sheet? a. Primary structure b. Secondary structure c. Tertiary structure d. Quaternary structure 61. Which structure of a protein molecule depends on the interaction between different peptides that make up the single multi-peptide structure? a. Primary structure b. Secondary structure c. Tertiary structure d. Quaternary structure

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62. Which structure of a protein molecule is made by multiple types of bonds between R chains, such as disulfide bonds, van der Waals forces, and ionic bonds? a. Primary structure b. Secondary structure c. Tertiary structure d. Quaternary structure 63. How many DNA bases are necessary in a group in order for them to be read into an amino acid message when DNA is transcribed? a. Two b. Three c. Four d. Six 64. What molecule ultimately gets made through the action of RNA polymerase? a. Amino acid molecules b. DNA strands c. Double-stranded ribosomal RNA d. Single-stranded messenger RNA 65. What part of the RNA transcription process involves the promotor region? a. Initiation b. Elongation c. Termination d. Splicing 66. Where does translation take place within the cell? a. Mitochondria b. Golgi apparatus c. Nucleus d. Ribosomes

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67. How many different or unique proteins are found in the human proteome? a. 5,000 b. 20,000 c. 1 million d. 1 billion 68. Which post-translational modification of proteins is likely to be irreversible? a. Proteolysis b. Glycosylation c. Phosphorylation d. Methylation 69. What does not happen in an enzymatic reaction with substrates and endproducts? a. The substrate is consumed or altered in the process, decreasing its concentration b. The end-product is capable of increasing its concentration, getting made in the reaction c. The enzyme is consumed in the reaction process d. The enzyme is temporarily altered but returns to its natural state for another reaction 70. What is true of enzymes and catalysts? a. Enzymes are all catalysts b. Catalysts are all enzymes c. Enzymes and catalysts are the same thing d. Enzymes and catalysts are unrelated to one another 71. What is not true of an ELISA test? a. Antibodies are fixed to a plastic plate b. If the protein is present, there will be a color change c. The antibody reacts to a color-changing molecule when bound d. The protein needs to be separated from other proteins to do the test

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72. In the DNA molecule, what nitrogenous base forms a hydrogen bond with cytosine? a. Guanine b. Thymine c. Adenine d. Uracil 73. What nitrogenous base is seen in RNA but not in DNA? a. Guanine b. Uracil c. Thymine d. Adenine 74. What is the major purpose of the histone proteins? a. To unwind DNA that has become condensed b. To participate in DNA synthesis c. To condense DNA into chromatin d. To help DNA make RNA strands 75. Where in a cell would DNA least likely be found? a. Nucleus b. Ribosomes c. Mitochondria d. Chloroplasts 76. What is not a difference between DNA and RNA? a. RNA contains ribose and DNA contains deoxyribose b. RNA has shorter strands than DNA c. RNA is more stable than DNA d. RNA is usually single-stranded and DNA is usually double-stranded

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77. Which nucleotide signals the end of the RNA transcript as it disconnects from the DNA template in the transcription process? a. Adenosine b. Guanine c. Cytosine d. Uracil 78. made of? a. Transfer RNA b. Ribosomal RNA c. Messenger RNA d. DNA 79. In what order does the DNA template get read by RNA polymerase? a. From the five-prime to three-prime end b. From the three-prime to the five-prime end c. The RNA segments get added on all at once d. It depends on the organism 80.What base pair makes up the tail on messenger RNA in eukaryotes in order to protect it? a. Adenine b. Uracil c. Cytosine d. Guanine 81. Which type of nucleic acid has enzymatic properties? a. rRNA b. DNA c. tRNA d. mRNA

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82. Which type of organism can make use of RNA as part of its genome? a. Archaea b. Viruses c. Bacteria d. Plant 83. Which enzyme in DNA replication participates in the elongation process the most? a. DNA helicase b. DNA primase c. Topoisomerase d. DNA polymerase 84. What enzyme attaches the end-caps on the parent strands of DNA after the DNA has been replicated in order to protect these ends? a. Topoisomerase b. DNA ligase c. Exonuclease d. Telomerase 85. What is another name for DNA gyrase, which is the molecule that unwinds and rewinds DNA to keep it from tangling or supercoiling during the replication process? a. DNA ligase b. DNA helicase c. Topoisomerase d. Exonuclease 86. What is the main effect of UV light on the structure of DNA? a. Methylation of purines b. Pyrimidine dimer formation c. Methylation of guanine d. Base pair replacement

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87. Which protein regulates most of the bacterial DNA sequences? a. Topoisomerase I b. Histone proteins c. DNA gyrase d. Factor for inversion stimulation 88. Where does translation take place in the prokaryotic cell? a. In the cytoplasm in general b. In ribosomes located in the cytoplasm c. In ribosomes within the nucleoid d. In the nucleoid unassociated with ribosomes 89. In the lac operon, what is the main inhibitory molecule involved in its transcription? a. Glucose b. RNA polymerase c. Terminator molecule d. Lactose 90. In prokaryotic and eukaryotic cells, what are cis-acting genes? a. These are genes that code for the same thing b. These are genes that are located on different chromosomes c. These are genes that are located adjacent to one another d. These are genes that bind to the RNA polymerase molecule 91. What gene sequence in eukaryotes allows for the more efficient transcription of a sequence of cis-enhancing genes? a. Enhancer b. Promotor c. Initiator d. Regulator

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92. Which type of transcription factor will cause the gene to become transcribed in eukaryotic cells? a. The general transcription factor b. The promotor factor c. The transcription activator d. The initiating factor 93. There is a trp repressor protein that will block the transcription of the trp operon. What is the corepressor that must be bound to the protein in order for it to function? a. RNA polymerase b. Specific protein 1 c. Tryptophan d. Lactose 94. What happens in a prokaryotic cell when the transcription process is attenuated in the process of attenuation? a. The mRNA is made but it cannot be translated b. The DNA molecule is methylated c. The transcription process cannot happen d. A short, nonfunctional mRNA molecule is made 95. What type of molecule acts in opposition to eukaryotic activator proteins? a. General transcription factors b. Eukaryotic repressor proteins c. RNA polymerase binding proteins d. Co-activator proteins

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96. What is most true of transposable DNA? a. It is found in prokaryotes in large numbers and in eukaryotes in small numbers b. It is found in prokaryotes and eukaryotes in large numbers c. It is found only in eukaryotes d. It is found in extremely small numbers in both prokaryotes and eukaryotes 97. What is the meaning of reverse transcription? a. It is when DNA is transcribed in the reverse direction b. It is when DNA doesn’t get transcribed unless it is acted upon by reverse transcriptase c. It is when RNA gets transcribed into DNA d. It is when viral DNA gets transcribed into RNA 98. What is the major end result of the jumping of a transposon? a. It causes a genetic mutation b. It causes cancer c. It causes other human diseases d. It has no effect on the individual 99. Sickle cell disease results in a protein being made that is different in characteristics from the original protein but differs by one amino acid. What type of mutation is this? a. Frameshift mutation b. Nonconservative missense point mutation c. Conservative missense point mutation d. Nonsense mutation 100.

Which type of mutation would be considered the most severe?

a. The deletion of a single base pair b. The deletion of three contiguous base pairs c. The insertion of three contiguous base pairs d. The switching of a purine into a pyrimidine

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101.

What is the least likely way to have DNA mutate?

a. Chemical mutation b. UV radiation mutation c. Gamma radiation mutation d. DNA polymerase error mutation 102.

What organic chemical is least likely to be part of chemoorganotrophy?

a. Fatty acids b. Amino acids c. Sugars d. Nucleic acids 103.

How many ATP molecules are gained per glucose molecule in glycolysis?

a. One b. Two c. Three d. Four 104.

Which cycle is different from the other three?

a. Citric acid cycle b. Tricarboxylic acid cycle c. Cori cycle d. Krebs cycle 105.

When all of glucose goes into making CO2 and water, how many molecules

of ATP are made when the electron transport chain is included in the process? a. 12 b. 32 c. 43 d. 64

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106.

In anaerobic respiration, what is least likely to be the common final

electron acceptor? a. Oxygen b. Ferric ion c. Carbonate d. Nitrate 107.

What happens when any kinase enzyme reacts?

a. A molecule is phosphorylated. b. A molecule is de-phosphorylated. c. A hydrogen atom is removed from the molecule. d. A hydrogen atom is added to a molecule from water. 108.

What is the end-product of the enzyme hexokinase?

a. Glucose b. Citric acid c. Pyruvate d. Glucose-6-phosphate 109.

How many phosphate molecules are on the end-product when

phosphofructokinase acts on fructose-6-phosphate? a. One b. Two c. Three d. None 110.

When a molecule in the glycolysis process gets phosphorylated, what is the

source of the phosphate molecule? a. GTP b. NADPH c. ATP d. Phosphate

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111.

In the second phase of glycolysis, what energy molecule or molecules are

produced? a. ATP and NADPH2 b. GTP and NADH c. ATP and NADH d. 2 molecules of NADH 112.

What is the end-product of glycolysis?

a. Pyruvate b. Acetyl-CoA c. Lactic acid d. Glycerol-3-phosphate 113.

What is the end-product of the electron transport chain in denitrifying

bacteria? a. Nitrate b. Nitrite c. Nitrogen gas d. Nitrous oxide 114.

Where do the protons go in eukaryotes in order to create the proton

motive force? a. Outside the cell b. Into the intramembranous space in mitochondria c. Into the cytoplasm d. Into the inside of the mitochondrion itself 115.

What is ATP synthase tied to?

a. The phosphorylation of NAD+. b. The transfer of electrons across the mitochondrial membrane. c. The hydrolysis of NADP+. d. The leakage of hydrogen ions across a membrane.

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116.

In oxidative phosphorylation, what is the source of energy for the making

of ATP molecules? a. Oxygen b. Phosphate c. The proton motive force d. High energy phosphate bonds 117.

Which of the following is not an electron carrier protein in the electron

transport system? a. Flavoprotein b. Cytochrome oxidase c. ATP synthase d. Ubiquinone 118.

How many NADH molecules are made in each turn of the Krebs cycle?

a. None b. One c. Two d. Three 119.

What molecule gets passed into the mitochondrion in order to participate

in the Krebs cycle? a. Pyruvate b. Acetic acid c. Acetyl-CoA d. Glyceraldehyde-3-phosphate 120.

What is the molecule made in the process of fatty acid oxidation?

a. Pyruvate b. Acetyl CoA c. Coenzyme A d. Glycerol

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121.

Under what circumstances does the alpha oxidation of fatty acids happen?

a. With branched-chain fatty acids b. With fatty acids of odd numbers of carbon atoms c. With extremely long fatty acids d. It does not occur at all because beta oxidation is the only reaction that happens with fatty acids 122.

What is least likely necessary for the participation in photosynthesis?

a. Carbon dioxide b. Sunlight c. Glucose d. Water 123.

What is one particle of light known as?

a. Thylakoid b. Stoma c. Granum d. Photon 124.

How many cycles of the Calvin cycle does it take in order to make a

molecule of glucose? a. One b. Three c. Five d. Six

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125.

Which is a true statement involving photosynthesis?

a. Oxygen, ATP, carbon dioxide, and NADPH are the reactants, while glyceraldehyde-3-phosphate and water are products. b. Chlorophyll, water, and carbon dioxide are reactants, while glyceraldehyde-3-phosphate and water are end-products. c. Water and carbon dioxide are reactants and glyceradehyde-3-phosphate and oxygen are end-products. d. Water, NADPH, carbon dioxide, and ATP are reactants, and ribulose bisphosphate and oxygen are end-products. 126.

What is not a component of the photosynthetic process used by

cyanobacteria? a. Chlorophyll b. Chloroplasts c. ATP d. CO2 127.

Where do the light-independent reactions take place in eukaryotic cells?

a. Stroma b. Cytoplasm c. Stomata d. Thylakoids 128.

What part of the definition of thylakoids isn’t correct?

a. Thylakoids are stacked membranes. b. The outside of thylakoids is called the stroma. c. Thylakoids are a maze of membranes like the endothelial reticulum. d. Thylakoids contain chlorophyll.

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129.

Which structure is not a part of a photosystem in a photosynthetic cell?

a. ATP synthase b. Antenna molecule c. Chlorophyll pigment d. Reaction center 130.

What drives ATP synthase in the chloroplast?

a. The reaction center b. The proton gradient c. Photons d. Electron transport chain 131.

What is the order of vesicular transport in the eukaryotic cell?

a. Cis Golgi, medial Golgi, trans Golgi, endoplasmic reticulum b. Endoplasmic reticulum, cis Golgi, medial Golgi, trans Golgi c. Endoplasmic reticulum, trans Golgi, medial Golgi, cis Golgi d. Trans Golgi, cis Golgi, medial Golgi, endoplasmic reticulum 132.

What is the purpose of the clathrin coating protein on vesicles in the cell?

a. It helps the vesicle get to the endoplasmic reticulum from the Golgi apparatus b. It helps the vesicle get from the endoplasmic reticulum to the Golgi apparatus c. It helps the vesicle get from the Golgi apparatus to the plasma membrane d. It helps the vesicle go between the various types of Golgi apparatuses 133.

What does clathrin require in order to pinch off a vesicle it’s coated with?

a. ATP b. Dynamin c. COPI d. COPII 134.

What milieu is necessary to aggregate proteins in the vesicles so the

concentration can be higher? 234

a. High pH and low calcium concentrations b. Low pH and high calcium concentrations c. High pH and high calcium concentrations d. Low pH and low calcium concentrations 135.

What type of protein is located on the target membrane that allows the

vesicle to attach for eventual discharge? a. t-SNARE b. v-SNARE c. Dynamin d. Clathrin 136.

Which protein type twists at the level of the vesicle and target membrane

in order to allow the vesicle to discharge into the target membrane space? a. Dynamin b. RAB-GTP c. SNARE d. Clathrin 137.

Which molecule is not a protein associated with synaptic vesicular

attachment in the nerve cell? a. SNAP-25 b. Synaptobrevin c. Dynamin d. Syntaxin

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138.

What proteins are responsible for holding vesicles in place before they can

release their neurotransmitters? a. SNAP-25 b. VAMPs c. Syntaxin d. Synaptobrevin 139.

When does the neurotransmitter get added to the vesicle in a

neurotransmitter situation? a. In the Golgi apparatus at the time the vesicle is made b. In the endosomal compartment, when the vesicle is made c. After the empty vesicle is made, it is filled with neurotransmitter d. When the vesicle recycles itself at the nerve cell membrane 140.

What part of the cytoskeleton attaches vesicles in nerve cells before they

are ready for release? a. Myosin b. Microtubules c. Intermediate filaments d. Actin 141.

Which protein causes a pore to open up in the presynaptic membrane

when vesicles are released? a. Synaptobrevin b. Synapsin I c. Synaptophysin d. Synaptotagmin

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142.

What does synaptophysin bind to in order to open up a pore in the

presynaptic nerve cell? a. Synaptotagmin b. SNAP-25 c. Synaptobrevin d. Physophilin 143.

What type of endocytosis is also referred to as clathrin-dependent

endocytosis? a. Receptor-mediated endocytosis b. Caveolae c. Pinocytosis d. Phagocytosis 144.

Where do the contents of vesicles that participate in potocytosis go to in

the cell? a. Lysosomes b. Golgi apparatus c. Cytosol d. Peroxisomes 145.

What happens to the LDL-receptor after it gets taken up by the endosome

in the process of endocytosis? a. It gets taken up by a vesicle and gets sent back to the exterior of the cell. b. It goes to the peroxisome, where it is broken down. c. It goes to the lysosome, where it gets stored. d. It gets broken down in the acidic environment of the endosome. 146.

Which structure is the most acidic?

a. Early endosome b. Coated vesicle c. Lysosome d. Late endosome

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147.

What is the most severe lysosomal storage disease?

a. Hurler’s disease b. Gaucher’s disease c. Tay-Sachs disease d. Mucolipidosis II 148.

What happens to the transferrin-receptor-iron complex in the early

endosomes after they are taken up by the cell? a. They go on to the lysosome as a group before getting broken down. b. The iron leaves separately from the transferrin-receptor complex, which gets recycled together. c. The three parts dissociate and the transferrin gets recycled. The receptor gets broken down and iron is released into the cytoplasm. d. They go on to the lysosome. The transferrin and the receptor get recycled and the iron is taken up by the cell. 149.

When a cell creates a signal for its own receptors, what type of cell

signaling is this? a. Autocrine b. Direct cell to cell contact c. Paracrine d. Endocrine 150.

What are the communicators that connect cells in animal cells called that

allow for direct cell to cell communication? a. Plasmodesmata b. Gap junctions c. Desmosomes d. Tight junctions

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151.

What is a good example of an intracellular ligand?

a. Calcium b. Norepinephrine c. Estrogen d. Insulin 152.

What happens when receptor tyrosine kinases get activated?

a. Tyrosine binds to itself b. Tyrosine is phosphorylated c. An ion channel is opened d. The amino acid is attached to a polypeptide molecule 153.

What ligand binds to the exterior of the cell rather than the interior of the

cell? a. Nitric oxide b. Estradiol c. Norepinephrine d. Vitamin D 154.

What is the most upstream of these events?

a. The DNA gene is activated b. The ligand is located by itself c. The ligand and receptor are bound d. An intracellular signaling molecule is activated 155.

Which ion often acts as a second messenger in the cell?

a. Sodium b. Calcium c. Potassium d. Phosphate

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156.

What does the enzyme adenylyl cyclase make?

a. ADP b. ATP c. Cyclic AMP d. GTP 157.

What is the second messenger in the contraction of muscle cells?

a. Cyclic AMP b. Inositol phosphate c. Magnesium d. Calcium 158.

In the signaling pathway involving phospholipids, which component exits

the plasma membrane to enter the cytosol in order to do its job? a. DAG b. IP3 c. PIP2 d. Phospholipase C 159.

How does a signaling pathway affect the making of a protein?

a. It can turn on gene expression at the transcription level only b. It can turn on translation of the protein only c. It can turn off gene expression at the transcription level only d. It can turn on translation, turn on transcription, or turn off a gene 160.

What effect on the cell in general happens when epinephrine binds to a cell

receptor? a. Gene transcription is turned on. b. There is a change in enzyme activity in the cell. c. Translation of a protein is initiated. d. Calcium influx into the cell takes place.

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161.

What is the major activity of a G protein-coupled receptor protein in

prokaryotes? a. It regulates cell division b. It involves cell to cell communication between intracellular organisms c. It regulates cell metabolism d. It is not found in prokaryotes 162.

Which aspect of the cytoskeleton participates in cytokinesis, or the

division of cells into two separate daughter cells? a. Myosin filaments b. Microtubules c. Microfilaments d. Intermediate tubules 163.

Which type of filament engages in cytoplasmic streaming in the cell?

a. Microtubules b. Myosin filaments c. Intermediate filaments d. Microfilaments 164.

Which type of cell filament in amoeba are responsible for cell movement

as it changes shape in certain directions? a. Microfilaments b. Myosin filaments c. Microtubules d. Intermediate filaments 165.

What type of filament in the cell is most responsible for maintaining the

cell shape? a. Microfilaments b. Myosin filaments c. Microtubules d. Intermediate filaments

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166.

Which type of filament participates in the movement of flagella?

a. Microtubules b. Microfilaments c. Intermediate filaments d. Myosin filaments 167.

What structure can be considered a microtubule organizing center?

a. Nucleolus b. Golgi apparatus c. Smooth endoplasmic reticulum d. Centrosome 168.

Which cell structure participates in the intake of vesicles because of

endocytosis? a. Microtubules b. Microfilaments c. Intermediate filaments d. Myosin filaments 169.

Which cytoskeleton structure is considered the thickest?

a. Actin filaments b. Intermediate filaments c. Microtubules d. Microfilaments 170.

What protein interacts with actin in order to sustain muscle contraction?

a. Tubulin alpha b. Tubulin beta c. Autoclampin d. Myosin

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171.

Which protein cinches off in the process where two daughter cells are

separate from one another? a. Myosin b. Actin c. Tubulin Alpha d. Tubulin Beta 172.

When referring to a muscle cell, what is a single muscle cell called?

a. Muscle fiber b. Myofibril c. Sarcomere d. Actinomycin complex 173.

When referring to a muscle cell, what is a single contractile unit called?

a. Muscle fiber b. Myofibril c. Sarcomere d. Actinomycin complex 174.

What protein acts like a spring to keep myosin sections linear and

organized? a. Nebulin b. Autoclampin c. Titin d. Actinomycin 175.

What part of the sarcomere does not disappear but becomes more

prominent during muscle contraction? a. I band b. H zone c. Z disc d. A band

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176.

What is the middle of the sarcomere called, where the myosin segments

reverse in polarity? a. Z disc b. M line c. H band d. A line 177.

Which ion is especially important in the contraction of the muscle fibers?

a. Calcium b. Potassium c. Sodium d. Phosphate 178.

What part of troponin and tropomyosin binds directly to calcium in order

for the muscle to contract? a. Troponin I b. Troponin C c. Tropomyosin d. Troponin T 179.

What ion gets added to myosin in non-muscle cells in order to allow for

muscle contraction? a. Calcium b. Sodium c. Phosphate d. Potassium 180.

Which ion gets attached to calmodulin in non-muscle cells in order for the

cell to contract? a. Calcium b. Sodium c. Phosphate d. Potassium

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181.

What molecule is most associated with cell migration?

a. Tubulin b. Actin c. Myosin d. Keratin 182.

What type of cell has a centrosome?

a. Bacteria b. Fungi c. Animals d. Plants 183.

Which type of microtubule binds to chromosomes in order to pull the

chromosomes apart during mitosis? a. Beta microtubules b. Astral microtubules c. Polar microtubules d. Kinetochore microtubules 184.

Which type of filament attaches the cell to desmosomes and

hemidesmosomes? a. Microfilaments b. Intermediate filaments c. Microtubules d. Actin filaments 185.

How many tubules together form a cilium or flagellum?

a. Ten b. Fourteen c. Eighteen d. Twenty

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186.

What is least likely to participate in the movement of a cilium or

flagellum? a. Dynein b. Nexin c. Nebulin d. Centriole 187.

What is the mitotic spindle made out of?

a. Chromosomes b. Centrosomes c. Nuclear envelope d. Microfilaments 188.

What phase of the cell cycle involves the making of the centrioles and

centrosomes? a. G1 b. S c. G2 d. M 189.

In which phase of the cell cycle do new proteins and mRNA get produced?

a. G1 b. S c. G2 d. M 190.

What type of cell is almost always going to be in the G0 phase of the cell

cycle? a. Neuron b. Epithelial cell c. Fibroblast d. Immune cell

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191.

During which phase of the cell cycle is the karyotype most visible?

a. G1 phase b. S phase c. G2 phase d. M phase 192.

A new, dividing cell starts the cell cycle in which phase?

a. G0 phase b. S phase c. G1 phase d. M phase 193.

After which phase of the cell cycle is the cell committed to cell division?

a. G0 phase b. G1 phase c. S phase d. G2 phase 194.

During which phase of mitosis does a checkpoint generally occur?

a. Prophase b. Metaphase c. Anaphase d. Telophase 195.

What happens when the cyclin-dependent kinase binds to the G1/S cyclin?

a. Proteins that start the S phase are activated b. Proteins that inhibit the S phase are activated c. Proteins that start the S phase are inactivated d. Proteins that inhibit the S phase are inactivated

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196.

What is the main function of anaphase-promoting complex/cyclosome or

APC/C in the cell? a. It causes the sister chromatids to separate b. It triggers the activity of RNA polymerase in the cell c. It triggers cytokinesis d. It stops the process of mitosis 197.

What would potentially happen if p53 is deficient or missing in a cell?

a. There is increased cellular apoptosis b. DNA repair is hyperactive c. The G0 phase will not occur d. There can be cancerous changes 198.

What is the longest phase involved in mitosis?

a. Prophase b. Anaphase c. Metaphase d. Telophase 199.

When does recombination occur in the process of meiosis?

a. Prophase I b. Anaphase I c. Prophase II d. Metaphase II 200. When in meiosis I does a plate develop, in which the chromosomes line up on either side? a. Prophase b. Prometaphase c. Metaphase d. Anaphase

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ANSWERS TO QUIZ ANSWERS TO CHAPTER ONE 1. Answer: c. Without photosynthesis by plant activity, which has oxygen as a byproduct or waste product of this process, there would be no oxygen on earth. 2. Answer: b. The specific heat of water is one calorie per gram per degree Celsius. This is much higher than the specific heat of similar substances, making it good for temperature regulation in living things. 3. Answer: a. When looking at the lattice energy of an ion, the energy will decrease with increased size and increase with increased charge on the ion. 4. Answer: b. Each of these is a suffix used to describe an anion in written form; however, the suffix -ous is used to describe certain atoms that are cations, such as ferrous, which is the cation in ferrous sulfate. 5. Answer: a. Van der Waals forces are weak forces between atoms. These are the weakest of the bonds between atoms and can be intermolecular. 6. Answer: b. While we think of life as carbon-based, the majority of human life by weight is actually oxygen, followed by carbon and the others. 7. Answer: a. Lactose is a disaccharide, although the rest are considered polysaccharides. Disaccharides are two-sugar compounds, while polysaccharides consist of many sugars. 8. Answer: c. The cholesterol molecule is a four-ring lipid molecule, made from a fatty acid that bonds in a specific way to make a ring structure. 9. Answer: a. An oxidation reaction happens alongside a reduction reaction. In an oxidation reaction, there is one atom that gains electron and one atom that loses an electron, with the electrons being transferred from one atom to another.

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10. Answer: b. A dehydration reaction or condensation reaction is one in which water is removed from a molecule in the reaction, usually creating a linkage between two atoms in the molecule.

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ANSWERS TO CHAPTER TWO 1. Answer: a. All cell types have DNA, membrane, ribosomes, and cytoplasm. Prokaryotes, however, do not have a nucleus. These are only found in eukaryotic cells. 2. Answer: d. The cell membrane is the innermost layer, with the cell wall, capsule, and pili being outside of this layer. 3. Answer: a. The smooth endoplasmic reticulum does not contain ribosomes so, rather than making proteins as is seen in rough endoplasmic reticulum, it makes lipids. 4. Answer: d. The Golgi apparatus is responsible for sorting and packaging the different substances made by a given cell. The structures act as the “post offices” of the cell. 5. Answer: d. The centrosome has two centrioles as part of it. The centrioles are where the cell’s microtubules ultimately are fabricated from. 6. Answer: a. The animal cell will have a centrosome, which is not seen in a plant cell. On the other hand, chloroplasts, central vacuoles, and cell walls are seen in plant cells but not in animal cells. 7. Answer: a. Connective tissue is found in all areas of the body and is supportive, providing structure to other tissue types. 8. Answer: b. Epithelial tissue will line body cavities or overlie organs. It also is the major tissue to form glands. 9. Answer: d. Elastic fibers can distend up to 150 times their original length, making them able to distend in tissues that need this, such as skin and lung tissue. 10. Answer: c. Gap junctions connect myocardial cells, which coordinate their movements across a given area of the heart by sending molecular and electrical signals from one cell to another.

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ANSWERS TO CHAPTER THREE 1. Answer: a. Almost all tight junctions exist in epithelial tissue. Their main function is to act as barriers to diffusion across the cells. They form watertight barriers between epithelial and endothelial cells. 2. Answer: c. Tight junctions are nearly impermeable to anything, which is why they are used for things like sealing the endothelium of blood vessels and the epithelium of the GI tract. Their lack of impermeability can lead to things like leaky gut syndrome. 3. Answer: a. The kidneys and GI tract have relatively permeable tight junctions, whereas in the brain, retina, bladder, and skin, the tight junctions are impermeable to most things. 4. Answer: c. The desmosomes are found in tissues that are under stress of some kind, particularly mechanical stress. The brain does not experience this type of mechanical stress so they will not use these types of cell adhesions. 5. Answer: c. Hemidesmosomes are similar to desmosomes in appearance but use integrin proteins in order to connect a cell to the basement membrane. 6. Answer: d. There are many types of collagen; however, type VII collagen is most associated with the formation of the basement membrane. 7. Answer: d. Collagen is laid out as a triple helix; it is laid out in long, thin strands wrapped around each other. 8. Answer: b. Collagen fibers are extremely strong so that their main purpose in connective tissue is to provide tensile strength in the tissue. 9. Answer: b. Gap junctions are extremely similar to plasmodesmata in plant cells. Both are able to allow for communication between the neighboring cells. 10. Answer: a. These plasmodesmata are direct channels between cells so that the small molecules get between the cells via simple diffusion.

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ANSWERS TO CHAPTER FOUR 1. Answer: b. Each of these is a part of the triglyceride molecule, except for a carboxylic acid portion. It is basically three fatty acids connected to glycerol via an ester bond. 2. Answer: d. The phospholipid is very similar to the triglyceride molecule; however, instead of three fatty acids, it has two fatty acids and a phosphate group in place of the third fatty acid moiety seen in the triglyceride molecule. 3. Answer: c. Each of these is associated with fatty acid synthesis except for muscle tissue. In each of the listed areas, fatty acids can be made after acetyl CoA is made through the glycolytic process from glucose in the cytoplasm. 4. Answer: b. Palmitic acid is a 16-carbon fatty acid that is the endpoint of fatty acid synthesis with fatty acid synthase. It takes other reactions to lengthen this fatty acid or to desaturate it. 5. Answer: a. Glycolipids are only found on the outside of the cell membrane. They have their carbohydrate portion sticking out from the cell. 6. Answer: c. Peripheral proteins lie on the outer surface of the cell. They are hydrophilic in general and can be isolated without necessarily disrupting the cell membrane. 7. Answer: d. The outer part of a cell is called the glycocalyx, because it has carbohydrates attached to the protein molecules, which can be transmembrane proteins or surface proteins. 8. Answer: a. Transporter proteins transport ions and small molecules across the cell membrane because otherwise the cell membrane would be more impermeable to these types of molecules. 9. Answer: c. Membrane receptor proteins allow for chemical signaling both inside and outside of the cell. 10. Answer: b. Integral monotopic proteins do not pass all the way through the membrane; however, transmembrane proteins can pass through the cell membrane bilayer several times.

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ANSWERS TO CHAPTER FIVE 1. Answer: d. In any system, including biological systems, the act of osmosis happens to solvents only. In biological systems, the solvent is always water. 2. Answer: a. Lipids are hydrophobic; therefore, they cross the cell membrane easily. Small gaseous molecules are also permeable across the membrane. Glucose, amino acids, and ions like sodium are not able to cross the membrane without assistance. 3. Answer: b. The driving force behind simple diffusion is the concentration gradient. The substance will go from a high concentration to a low concentration, regardless of the type of solute. 4. Answer: a. Oxygen can pass through the membrane without the use of a channel of any kind. This means that it can pass via simple diffusion. The others involve active transport or facilitated diffusion because ion channels are necessary to allow these to get through the nonpolar membrane. 5. Answer: c. The P-pump is the main category of pump that belongs to the class of pumps known as sodium-potassium ATPase pumps. 6. Answer: a. The V-pump will only pump hydrogen ions across the membranes of vacuoles, endosomes, and lysosomes, allowing for the inside of the structures to have a lower pH for the function of enzymes within them. 7. Answer: c. With an antiporter system, the energy is gotten from the electrochemical gradient produced by sodium. Sodium diffuses back into the cell, while calcium is pumped out of the cell in this process. 8. Answer: a. The glucose-sodium transport is a symporter mechanism in which the sodium and glucose both get transported in the same direction. 9. Answer: b. The nerve cell depolarizes when the voltage-gated sodium channels open up and allow sodium to enter the cell. 10. Answer: c. There are voltage-gated potassium channels that allow potassium to leave the cell so that it becomes more electronegative again. Once this has occurred, the channels close and the sodium-potassium ATPase pump reestablishes the resting potential.

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ANSWERS TO CHAPTER SIX 1. Answer: a. The primary structure of a protein is determined by the order of amino acids, which specifically depends on the genetic code that encodes for the protein. 2. Answer: d. While the term “protein” defines any of these, it is the amino acid that is considered the smallest subunit of these structures. 3. Answer: a. DNA will only code for peptides or proteins. It can code for proteins that make the other two substances but does not encode directly for other substances. 4. Answer: b. It is estimated that there are about 20,000 genes in the human genome, although this number is continually being downsized as more information comes out about coding versus noncoding genetic material. 5. Answer: b. The exon is the part of the messenger RNA molecule that remains after splicing in order to make the protein molecule through the translation process. The intron is the part that gets spliced out of the precursor molecule. 6. Answer: c. Each of these is something that happens in the cell to DNA, RNA, and proteins; however, the actual process that starts with messenger RNA and makes protein or polypeptides is called translation. 7. Answer: d. Only the activation energy of the reaction is changed. The total change in energy between substrate and end-product will remain the same and the reaction must be favorable to begin with. 8. Answer: b. The transition state is the unstable state that marks the transition between the substrate and end-product. This energy level is reduced in enzymatic reaction so the reaction happens more quickly and efficiently. 9. Answer: b. This is an immunoassay that is similar to the ELISA test but is harder to do and requires separation of the antibodies with gel electrophoresis in order to do the test. 10. Answer: d. Proteins in gel electrophoresis are separated in the system based on their size and electrical charge.

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ANSWERS TO CHAPTER SEVEN 1. Answer: a. The nucleoside takes on a phosphate group in order to become a nucleotide. 2. Answer: d. In the DNA molecule, there is hydrogen bonding. The adenine molecule forms a hydrogen bond with thymine in all cases. 3. Answer: a. The histone proteins are the smallest, followed by the nucleosome, solenoid, and chromosome, in order of larger size. 4. Answer: d. A nucleosome consists of an octet of histone proteins that have DNA wrapped around them. 5. Answer: a. In the mRNA molecule, the introns are spliced out and the exons remain as part of the complete, finished molecule. It gets a cap and a tail as well. 6. Answer: c. The transcript is made from messenger RNA and is the strand that is made during the transcription process. 7. Answer: c. Ribosomal RNA gets made and assembled in the nucleolus, where it later goes to the ribosomes in order to participate in the translation process. 8. Answer: d. tRNA or transfer RNA has a covalent linkage to an amino acid so that it can transfer the amino acid to a peptide chain in the making of proteins. 9. Answer: a. The DNA helicase enzyme separates the two DNA strands and unwinds them so that a new strand can be added in the process of DNA replication. 10. Answer: b. DNA ligase is the enzyme that joins the different Okazaki fragments after the DNA is completely replicated on the lagging strand.

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ANSWERS TO CHAPTER EIGHT 1. Answer: b. Most prokaryotic genes are circular without a nucleus, although plasmids can exist. 2. Answer: a. The prokaryotic genes are usually negatively supercoiled, against the grain of the double helix. There are no histone or non-histone proteins involved. 3. Answer: a. The promotor sequence binds selectively to the RNA polymerase enzyme so that transcription can take place under the right circumstances. 4. Answer: b. These parts of a eukaryotic cell all contain individual DNA molecules. The eukaryotic cell does not have a nucleoid so there is no “nucleoid DNA” in a eukaryotic cell. 5. Answer: d. Luteinizing hormone is protein-based so it does not enter the nucleus. The others are steroid hormones that can enter the nucleus and can act as transcription factors. 6. Answer: a. The operator contains a sequence that can attach to an inhibitory protein in order to stop the production of the trp gene sequence. 7. Answer: d. Histone acetylation will decrease the binding activity of histone proteins to the DNA molecule so that transcription of the DNA sequence can happen. 8. Answer: a. In genomic printing, certain DNA segments get methylated so that DNA gets distinguished as being maternal or paternal in origin. Some genes, as a result, get expressed while others do not. 9. Answer: a. Most of the time, a mutation has no effect on the cell. Less commonly, some of the other effects can be seen, which are more dangerous complications for the cell. 10. Answer: c. A point mutation involves simply the substitution of one base for another. In sickle cell disease, glutamine is substituted for valine, leading to an abnormal hemoglobin protein.

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ANSWERS TO CHAPTER NINE 1. Answer: b. The reactions that occur in the process of chemoorganotrophy is oxidation, which is the taking of an organic substance, progressively oxidizing it, and turning it into a more oxidized substance, such as into CO2 and water. 2. Answer: a. In this process, glucose and other organic chemicals have electrons to donate. They donate them to the final electron acceptor in aerobic respiration to create energy. In this case, the final electron acceptor is oxygen. 3. Answer: d. The major difference is that the Krebs cycle is not used in fermentation but it is used in anaerobic metabolism. 4. Answer: c. All glycolysis in the cell takes place in the cytoplasm. This is true for both prokaryotic cells and eukaryotic cells. 5. Answer: a. The first phase of glycolysis ends with two molecules of glyceraldehyde-3-phosphate, using up two ATP molecules in the process. 6. Answer: d. The molecule gets rearranged with any type of isomerase molecule. 7. Answer: d. Anaerobic metabolism cannot take place if cytochrome oxidase is unavailable to pass electrons to oxygen. 8. Answer: a. It is electrons that get transferred through the electron transport system so that hydrogen ions get pumped out of the cell, creating the proton motive force and a pH gradient. 9. Answer: b. The light-dependent reactions will make the high-energy products, which are ATP and NADPH, which are later used in the light-independent reactions. 10. Answer: a. There is ATP, NADPH, and CO2 that enter the cycle, which glyceraldehyde-3-phosphate used as its end product. This goes on outside of the cycle to make glucose.

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ANSWERS TO CHAPTER TEN 1. Answer: a. Ribosomes are not one of the membrane-bound organelles that will participate in vesicular budding. This budding only happens when an organelle is membrane-bound. 2. Answer: d. Because vesicles are most likely to bud off of a membrane, they are actually surrounded by these membranes, making them glycerophospholipids, made in the endoplasmic reticulum. 3. Answer: a. Each of these is a typical vesicle coat protein except for dynamin, which is used to pinch off clathrin-coated vesicles. 4. Answer: d. These accidental proteins are sent back to the endoplasmic reticulum, where they belong. 5. Answer: d. There are endosomal compartments that will make the vesicles necessary for neurotransmitter release. The neurotransmitters are filled after the vesicles are made. 6. Answer: a. Calcium is increased in concentration in the presynaptic cell, causing the release of neurotransmitters into the synaptic cleft. 7. Answer: a. Synapsin I gets a phosphate group attached to it by ATP so it has a decreased affinity for actin. This allows the vesicle to move toward the active zone in the presynaptic area. 8. Answer: b. It is in the active zone where the neurotransmitters get released by the presynaptic nerve cell into the synaptic cleft. 9. Answer: b. The first place the vesicles go in the endocytic pathway is the early endosome, where they are uncoated and start the sorting process. 10. Answer: d. There are other proteins but clathrin is the main protein that forms a pit so the membrane is drawn into the vesicle in the process of endocytosis.

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ANSWERS TO CHAPTER ELEVEN 1. Answer: c. Neurotransmitters are associated with paracrine cell signaling, which involves connection between nearby cells that does not involve direct cell to cell contact. Neurotransmitters mediate this sort of thing. 2. Answer: d. Endocrine signaling happens over very large distances in the organism—often spanning the entire organism. 3. Answer: a. The main effect of the binding of an intracellular ligand is the induction of transcription of DNA. There is gene regulation so that certain genes get turned on. 4. Answer: d. Plasmodesmata involves cell to cell signaling between two different cells that are next to each other in plant organisms. 5. Answer: a. Threonine, serine, and tyrosine have a hydroxyl group, allowing for these to be phosphorylated. The glutamate amino acid does not have this hydroxyl group so it cannot be phosphorylated. 6. Answer: d. The MAP kinase signaling pathway is a growth factor pathway that involves the promotion of cell division. When overactive, the pathway can lead to cancerous changes in the cell. 7. Answer: b. Each of these is a typical second messenger except for ATP, which does not normally act specifically as a second messenger inside a cell. 8. Answer: a. When phosphodiesterase acts on cyclic AMP, it becomes AMP, which is completely inactive. In that way, the enzyme deactivates cyclic AMP. 9. Answer: c. This is also referred to as a seven-pass receptor because it passes through the membrane seven times as part of its structure. 10. Answer: a. When the ligand gets bound, there is a conformational change that allows GTP to replace GDP on the G protein.

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ANSWERS TO CHAPTER TWELVE 1. Answer: b. The cytoskeleton is a highway for molecular transport and holds ribosomes in place in prokaryotic cells. They do not have organelles and it does not participate in cell to cell communication. 2. Answer: a. Actin is considered the thinnest filaments because it takes two of these wound together to make the very thin microfilaments. 3. Answer: b. The lamin protein is found exclusively in the nucleus, where it is responsible for holding up the nuclear envelope. 4. Answer: c. It is the microtubules that participate in the separation of sister chromatids in cells that are actively dividing. 5. Answer: a. The microfilaments of the cell do all of these things but they do not draw chromosomes apart in the process of cell division. 6. Answer: a. Two actin filament strands wind together in order to make microfilaments, which are the thinnest filaments—only six to seven nanometers in diameter. 7. Answer: b. I bands are light bands that are seen on electron microscope of muscle cells. They contain only actin filaments. 8. Answer: a. The Z bands are physically seen as the structures that are at the ends of the sarcomere. These can be seen as jagged lines across the myofibril on electron microscopy. 9. Answer: c. The hydrolysis of ATP must take place in order to drive the interaction between actin and myosin in the act of contracting the muscle. 10. Answer: d. Each of these is directly linked to the actin molecule but the titin molecule isn’t associated to actin but is instead associated with myosin.

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ANSWERS TO CHAPTER THIRTEEN 1. Answer: a. During the S phase, DNA polymerase is active in the synthesis of new DNA. 2. Answer: d. Interphase involves the G1 phase, S phase, and G2 phase. The M phase is not a part of this process as it involves mitosis or the “mitotic phase”. 3. Answer: c. In the G2 phase, the cytoskeleton gets broken down and its components get ready for the process of mitosis. 4. Answer: d. G0 is a quiescent phase, in which the cell does not participate at all in the cell division process. The rest of the phases are participatory in the cell division process in some way. 5. Answer: b. In the late G1 phase, if there is too much of the protein made in the tumor repressor gene p53, the cell cycle does not continue and the process of cell apoptosis takes place. 6. Answer: a. Cells undergoing uncontrolled cell growth will participate in the M phase more commonly and to a greater degree. 7. Answer: d. Maturation-promoting factor will trigger a cell to enter the M phase of the cell cycle. 8. Answer: c. Its main job is to break down the nuclear envelope so that mitosis can proceed. 9. Answer: c. The sister chromatids get pulled apart in mitosis during the anaphase part of the process. They then are called daughter chromosomes. 10. Answer: b. During telophase, the nuclear envelope gets rebuilt in order to have the daughter chromosomes encapsulated again.

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ANSWERS TO COURSE QUESTIONS 1. Answer: a. Cations are positively charged because they have lost an electron. On the other hand, anions have gained an electron and are negatively charged. 2. Answer: c. Each of these is true of water except that it has a high surface tension and not a low surface tension. This means that it will take increased force to break a liquid water surface. 3. Answer: d. The lattice energy is another way to describe the bond strength of an ionic molecule. A high bond strength means that the energy it takes for the molecule to form a solid lattice is favorable. 4. Answer: d. Covalent compounds can be seen in either gases, liquids, or solids at normal room temperature and pressure. 5. Answer: c. Ionic compounds can be seen only in solid form at room temperature and pressure. They have high melting points so it would be rare to see them in liquid or gaseous form. Remember that, while ionic compounds easily dissolve in water under these conditions but, without water, they would be solidified. 6. Answer: d. Each of these statements is true of covalent molecules and covalent bonds; however, they have low boiling points as well as low melting points. 7. Answer: d. Sugars and carbohydrates are made only from carbon, oxygen, and hydrogen. There is no nitrogen in sugars. 8. Answer: c. Ribose is a five-carbon sugar used in the making of the RNA molecule. The rest are six-carbon sugars. 9. Answer: b. Each of these is a disaccharide except for galactose, which is a sixcarbon monosaccharide sugar. 10. Answer: b. Each of these is considered part of a nucleotide except for amino acids, which are part of a protein molecule and not a nucleic acid. 11. Answer: d. Hydrogen bonds between the nitrogenous bases make the DNA double stranded.

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12. Answer: c. Adenosine triphosphate or ATP is a high-energy molecule that gives of a great deal of energy when the phosphate linkage is broken to make ADP or adenosine diphosphate. 13. Answer: d. Enzymes can do each of these things but it does not change the starting or finishing energy levels of a given reaction. Instead, it changes the energy of activation. 14. Answer: c. Plasmids contain DNA within them. This DNA is considered extrachromosomal DNA because it is not part of the regular genome. 15. Answer: a. The cell wall determines the different ways that an organism stains with a gram staining technique. Gram-positive organisms stain positively because they have a thick peptidoglycan wall, which is not seen in gramnegative organisms. 16. Answer: c. Each of these is a way to transfer DNA from one cell to another. True sexual reproduction does not happen in bacteria but they do undergo conjugation, in which one bacterium injects DNA into another via one of their pili. 17. Answer: b. The rough endoplasmic reticulum is the part of the eukaryotic cell that makes proteins. It is continuous with the nuclear envelope in order to allow RNA to pass from the nucleus to the part of the cell that participates in protein synthesis. 18. Answer: a. The peroxisomes contain oxidative molecules that get rid of toxins and waste products within the cell. 19. Answer: c. The process of osmosis applies only to water as it travels from an area of high concentration to an area of low concentration across a semipermeable membrane. 20. Answer: a. The nucleolus is the part of the nucleus that makes ribosomes as one of its major functions. The nucleolus resides within the nucleus of the cell. 21. Answer: b. The mitochondrion is an energy-making part of the cell, essential because it has multiple chemical reactions that participate in the making of ATP energy, turning nutrients into carbon dioxide and water.

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22. Answer: c. The main byproduct of the photosynthetic process, the purpose of which is to make glucose, is oxygen, which is not used by the plant cell but is given off after glucose is synthesized. 23. Answer: b. Each of these is contained within the chloroplast and the mitochondria; however, the thylakoids are just seen in the chloroplasts but not in the mitochondria. 24. Answer: d. Cellulose is what the cell wall of plants are made from. The other substances can be components of other cell walls. 25. Answer: a. Each of these is a signaling method that acts on a specific cell. Only endocrine signaling can act, however, over a long distance within the organism. 26. Answer: c. Epithelial cells have a nerve supply so they are innervated; however, they do not have capillaries that reach up into the tissue so these cells are not vascular. 27. Answer: d. It is the apical side of the epithelium that has microvilli, which extend into the lumen of ducts and body cavities of different types. Not all epithelial cells have microvilli. 28. Answer: c. Gap junctions are connections between cells of the same tissue type to have small molecules pass between the cells. They connect these cells chemically as well as physically. 29. Answer: a. Adipose cells or fat cells are considered connective tissue cells that serve an energy reservoir function in the body. 30. Answer: a. These cells have each of these descriptions; however, they are irregularly arranged so they do not appear striated. 31. Answer: d. The microglia or microglial cells are responsible for clearing out pathogens and cellular debris in the nervous system. 32. Answer: d. Tight junctions allow for paracellular transport, which is the transport of certain molecules and ions between the cells that are semi-fused together with these types of junctions. 33. Answer: b. Each of these represents a protein that is part of making the tight junction, except for elastin, which is a connective tissue protein that is not part of the tight junction. 267

34. Answer: c. The hemidesmosome does not connect a cell to another cell. Instead it connects the cell to connective tissue or to the basement membrane in the tissues. The others directly connect one cell to another. 35. Answer: d. While adherens junctions and desmosomes have the same cadherins proteins, they also have dissimilar proteins such as intermediate filaments, plakophilin, and desmoplakin. 36. Answer: b. Gap junctions are connecting adhesions between two cells that will allow an electrical signal to pass from one cell to its neighboring cell. 37. Answer: a. The gap junction involves two connexons that connect between two cells and allow for chemical and electrical activity to occur from cell to cell. 38. Answer: a. Laminin is the main protein in the basement membrane, forming a lattice network that attaches the cell to the underlying connective tissue. 39. Answer: d. The thymus is a gland so it is not connective tissue. Blood, bone, and fatty tissue are considered types of connective tissue. 40. Answer: c. The main cell seen in connective tissue is the fibroblast, which makes collagen. The other cells are seen less commonly in connective tissue of different types. 41. Answer: b. Type II collagen is the type of collagen seen in cartilage. You need to know that there are different types of collagen and that type I is in normal connective tissue and type II is in cartilage. 42. Answer: a. Cardiac muscle gets its elasticity from the myofibrils and not from the presence of elastin. The skin, lungs, bladder, and arteries all rely on elastin as a major component of the tissue; elastin is necessary to keep these tissues stretchy. 43. Answer: c. Fibrillin-1 gives the elastic fiber its fibrous nature. It combines with elastin to make the elastic fiber more fibrous. 44. Answer: a. Fatty acid synthesis takes molecules in the cytoplasm and makes fatty acids using multiple enzymes called fatty acid synthases. 45. Answer: b. Phospholipids are similar in structure to triglyceride molecules. The main difference is that there are just two fatty acids on the phospholipid

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molecule; there is a phosphate group in place of one of the fatty acids, which is attached to an alcohol group on the glycerol molecule. 46. Answer: b. Aquaporins are, for the most part, unable to pass any other molecule through it except for water, which is rapidly transported across the cell membrane via this mechanism. 47. Answer: c. Plant cells in pure water draw the water into the cells via osmosis, making them turgid. Only in saltwater will the plant cells become flaccid or plasmolyzed. Transpiration is evaporation from the leaves of the plant. 48. Answer: d. While each of these will dissolve in water, sodium chloride has two solutes—sodium and chloride—so that its osmotic pressure will be greater. 49. Answer: c. Filtration happens in the glomerulus of the kidneys, because of the hydrostatic pressure of the cardiovascular system that forces solutes and water through small pores in the glomeruli. 50. Answer: d. The concentration gradient for primary active transport can be downward or upward. It can just as easily go in an upward concentration gradient—from a low to a high concentration across the membrane. 51. Answer: a. The sarcoplasmic reticulum acts to pump and release calcium ions in the muscle cell in order to participate in muscle contraction. There are special P-class pumps that pump calcium into the sarcoplasmic reticulum after they are used for muscle contraction. 52. Answer: d. F-class pumps are located on mitochondria, chloroplasts, and bacterial cell membranes. They make ATP so these are also referred to as ATP synthases. 53. Answer: b. The ABC-class pump is actually a superfamily of pumps that will pump both small ions and molecules across the cell membrane. This is the only classification of pumps that pumps small molecules across the membrane. 54. Answer: a. It is the primary active transport of sodium ions, creating an electrochemical gradient, that causes the secondary transport of other molecules. This is referred to as either a symport or antiport mechanism. 55. Answer: b. Each pass of the sodium-potassium ATPase pump requires just one ATP molecule to be used up. 269

56. Answer: d. With each pass of the sodium-potassium ATPase pump, three molecules of sodium leave the cell and two molecules of potassium enter the cell. 57. Answer: a. While the sodium-potassium ATPase pump does each of these things, it does not affect the pH of the inside or outside of the cell. 58. Answer: d. The polarized cell under normal, resting conditions has a resting membrane potential of – 70 millivolts. 59. Answer: d. All cells have a sodium-potassium ATPase pump. The voltagegated channels that lead to depolarization and repolarization happen only in certain cells. 60. Answer: b. The secondary structure of a protein molecule comes from hydrogen bonding between amino acids, leading to an alpha helix or a beta pleated sheet. 61. Answer: d. The quaternary structure is what is created by a protein when more than one peptide interacts with others within the protein. 62. Answer: c. The tertiary structure of a protein is the three-dimensional shape that is made by several different types of bonds between the R groups of the amino acids. 63. Answer: b. There needs to be three bases or a triplet of bases in order to have enough to encode for specific amino acids (of which there are twenty) plus triplets that stand for starting and stopping the reading process. 64. Answer: d. RNA polymerase is an enzyme that acts on DNA in the making of single-stranded messenger RNA molecules that go on to make proteins. 65. Answer: a. The promotor region is involved in the initiation process of RNA transcription, where the process of reading the gene first begins. 66. Answer: d. The process of translation takes place within the ribosomes of the cell. Transcription, on the other hand, is what happens in the nucleus of the cell. 67. Answer: c. While there are just 20,000 different genes in the genome, there are more than a million unique proteins in the human proteome. 68. Answer: a. Most of these processes listed are reversible except for peptide cleavage or proteolysis, which tends to be an irreversible process. 270

69. Answer: d. In an enzyme system, each of these things happens; however, the enzyme is not consumed and will return to its natural state so that another reaction can occur. 70. Answer: a. Enzymes are all catalysts but not all catalysts are enzymes. Both help a reaction happen faster but enzymes are seen in biological processes. Catalysts can be chemical substances. 71. Answer: d. The protein does not need to be separated from other proteins in order to do the test. The protein is selected from the other proteins in the sample because it is selectively bound to the antibody that is affixed to a plate. 72. Answer: a. There is hydrogen bonding in the DNA molecule that causes cytosine to bond with guanine. 73. Answer: b. Uracil takes the place of thymine in the RNA molecule so that there is no thymine in RNA but only uracil. There is no uracil in the DNA molecule. 74. Answer: c. The main purpose of histone proteins is to condense DNA into chromatin. Without histones, DNA would be one long strand that would stretch too long to fit in the nucleus. 75. Answer: b. DNA is found in each of these structures; however, it is not found in the ribosomes of the cell. Because chloroplasts and mitochondria were probably evolutionarily derived from bacterial organisms, they do contain DNA. 76. Answer: c. In general, the structure of DNA makes DNA more structurally stable than RNA. RNA is generally single-stranded, contains ribose instead of deoxyribose, and has shorter strands than DNA. 77. Answer: d. A string of uracils together cause weak linkage in the connection between the DNA and RNA molecule, which causes the RNA molecule to slip off the DNA, freeing itself from RNA polymerase. 78. Answer: d. The template strand is the strand that is the original DNA strand that gets made into the transcript. The coding strand is the opposite DNA strand to the template strand; it is also made of DNA. 79. Answer: b. The DNA template strand gets read from the three-prime end to the five-prime end, adding RNA bases one at a time. 271

80.Answer: a. Adenine is added in sequence to make the poly-A tail on messenger RNA. It protects the messenger RNA so that it can leave the nucleus for transcription. 81. Answer: a. Ribosomal RNA is more than just a structural RNA. It has enzymatic properties that catalyzes the connection between the amino acid and the messenger RNA. 82. Answer: b. Only viruses can have their genome be based on RNA, which can be double-stranded or single-stranded RNA. 83. Answer: d. DNA polymerase participates in elongation of the DNA strand during the process of DNA replication. 84. Answer: d. Telomerase forms telomers, which are the protective caps added to the ends of the DNA molecule in order to protect the ends and keep them from binding to one another. 85. Answer: c. Topoisomerase and DNA gyrase are the same enzymes necessary for unwinding and rewinding DNA in the replication process. 86. Answer: b. The main effect of UV light on the structure of DNA is the formation of pyrimidine dimers, where two dimers connect covalently to one another on the DNA molecule. 87. Answer: d. Factor for inversion stimulation most participates in the regulation of bacterial DNA sequences. Remember that bacterial DNA does not contain histone proteins; topoisomerase I and DNA gyrase both help to supercoil the bacterial genome. 88. Answer: b. The DNA projects out of the nucleoid, where it transcribes and translates at the same time associated with ribosomes located in the cytoplasm. 89. Answer: d. Lactose is the main inhibitory molecule. It binds to the regulator regions when lactose is present. This prevents the transcription of molecules that would normally cause lactose uptake and metabolism, which would be used for food. If lactose is present, these enzymes are not necessary. 90. Answer: c. Cis-acting genes are genes that are located adjacent to one another. There is usually one promotor site for the genes that are cis-acting genes.

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91. Answer: a. An enhancer sequence helps a gene or gene sequence get transcribed to a higher degree of efficiency. 92. Answer: c. The transcription activator has two parts. It binds to specific DNA sequences and activates gene transcription by also interacting with transcription machinery. 93. Answer: c. In this case, tryptophan is a corepressor that binds to the trp repressor gene so that the transcription of the trp operon can be blocked. 94. Answer: d. In the attenuation process, transcription can happen but a short, non-functional mRNA molecule is made and the transcription process does not complete itself. 95. Answer: b. Eukaryotic repressor proteins will bind to regulator sites, acting in direct opposition to eukaryotic activator proteins. 96. Answer: b. Transposable DNA is found in prokaryotes and eukaryotes in large numbers, making up about half of all human DNA. 97. Answer: c. Reverse transcription is when RNA gets transcribed into DNA. It happens in virus particles as well as in other cells that have class 1 transposable DNA. 98. Answer: d. The majority of the time, the effect of a transposon is silent and it causes no specific human disease whatsoever. 99. Answer: b. The mutation is a point mutation that is nonconservative, meaning that the protein does not behave the same way as the original protein. This makes it a nonconservative missense point mutation. 100.

Answer: a. The deletion of a single base pair is the most dangerous because

it results in a frameshift mutation so that the rest of the DNA message is completely garbled and makes no sense. 101.

Answer: d. Very rarely, DNA polymerase can put in the wrong base pair,

resulting in a mutation. This is rare because there are proofreading enzymes that will fix the error before the next replication. 102.

Answer: d. There are direct pathways that turn amino acids, fatty acids,

and sugars into energy and oxidized substances. In general, this does not occur with nucleic acids unless they are broken down into sugars or other substances. 273

103.

Answer: b. Because energy is required to start the process of glycolysis,

only two ATP molecules are generated per glucose molecule in the process. 104.

Answer: c. Each of these names is synonymous with the other; however,

the Cori cycle is something completely different and involves the conversion of lactic acid into glucose by the liver after anaerobic metabolism. 105.

Answer: c. About 32 molecules of ATP are made per molecule of glucose

when all parts of aerobic respiration are taken into account. 106.

Answer: a. Each of these can be a final common electron acceptor in

anaerobic respiration. Because the process is anaerobic, however, the process does not include oxygen. 107.

Answer: a. All kinase enzymes cause the phosphorylation of a molecule.

108.

Answer: d. Hexokinase is an enzyme that turns the glucose or hexose

molecule into glucose-6-phosphate. 109.

Answer: b. Because this is a kinase, it takes fructose-6-phosphate, and

turns it into fructose-1,6 bisphosphate, which has two phosphate molecules attached to it. 110.

Answer: c. ATP provides the phosphate to the molecules in the glycolysis

pathway, turning it into ADP, which is an energy-requiring step. 111.

Answer: c. Both ATP and NADH are produced by the second half of the

glycolysis pathway. These make up for the lost ATP molecules in the first half of glycolysis, yielding two extra ATP molecules plus 2 NADH molecules—both of which are high energy. 112.

Answer: a. The end-product of glycolysis is pyruvate. Two molecules of

pyruvate are made for every molecule of glucose that begins the process. 113.

Answer: c. Denitrifying bacteria will use nitrate and nitrite as final electron

acceptors to yield the end product, which is nitrogen gas. 114.

Answer: b. The protons get pumped into the intramembranous space in

the mitochondria, creating an electrochemical gradient as well as a pH gradient. 115.

Answer: d. The enzyme ATP synthase is directly tied to the leakage of

hydrogen ions across the mitochondrial or cytoplasmic membrane.

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116.

Answer: c. The source of energy for oxidative phosphorylation is the

proton motive force, which is generated across a membrane. 117.

Answer: c. ATP synthase is the only one of these proteins that does not

participate within the electron transport system. 118.

Answer: d. Three NADH molecules are made with each turn of the Krebs

cycle, along with one molecule of FADH2 and one molecule of ATP. 119.

Answer: a. It is pyruvate that gets transported from the cytoplasm to the

mitochondrion in order to eventually get transformed into what participates in the Krebs cycle. 120.

Answer: b. Acetyl CoA is released in the oxidation of fatty acids. This

process is also referred to as beta-oxidation. 121.

Answer: a. Normally, beta oxidation occurs but, in branched-chain fatty

acids, alpha oxidation may occur as a minor metabolic pathway. 122.

Answer: c. Glucose is not necessary for photosynthesis; however, it is an

end-product of photosynthesis and not a starting substrate. 123.

Answer: d. One particle of light is referred to as a photon. This is what

gets absorbed in order to have photosynthesis take place. 124.

Answer: d. It takes six turns of the cycle, in which one CO2 molecule is

built into a six-carbon sugar, such as glucose. Three actual turns make glyceraldehyde-3-phosphate, which is the cycle’s endpoint. 125.

Answer: c. In photosynthesis, water and carbon dioxide are reactants and

glyceraldehyde-3-phosphate and oxygen are end-products of the reactions. 126.

Answer: b. Cyanobacteria use each of these things as part of

photosynthesis but they do not make use of chloroplasts because these are prokaryotic cells that do not have chloroplasts. 127.

Answer: a. The light-independent reactions take place in the stroma of the

chloroplasts in eukaryotic cells. 128.

Answer: c. Thylakoids are stacked membranes but they are not a maze of

membranes. They contain chlorophyll and the outside of them is called the stroma.

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129.

Answer: a. The photosystem has antenna molecules attached to

chlorophyll pigments in what’s called a reaction center. It does not include ATP synthase, which is a separate component that relies on a proton gradient. 130.

Answer: b. Similar to what’s seen in mitochondria, it is the proton gradient

that drives the ATP synthase in the chloroplast. 131.

Answer: b. The transport of vesicles in the eukaryotic cell is from the

endoplasmic reticulum to the cis Golgi to the medial Golgi, and to the trans Golgi. The reverse can happen rarely if the original transport was in error. This would mean that the errant proteins are returned back to the endoplasmic reticulum. 132.

Answer: c. The clathrin coating protein on vesicles allow the vesicle to get

from the Golgi apparatus to the plasma membrane. 133.

Answer: b. Clathrin requires dynamin and GTP energy in order to pinch

off a vesicle. COPI and COPII do not require anything in order to do this process. 134.

Answer: b. It takes a low pH and high calcium concentration milieu in

order to aggregate proteins in the vesicles so that there can be high concentrations of these proteins inside the vesicle. When discharged, though, the opposite situation occurs so that there is release of the proteins into whatever space they are discharged into. 135.

Answer: a. It is a t-SNARE protein on the target membrane that docks

with the v-SNARE protein on the vesicle. When these proteins match, there is attachment and ultimately the release of the vesicle outside of the target membrane. 136.

Answer: c. The SNARE proteins will twist with one another so that the

vesicle can be attached and so that it can be discharged into the target membrane lumen. 137.

Answer: c. Each of these is a SNARE-type protein, which participates in

the connection of synaptic vesicles to the presynaptic cell membrane. The exception is dynamin, which does not participate in this process.

276

138.

Answer: b. VAMPs are vesicle-associated membrane proteins that hold

vesicles in place before they need to be discharged in the nerve cells. They attach the vesicles to the cytoskeleton. 139.

Answer: c. After the empty vesicle is made or recycled, it is filled with

neurotransmitter for eventual release at the time of the action potential. 140.

Answer: d. Actin is the part of the cytoskeleton that attaches vesicles in

nerve cells before they are ready for release into the synaptic cleft. 141.

Answer: c. Synaptophysin has properties that help the presynaptic

membrane open up a pore when the vesicle is ready to be released. 142.

Answer: d. Physophilin and synaptophysin bind together to make the pore

necessary for the vesicle to empty itself of neurotransmitters through the presynaptic cell membrane. 143.

Answer: a. Clathrin-dependent endocytosis is also referred to as receptor-

mediated endocytosis. The others listed are other types of endocytosis. 144.

Answer: c. The act of potocytosis involves the uptake of molecules into

buds and vesicles that just get released into the cytosol of the cell rather than to a lysosome or other organelle. 145.

Answer: a. The LDL-receptor gets recycled. It gets taken up by a vesicle

and is sent back to the exterior of the cell. 146.

Answer: c. Things get increasingly acidic from the exterior of the cell to the

coated vesicle to the early endosome to the late endosome and finally, to the lysosome, which is the most acidic, having a pH of 4.8. 147.

Answer: d. Mucolipidosis II disease is the most serious lysosomal storage

disease because nearly none of the lysosomal enzymes are present due to a genetic defect involving the function of all of these enzymes. 148.

Answer: b. The iron leaves after being bound to an intracellular protein.

The transferrin-receptor complex gets recycled back to the cell surface, where they then dissociate from one another. 149.

Answer: a. Autocrine cell signaling involves a cell making a ligand or signal

for its own receptors. It can have a separate paracrine function as well. 150.

Answer: b. In animal cells, gap junctions connect two cells together to

allow for direct cell to cell communication. 277

151.

Answer: c. Intracellular ligands are usually hydrophobic molecules that

can pass the plasma membrane by themselves. Examples include the sex hormones like estrogen and testosterone. 152.

Answer: b. When the receptor gets activated, tyrosine on the inside of the

cell is able to be phosphorylated. 153.

Answer: c. Norepinephrine is not hydrophobic nor can it pass through the

cell membrane. It therefore needs to bind on the outside of the cell. The rest will bind inside the cell as intracellular ligands. 154.

Answer: b. The ligand located by itself is the most upstream of the events

that occur with the ligand itself binding to the receptor, activating an intracellular signaling molecule, and ultimately doing something like activating a gene. 155.

Answer: b. Calcium is a frequent second messenger in the cell. Its

concentration is increased through ligand-gated calcium channels that increase its concentration in the cell, where it affects the ability of a protein to do its job. 156.

Answer: c. Adenylyl cyclase is an enzyme that catalyzes the conversion of

ATP to cyclic AMP because cyclic AMP is necessary as a second messenger. 157.

Answer: d. Calcium is the second messenger in the contraction of muscle

cells. Calcium concentration is increased so that the activity of the cell is to contract. 158.

Answer: b. Each of these stays as part of the plasma membrane; however,

IP3 is able to enter the cytoplasm in order to continue a signaling cascade. 159.

Answer: d. The making of a protein can be changed through the turning off

of a gene, the turning on of gene transcription, or the turning on of protein translation. 160.

Answer: b. There is a change in enzyme activity so that the activity of

glycogen synthase is turned off and the activity of glycogen phosphorylase gets turned on, making more glucose molecules. 161.

Answer: d. G protein-coupled receptors are not found in prokaryotic cells

but it is found in eukaryotic cells only.

278

162.

Answer: c. The microfilaments are the filaments that participate in the

process of cytokinesis in the cell. This is when a cell becomes two daughter cells after the division of nuclear material. 163.

Answer: d. Microfilaments aid in cytoplasmic streaming, which is the

movement of cell structures and molecules within the cell. 164.

Answer: a. It is the microfilaments that aid in amoeba movements,

allowing them to move in response to certain chemical or physical situations. 165.

Answer: d. It is the intermediate filaments that give the cell its basic shape

by creating a specific cell structure. These are sturdier than other filaments in the cytoskeleton. 166.

Answer: a. The microtubules get together and react to make the flagella of

the cell move. 167.

Answer: d. A centrosome is also called a microtubule organizing center

because microtubules exit this structure. 168.

Answer: b. When microfilaments contract, they draw in vesicles that

contain substance in the act of endocytosis. 169.

Answer: c. Microtubules are tubular and are made from alpha and beta

tubulin. These are the thickest of the different filaments in the cell. 170.

Answer: c. Myosin interacts with actin in order to cause muscles to

contract. Tubulin proteins are used in microtubules and autoclampin participates in actin creation when it assembles. 171.

Answer: b. Actin forms a cinch that pinches off a cell after the nuclear

material has separated so that there can be physical separation of a dividing cell into two cells. 172.

Answer: a. A single contractile cell in muscle tissue is called a muscle fiber.

173.

Answer: c. A sarcomere is what’s referred to when talking about a single

contractile unit. 174.

Answer: c. The titin molecule is large and acts like a spring that keeps the

myosin fragments organized as the muscle contraction occurs. 175.

Answer: d. The A band is the actin-myosin complex. It increases in length

during muscle contraction, allowing the H zone, which is myosin only, and the I band, which is actin only, to come together. 279

176.

Answer: b. The M line is the middle of the sarcomere. It is here when the

myosin segments reverse in their polarity so the sarcomere is symmetric from one side to another. 177.

Answer: a. Calcium is released by the sarcoplasmic reticulum. The

concentration of calcium determines whether or not the muscle contracts. 178.

Answer: b. Troponin C is the polypeptide that binds to calcium in order for

there to be an interaction between troponin and tropomyosin. 179.

Answer: c. There is a part of the myosin molecule that gets phosphorylated

in order to allow for muscle contraction. There is a kinase that performs this process. 180.

Answer: a. Calcium binds to calmodulin in non-muscle cells in order for

the contraction of the cell to occur. 181.

Answer: a. The tubulin is a part of the microtubules that gets built at the

leading edge of the migrating cell. It forms microtubules that adhere to the matrix and help the cell migrate from one place to another. 182.

Answer: c. Animal cells only have centrosomes. The microtubule

organizing center in plants and fungi is the nuclear envelope and not the centrosomes. 183.

Answer: d. The kinetochore microtubules will actually connect to the

chromosomes in order to pull them apart during the process of mitosis. 184.

Answer: b. Intermediate filaments will attach to the desmosomes and

hemidesmosomes outside of the cell in order to provide structure to the cell in relation to other cells near it. 185.

Answer: d. There are eighteen tubules around the structure and a central

doublet for a total of twenty microtubules in a structure that makes up a flagellum or cilium. 186.

Answer: c. Each of these is participatory in the process of making a

flagellum or cilium move. Nebulin, however, is not involved. 187.

Answer: b. The mitotic spindle is made out of a pair of centrosomes that

together form the mitotic spindle during the S phase of interphase. 188.

Answer: b. It is during the S phase that centrioles and centrosomes get

made and duplicated. 280

189.

Answer: a. The G1 phase is biochemically active with a great many nucleic

acids and proteins getting made in the process, even though the cell itself does not change much in appearance. 190.

Answer: a. A neuron is almost always going to be in the G0 phase because,

once it is made, it is quiescent and doesn’t undergo cell division. 191.

Answer: d. In the M phase, the karyotype is most visible. It is generally not

visible under light microscopy in the other phases. 192.

Answer: c. The newly dividing cell starts out the cell cycle in the G1 phase,

where it prepares to divide again. Only nondividing cells go through a G0 phase. 193.

Answer: d. Only after getting through the G2 phase is the cell completely

committed to cell division. It needs to get through the G2 checkpoints. 194.

Answer: b. There is a well-known metaphase checkpoint that makes sure

the microtubules are attached and that the karyotype is aligned before the cell cycle can continue. 195.

Answer: a. Proteins that start the S phase get activated when the G1/S

cyclin binds to the cyclin-dependent kinase. 196.

Answer: a. It causes the sister chromatids to separate by causing the

breakdown of the cohesin protein, which will normally hold the sister chromatids together. 197.

Answer: d. If p53 is deficient, missing, or damaged, there can be cancerous

changes in the cell because mutations get passed on to the next generation. 198.

Answer: a. Prophase takes up over half of the entire mitosis cycle, which

itself is about an hour long. 199.

Answer: a. It is during prophase I that recombination or crossing over

occurs, leading to unique chromosomes that separate after meiosis I occurs. 200. Answer: c. In both mitosis and meiosis I, there is a metaphase plate that develops, with the chromosomes lined up on either side of the plate.

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College Level Molecular Biology

Articles inside

Answers to Chapter Eight

Answers to Chapter Four

Answers to Chapter Seven

Answers to Chapter Six

Answers to Chapter Five

Answers to Chapter Three

Answers to Chapter Two

Summary

Quiz

Apoptosis

Key Takeaways

Meiosis

Mitosis and its Regulation

Cell Cycle Regulators

Quiz

Key Takeaways

Cilia, Centrioles and Flagella

Intermediate Filaments

Microtubules

Cell Migration

Microfilaments

Quiz

G Protein-coupled Receptors

Key Takeaways

Signaling Processes

Ligands

Receptors

Key Takeaways

Receptor-Mediated Endocytosis

Secretory Pathways in Nerve Cells

Quiz

Fatty Acid Oxidation

Key Takeaways

Photosynthesis

Citric Acid Cycle

Mitochondrial Respiration

Glycolysis

Quiz

Key Takeaways

Gene Mutations

Genomics

Transposable DNA

Key Takeaways

Eukaryotic Genes

Quiz

DNA Repair

DNA Replication

Types and Function of RNA

Key Takeaways

Quiz

Post-Translational Modification

Protein Detection and Characterization

Enzymology

Protein Synthesis

Key Takeaways

Quiz

Diffusion

Composition of Membranes

Active Transport

Quiz

Membrane Proteins

Quiz

Tissue Differentiation

Plant Cell Adhesions

Desmosomes

Key Takeaways

Connective Tissue and Connective Tissue Proteins

Quiz

Key Takeaways

Cell to Cell Communication

Chemical Reactions in Living Things

Chapter One: Chemical Foundations of Life

Quiz

Preface

Chemical Building Blocks of Life

Key Takeaways

Covalent Bonds

Eukaryotic Cell Structures