SCIENCE 8

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1st Quarter Module (Lesson: Introduction to Biology) Biology deals with the study of the many living organismsBiology is a natural science concerned with the study of life and living organisms, including their structure, function, growth, evolution, distribution, and taxonomy. Modern biology is a vast and eclectic field, composed of many branches and sub disciplines. However, despite the broad scope of biology, there are certain general and unifying concepts within it that govern all study and research, consolidating it into single, coherent fields. In general, biology recognizes the cell as the basic unit of life, genes as the basic unit of heredity, and evolution as the engine that propels the synthesis and creation of new species. It is also understood today that all organisms survive by consuming and transforming energy and by regulating their internal environment to maintain a stable and vital condition.

Sub disciplines of biology are defined by the scale at which organisms are studied, the kinds of organisms studied, and the methods used to study them: Biochemistry examines the rudimentary chemistry of life; molecular biology studies the complex interactions among biological molecules; botany studies the biology of plants; cellular biology examines the basic building-block of all life, the cell; physiology examines the physical and chemical functions of tissues, organs, and organ systems of an organism; evolutionary biology examines the processes that produced the diversity of life; and ecology examines how organisms interact in their environment.

Features of Living Things  Growth Living things grow by developing new parts between or within older ones and may be replaced during life. Living things exhibit internal growth called intussusceptions while non-living things external growth called accretion. If non-living things grow, they do that by external addition. 

Form and Size Living things have such characteristics as size and form within certain limits.

Most of them are also arranged as definite individuals while in non-living things, materials vary widely in size and form.

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Locomotion or Movement Living things can move by themselves while non-living things move with the help of living things or other external forces.

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Irritability or Sensitiveness Living things react to changes in the environment. These environmental factors that cause the organism to react are called stimuli. The degree of response is often proportionate to the type of stimulus and the organism is only temporarily altered by the stimulus.

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Cell theory

Human cancer cells with nuclei (specifically the DNA) stained blue. The central and rightmost cells are in interphase, so the entire nuclei are labeled. The cell on the left is going through mitosis and its DNA has condensed.

Cell theory Cell theory states that the cell is the fundamental unit of life, and that all living things are composed of one or more cells or the secreted products of those cells (e.g. shells). All cells arise from other cells through cell division. In multicellular organisms, every cell in the organism's body derives ultimately from a single cell in a fertilized egg. The cell is also considered to be the basic unit in many pathological processes. In addition, the phenomenon of energy flow occurs in cells in processes Young Ji International School / College

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that are part of the function known as metabolism. Finally, cells contain hereditary information (DNA), which is passed from cell to cell during cell division.

Evolution

Natural selection of a population for dark coloration.

Evolution A central organizing concept in biology is that life changes and develops through evolution, and that all life-forms known have a common origin. The theory of evolution postulates that all organisms on the Earth, both living and extinct, have descended from a common ancestor or an ancestral gene pool. This last universal common ancestor of all organisms is believed to have appeared about 3.5 billion years ago. Biologists generally regard the universality and ubiquity of the genetic code as definitive evidence in favor of the theory of universal common descent for all bacteria, archaea, and eukaryotes .

Introduced into the scientific lexicon by Jean-Baptiste de Lamarck in 1809, evolution was established by Charles Darwin fifty years later as a viable scientific model when he articulated its driving force: natural selection. (Alfred Russel Wallace is recognized as the co-discoverer of this concept as he helped research and experiment with the concept of evolution. Evolution is now used to explain the great variations of life found on Earth.

Darwin theorized that species and breeds developed through the processes of natural selection and artificial selection or selective breeding. Genetic drift was embraced as an additional mechanism of evolutionary development in the modern synthesis of the theory.

The evolutionary history of the species—which describes the characteristics of the various species from which it descended—together with its genealogical relationship to every other species is known as its phylogeny. Widely varied approaches to biology generate information about phylogeny. These include the comparisons of DNA sequences conducted with in molecular biology or genomics, and comparisons of fossils or other records of ancient organisms in paleontology.

Biologists organize and analyze evolutionary relationships through various methods, including phylogenetics, phenetics, and cladistics. (For a summary of major events in the evolution of life as currently understood by biologists, see evolutionary timeline.)

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Genetics

A Punnett square depicting a cross between two pea plants heterozygous for purple (B) and white (b) blossoms Genetics Genes are the primary units of inheritance in all organisms. A gene is a unit of heredity and corresponds to a region of DNA that influences the form or function of an organism in specific ways. All organisms, from bacteria to animals, share the same basic machinery that copies and translates DNA into proteins.

Cells transcribe a DNA gene into an RNA version of the gene, and aribosome then translates the RNA into a protein, a sequence of amino acids.

The translation code from RNA codon to amino acid is the same for most organisms, but slightly different for some. For example, a sequence of DNA that codes for insulin in humans also codes for insulin when inserted into other organisms, such as plants.

DNA usually occurs as linear chromosomes in eukaryotes, and circular chromosomes in prokaryotes. A chromosome is an organized structure consisting of DNA and histones. The set of chromosomes in a cell and any other hereditary information found in the mitochondria, chloroplasts, or other locations is collectively known as its genome. In eukaryotes, genomic DNA is located in the cell nucleus, along with small amounts in mitochondria and chloroplasts. In prokaryotes, the DNA is held within an irregularly shaped body in the cytoplasm called the nucleoid. The genetic information in a genome is held within genes, and the complete assemblage of this information in an organism is called its genotype.

Homeostasis

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The hypothalamus secretes CRH, which directs the pituitary gland to secrete ACTH. In turn, ACTH directs the adrenal cortex to secrete glucocorticoids, such as cortisol. The GCs then reduce the rate of secretion by the hypothalamus and the pituitary gland once a sufficient amount of GCs has been released.

Homeostasis is the ability of an open system to regulate its internal environment to maintain stable conditions by means of multiple dynamic equilibrium adjustments controlled by interrelated regulation mechanisms. All living organisms, whether unicellular or multicellular, exhibit homeostasis.

To maintain dynamic equilibrium and effectively carry out certain functions, a system must detect and respond to perturbations. After the detection of a perturbation, a biological system normally responds through negative feedback. This means stabilizing conditions by either reducing or increasing the activity of an organ or system. One example is the release of glucagon when sugar levels are too low.

Energy The survival of a living organism depends on the continuous input of energy.

Chemical reactions that are responsible for its structure and function are tuned to extract energy from substances that act as its food and transform them to help form new cells and sustain them. In this process, molecules of chemical substances that constitute food play two roles; first, they contain energy that can be transformed for biological chemical reactions; second, they develop new molecular structures made up of biomolecules.

The organisms responsible for the introduction of energy into an ecosystem are known as producers or autotrophs. Nearly all of these organisms originally draw energy from the sun. Plants and other phototrophs use solar energy via a process known as photosynthesis to convert raw materials into organic molecules, such as ATP, whose bonds can be broken to release energy. A few ecosystems, however, depend entirely on energy extracted by chemotrophs from methane, sulfides, or other non-luminal energy sources.

Some of the captured energy is used to produce biomass to sustain life and provide energy for growth and development. The majority of the rest of this energy is lost as heat and waste molecules. The most important processes for converting the energy trapped in chemical substances into energy useful to sustain life are metabolismand cellular respiration.

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Structural

Schematic of typical animal cell depicting the various organelles and structures.

Molecular biology is the study of biology at a molecular level. This field overlaps with other areas of biology, particularly with genetics and biochemistry. Molecular biology chiefly concerns itself with understanding the interactions between the various systems of a cell, including the interrelationship of DNA, RNA, and protein synthesis and learning how these interactions are regulated.

Cell biology studies the structural and physiological properties of cells, including their behaviors, interactions, and environment. This is done on both the microscopic and molecular levels, for unicellular organisms such as bacteria, as well as the specialized cells in multicellular organisms such as humans.

Understanding the structure and function of cells is fundamental to all of the biological sciences. The similarities and differences between cell types are particularly relevant to molecular biology.

Anatomy considers the forms of macroscopic structures such as organs and organ systems.

Genetics is the science of genes, heredity, and the variation of organisms. Genes encode the information necessary for synthesizing proteins, which in turn play a central role in influencing the final phenotype of the organism. In modern research, genetics provides important tools in the investigation of the function of a particular gene, or the analysis of genetic interactions. Within organisms, genetic information generally is carried in chromosomes, where it is represented in the chemical structure of particular DNA molecules.

Developmental biology studies the process by which organisms grow and develop. Originating in embryology, modern developmental biology studies the genetic control of cell growth, differentiation, and "morphogenesis," which is the process that progressively gives rise to tissues, organs, and anatomy. Model organisms for developmental biology include the round worm Caenorhabditiselegans,[44] the fruit fly Drosophila melanogaster, the zebrafish Daniorerio, the mouse Musmusculus, and the weed Arabidopsis thaliana.

(A model organism is a species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in that organism provide insight into the workings of other organisms.)

Physiological Physiology studies the mechanical, physical, and biochemical processes of living organisms by attempting to understand how all of the structures function as a whole. The theme of "structure to function" is central to biology. Physiological studies have traditionally been divided into plant physiology and animal physiology, but some principles of physiology are universal, no matter what particular organism is Young Ji International School / College

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being studied. For example, what is learned about the physiology of yeast cells can also apply to human cells. The field of animal physiology extends the tools and methods of human physiology to non-human species. Plant physiology borrows techniques from both research fields.

Physiology studies how for example nervous, immune, endocrine, respiratory, and circulatory systems, function and interact. The study of these systems is shared with medically oriented disciplines such as neurology and immunology.

Evolutionary Evolutionary research is concerned with the origin and descent of species, as well as their change over time, and includes scientists from many taxonomically oriented disciplines. For example, it generally involves scientists who have special training in particular organisms such as mammalogy, ornithology, botany, or herpetology, but use those organisms as systems to answer general questions about evolution.

Evolutionary biology is partly based on paleontology, which uses the fossil record to answer questions about the mode and tempo of evolution, and partly on the developments in areas such as population genetics. In the 1980s, developmental biology re-entered evolutionary biology from its initial exclusion from the modern synthesis through the study of evolutionary developmental biology. Related fields often considered part of evolutionary biology are phylogenetics, systematics, and taxonomy.

Systematic

A phylogenetic tree of all living things, based on rRNA gene data, showing the separation of the three domains bacteria, archaea, and eukaryotes as described initially by Carl Woese. Trees constructed with other genes are generally similar, although they may place some early-branching groups very differently, presumably owing to rapid rRNA evolution. The exact relationships of the three domains are still being debated.

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The hierarchy of biological classification's eight major taxonomic ranks. Intermediate minor rankings are not shown. This diagram uses a 3Domains / 6 Kingdoms format Systematics Multiple speciation events create a tree structured system of relationships between species. The role of systematics is to study these relationships and thus the differences and similarities between species and groups of species. However, systematics was an active field of research long before evolutionary thinking was common.

Traditionally, living things have been divided into five kingdoms: Monera; Protista;Fungi; Plantae; Animalia. However, many scientists now consider this fivekingdom system outdated. Modern alternative classification systems generally begin with the three-domain system: Archaea (originally Archaebacteria); Bacteria(originally Eubacteria) and Eukaryota (including protists, fungi, plants, and animals) These domains reflect whether the cells have nuclei or not, as well as differences in the chemical composition of key biomolecules such as ribosomes.

Further, each kingdom is broken down recursively until each species is separately classified.

The order is: Domain;Kingdom; Phylum; Class; Order; Family; Genus; Species.

Outside of these categories, there are obligate intracellular parasites that are "on the edge of life" in terms of metabolic activity, meaning that many scientists do not actually classify these structures as alive, due to their lack of at least one or more of the fundamental functions or characteristics that define life. They are classified as viruses, viroids, prions, orsatellites.

The scientific name of an organism is generated from its genus and species.

For example, humans are listed as Homo sapiens. Homo is the genus, and sapiens the species. When writing the scientific name of an organism, it is proper to capitalize the first letter in the genus and put all of the species in lowercase. Additionally, the entire term may be italicized or underlined.

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The dominant classification system is called the Linnaean taxonomy. It includes ranks and binomial nomenclature. How organisms are named is governed by international agreements such as the International Code of Nomenclature for algae, fungi, and plants (ICN), the International Code of Zoological Nomenclature (ICZN), and the International Code of Nomenclature of Bacteria (ICNB). The classification of viruses, viroids, prions, and all other sub-viral agents that demonstrate biological characteristics is conducted by the International Committee on Taxonomy of Viruses (ICTV) and is known as the International Code of Viral Classification and Nomenclature (ICVCN). However, several other viral classification systems do exist.

A merging draft, BioCode, was published in 1997 in an attempt to standardize nomenclature in these three areas, but has yet to be formally adopted. The BioCode draft has received little attention since 1997; its originally planned implementation date of January 1, 2000, has passed unnoticed. A revised BioCode that, instead of replacing the existing codes, would provide a unified context for them, was proposed in 2011. However, the International Botanical Congress of 2011 declined to consider the BioCode proposal. The ICVCN remains outside the BioCode, which does not include viral classification.

Ecological and environmental

Mutual symbiosis between clownfish of the genus Amphiprion that dwell among the tentacles of tropical sea anemones. The territorial fish protects the anemone from anemone-eating fish, and in turn the stinging tentacles of the anemone protects the clown fish from its predators.

Ecology studies the distribution and abundance of living organisms, and the interactions between organisms and their environment. The habitat of an organism can be described as the local abiotic factors such as climate and ecology, in addition to the other organisms and biotic factors that share its environment. One reason that biological systems can be difficult to study is that so many different interactions with other organisms and the environment are possible, even on small scales. A microscopic bacterium in a local sugar gradient is responding to its environment as much as a lion searching for food in the African savanna. For any species, behaviors can be co-operative,competitive, parasitic, or symbiotic. Matters become more complex when two or more species interact in an ecosystem.

Ecological systems are studied at several different levels, from individuals and populations to ecosystems and the biosphere. The term population biology is often used interchangeably with population ecology, although population biology is more frequently used when studying diseases, viruses, and microbes, while population

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ecology is more commonly used when studying plants and animals. Ecology draws on many subdisciplines.

Ethology studies animal behavior (particularly that of social animals such as primates and canids), and is sometimes considered a branch of zoology.

Ethologists have been particularly concerned with the evolution of behavior and the understanding of behavior in terms of the theory of natural selection. In one sense, the first modern ethologist was Charles Darwin, whose book, The Expression of the Emotions in Man and Animals, influenced many ethologists to come.

Biogeography studies the spatial distribution of organisms on the Earth, focusing on topics like plate tectonics, climate change, dispersal and migration, and cladistics.

Basic unresolved problems in biology Despite the profound advances made over recent decades in our understanding of life's fundamental processes, some basic problems have remained unresolved. For example, one of the major unresolved problems in biology is the primary adaptive function of sex, and particularly its key processes in eukaryotes, meiosis and homologous recombination. One view is that sex evolved primarily as an adaptation for increasing genetic diversity. An alternative view is that sex is an adaptation for promoting accurate DNA repair in germ-line DNA, and that increased genetic diversity is primarily a byproduct that may be useful in the long run.

Another basic unresolved problem in biology is the biologic basis of aging. At present, there is no consensus view on the underlying cause of aging.

These are the main branches of biology:  Aerobiology – the study of airborne organic particles  Agriculture – the study of producing crops and raising livestock, with an emphasis on practical applications  Anatomy – the study of form and function, in plants, animals, and other organisms, or specifically in humans  Histology – the study of cells and tissues, a microscopic branch of anatomy  Astrobiology (also known as exobiology, exopaleontology, and bioastronomy) – the study of evolution, distribution, and future of life in the universe  Biochemistry – the study of the chemical reactions required for life to exist and function, usually a focus on the cellular level  Bioengineering – the study of biology through the means of engineering with an emphasis on applied knowledge and especially related to biotechnology  Biogeography – the study of the distribution of species spatially and temporally  Bioinformatics – the use of information technology for the study, collection, and storage of genomic and other biological data  Biomathematics (or Mathematical biology) – the quantitative or mathematical study of biological processes, with an emphasis on modeling  Biomechanics – often considered a branch of medicine, the study of the mechanics of living beings, with an emphasis on applied use through prosthetics or orthotics  Biomedical research – the study of health and disease  Pharmacology – the study and practical application of preparation, use, and effects of drugs and synthetic medicines  Biomusicology – the study of music from a biological point of view.

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Biophysics – the study of biological processes through physics, by applying the theories and methods traditionally used in the physical sciences Biotechnology – the study of the manipulation of living matter, including genetic modification and synthetic biology  Synthetic Biology – research integrating biology and engineering; construction of biological functions not found in nature Building biology – the study of the indoor living environment Botany – the study of plants Cell biology – the study of the cell as a complete unit, and the molecular and chemical interactions that occur within a living cell Cognitive biology – the study of cognition as a biological function Conservation biology – the study of the preservation, protection, or restoration of the natural environment, natural ecosystems, vegetation, and wildlife Cryobiology – the study of the effects of lower than normally preferred temperatures on living beings Developmental biology – the study of the processes through which an organism forms, from zygote to full structure  Embryology – the study of the development of embryo (from fecundation to birth) Ecology – the study of the interactions of living organisms with one another and with the non-living elements of their environment Environmental biology – the study of the natural world, as a whole or in a particular area, especially as affected by human activity Epidemiology – a major component of public health research, studying factors affecting the health of populations Evolutionary biology – the study of the origin and descent of species over time Genetics – the study of genes and heredity.  Epigenetics – the study of heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence Hematology (also known as Haematology) – the study of blood and bloodforming organs.

Integrative biology – the study of whole organisms Limnology – the study of inland waters Marine biology (or Biological oceanography) – the study of ocean ecosystems, plants, animals, and other living beings Microbiology – the study of microscopic organisms (microorganisms) and their interactions with other living things  Parasitology – the study of parasites and parasitism  Virology – the study of viruses and some other virus-like agents Molecular biology – the study of biology and biological functions at the molecular level, some cross over with biochemistry Mycology – the study of fungi Neurobiology – the study of the nervous system, including anatomy, physiology and pathology Population biology – the study of groups of conspecific organisms, including  Population ecology – the study of how population dynamics and extinction  Population genetics – the study of changes in gene frequencies in populations of organisms

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Paleontology – the study of fossils and sometimes geographic evidence of prehistoric life Pathobiology or pathology – the study of diseases, and the causes, processes, nature, and development of disease Physiology – the study of the functioning of living organisms and the organs and parts of living organisms Phytopathology – the study of plant diseases (also called Plant Pathology) Psychobiology – the study of the biological bases of psychology Sociobiology – the study of the biological bases of sociology Structural biology – a branch of molecular biology, biochemistry, and biophysics concerned with the molecular structure of biological macromolecules Zoology – the study of animals, including classification, physiology, development, and behavior.

Sub branches include : Ethology (animal behavior), Entomology(insects), Herpetology(reptiles and amphibians), Ichthyology(fish),Mamma logy(mammals), and Ornithology(birds)

Activity 1 Areas of Biology 1. Make a tour of your neighborhood and list down the profession or occupation of the residents there. ______________________________________________________________ ______________________________________________________________ ______________________________________________________________ 2. Classify the occupation as ether biology-related or not biology-related. Explain your answer. ______________________________________________________________ ______________________________________________________________ ______________________________________________________________ 3. If you are to select among those professionals/occupations, what would you choose? What would you like to be in the future? Why? ______________________________________________________________ ______________________________________________________________ ______________________________________________________________ ______________________________________________________________

Lesson 2

Ecosystem

An ecosystem is a community of living organisms (plants, animals and microbes) in conjunction with the nonliving components of their environment (things like air, water and mineral soil), interacting as a system. These biotic and abiotic components are regarded as linked together through nutrient cycles and energy flows. As ecosystems are defined by the network of interactions among organisms, and between organisms and their environment, they can be of any size but usually encompass specific, limited spaces (although some scientists say that the entire planet is an ecosystem).

Energy, water, nitrogen and soil minerals are other essential abiotic components of an ecosystem. The energy that flows through ecosystems is obtained primarily from the sun. It generally enters the system through photosynthesis, a process that also captures carbon from the atmosphere. By feeding on plants and on Young Ji International School / College

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one another, animals play an important role in the movement of matter and energy through the system. They also influence the quantity of plant and microbial biomass present.

By breaking down dead organic matter, decomposers release carbon back to the atmosphere and facilitate nutrient cycling by converting nutrients stored in dead biomass back to a form that can be readily used by plants and other microbes.

Ecosystems are controlled both by external and internal factors. External factors such as climate, the parent material which forms the soil and topography, control the overall structure of an ecosystem and the way things work within it, but are not themselves influenced by the ecosystem. Other external factors include time and potential biota. Ecosystems are dynamic entities—invariably, they are subject to periodic disturbances and are in the process of recovering from some past disturbance. Ecosystems in similar environments that are located in different parts of the world can have very different characteristics simply because they contain different species. The introduction of non-native species can cause substantial shifts in ecosystem function. Internal factors not only control ecosystem processes but are also controlled by them and are often subject to feedback loops. While the resource inputs are generally controlled by external processes like climate and parent material, the availability of these resources within the ecosystem is controlled by internal factors like decomposition, root competition or shading. Other internal factors include disturbance, succession and the types of species present. Although humans exist and operate within ecosystems, their cumulative effects are large enough to influence external factors like climate.

Coral reefs are a highly productive marine ecosystem.

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Rainforest ecosystems are rich in biodiversity. This is the Gambia River in Senegal's Niokolo-Koba National Park.

Biodiversity affects ecosystem function, as do the processes of disturbance and succession. Ecosystems provide a variety of goods and services upon which people depend; the principles of ecosystem management suggest that rather than managing individual species, natural resources should be managed at the level of the ecosystem itself. Classifying ecosystems into ecologically homogeneous units is an important step towards effective ecosystem management, but there is no single, agreed-upon way to do this.

History and development The term "ecosystem" was first used in a publication by British ecology Arthur Tansley. Tansley devised the concept to draw attention to the importance of transfers of materials between organisms and their environment. He later refined the term, describing it as "The whole system, ... including not only the organismcomplex, but also the whole complex of physical factors forming what we call the environment".Tansley regarded ecosystems not simply as natural units, but as mental isolates. Tansleylaterdefined the spatial extent of ecosystems using the term ecotope.

Ecosystem processes Energy and carbon enter ecosystems through photosynthesis, are incorporated into living tissue, transferred to other organisms that feed on the living and dead plant matter, and eventually released through respiration. Most mineral nutrients, on the other hand, are recycled within ecosystems.

Ecosystems are controlled both by external and internal factors. External factors, also called state factors, control the overall structure of an ecosystem and the way things work within it, but are not themselves influenced by the ecosystem.

The most important of these is climate. Climate determines the biome in which the ecosystem is embedded. Rainfall patterns and temperature seasonality determine the amount of water available to the ecosystem and the supply of energy available (by influencing photosynthesis). Parent material, the underlying geological material that gives rise to soils, determines the nature of the soils present, and influences the supply of mineral nutrients. Topography also controls ecosystem processes by affecting things like microclimate, soil development and the movement of water through a system. This may be the difference between the ecosystem present in wetland situated in a small depression on the landscape, and one present on an adjacent steep hillside.

Other external factors that play an important role in ecosystem functioning include time and potential biota. Ecosystems are dynamic entities—invariably, they are subject to periodic disturbances and are in the process of recovering from some past disturbance. Time plays a role in the development of soil from bare rock and the recovery of a community from disturbance. Similarly, the set of organisms that can potentially be present in an area can also have a major impact on ecosystems.

Ecosystems in similar environments that are located in different parts of the world can end up doing things very differently simply because they have different pools of species present. The introduction of non-native species can cause substantial shifts in ecosystem function.

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Unlike external factors, internal factors in ecosystems not only control ecosystem processes, but are also controlled by them. Consequently, they are often subject to feedback loops. While the resource inputs are generally controlled by external processes like climate and parent material, the availability of these resources within the ecosystem is controlled by internal factors like decomposition, root competition or shading. Other factors like disturbance, succession or the types of species present are also internal factors. Human activities are important in almost all ecosystems. Although humans exist and operate within ecosystems, their cumulative effects are large enough to influence external factors like climate.

Primary production

Global oceanic and terrestrial phototroph abundance, from September 1997 to August 2000. As an estimate of autotroph biomass, it is only a rough indicator of primary production potential, and not an actual estimate of it. Provided by the SeaWiFS Project, NASA/Goddard Space Flight Center and ORBIMAGE. Primary production Primary production is the production of organic matter from inorganic carbon sources. Overwhelmingly, this occurs through photosynthesis. The energy incorporated through this process supports life on earth, while the carbon makes up much of the organic matter in living and dead biomass, soil carbon and fossil fuels. It also drives the carbon cycle, which influences global climate via the greenhouse effect.

Through the process of photosynthesis, plants capture energy from light and use it to combine carbon dioxide and water to produce carbohydrates and oxygen.

The photosynthesis carried out by all the plants in an ecosystem is called the gross primary production (GPP). About 48–60% of the GPP is consumed in plant respiration. The remainder, that portion of GPP that is not used up by respiration, is known as the net primary production (NPP). Total photosynthesis is limited by a range of environmental factors. These include the amount of light available, the amount of leaf area a plant has to capture light (shading by other plants is a major limitation of photosynthesis), rate at which carbon dioxide can be supplied to the chloroplasts to support photosynthesis, the availability of water, and the availability of suitable temperatures for carrying out photosynthesis.

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Energy flow

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Left: Energy flow diagram of a frog. The frog represents a node in an extended food web. The energy ingested is utilized for metabolic processes and transformed into biomass. The energy flow continues on its path if the frog is ingested by predators, parasites, or as a decaying carcass in soil. This energy flow diagram illustrates how energy is lost as it fuels the metabolic process that transforms the energy and nutrients into biomass.

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Right: An expanded three link energy food chain (1. plants, 2. herbivores, 3. carnivores) illustrating the relationship between food flow diagrams and energy transformity. The transformity of energy becomes degraded, dispersed, and diminished from higher quality to lesser quantity as the energy within a food chain flows from one trophic species into another. Abbreviations: I=input, A=assimilation, R=respiration, NU=not utilized, P=production, B=biomass.

Energy flow (ecology) The carbon and energy incorporated into plant tissues (net primary production) is either consumed by animals while the plant is alive, or it remains uneaten when the plant tissue dies and becomes detritus. In terrestrial ecosystems, roughly 90% of the NPP ends up being broken down by decomposers. The remainder is either consumed by animals while still alive and enters the plant-based trophic system, or it is consumed after it has died, and enters the detritus-based trophic system. In aquatic systems, the proportion of plant biomass that gets consumed by herbivores is much higher. In trophic systems photosynthetic organisms are the primary producers. The organisms that consume their tissues are called primary consumers or secondary producers—herbivores. Organisms which feed on microbes (bacteria and fungi) are termed microbivores. Animals that feed on primary consumers—carnivores—are secondary consumers. Each of these constitutes atrophic level. The sequence of consumption—from plant to herbivore, to carnivore—forms a food chain. Real systems are much more complex than this— organisms will generally feed on more than one form of food, and may feed at more than one trophic level. Carnivores may capture some preys which are part of a plantbased trophic system and others that are part of a detritus-based trophic system (a bird that feeds both on herbivorous grasshoppers and earthworms, which consume detritus). Real systems, with all these complexities, form food webs rather than food chains.

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Decomposition The carbon and nutrients in dead organic matter are broken down by a group of processes known as decomposition. This releases nutrients that can then be reused for plant and microbial production, and returns carbon dioxide to the atmosphere (or water) where it can be used for photosynthesis. In the absence of decomposition, dead organic matter would accumulate in an ecosystem and nutrients and atmospheric carbon dioxide would be depleted. Approximately 90% of terrestrial NPP goes directly from plant to decomposer.

Decomposition processes can be separated into three categories—leaching, fragmentation and chemical alteration of dead material. As water moves through dead organic matter, it dissolves and carries with it the water-soluble components.

These are then taken up by organisms in the soil, react with mineral soil, or are transported beyond the confines of the ecosystem (and are considered "lost" to it).

Newly shed leaves and newly dead animals have high concentrations of watersoluble components, and include sugars, amino acids and mineral nutrients.

Leaching is more important in wet environments, and much less important in dry ones.

Fragmentation processes break organic material into smaller pieces, exposing new surfaces for colonization by microbes. Freshly shed leaf litter may be inaccessible due to an outer layer of cuticle or bark, and cell contents are protected by a cell wall. Newly dead animals may be covered by an exoskeleton.

Fragmentation processes, which break through these protective layers, accelerate the rate of microbial decomposition. Animals fragment detritus as they hunt for food, as does passage through the gut. Freeze-thaw cycles and cycles of wetting and drying also fragment dead material.

The chemical alteration of dead organic matter is primarily achieved through bacterial and fungal action. Fungal hyphae produce enzymes which can break through the tough outer structures surrounding dead plant material. They also produce enzymes which break down lignin, which allows to them access to both cell contents and to the nitrogen in the lignin. Fungi can transfer carbon and nitrogen through their hyphal networks and thus, unlike bacteria, are not dependent solely on locally available resources.

Decomposition rates vary among ecosystems. The rate of decomposition is governed by three sets of factors—the physical environment (temperature, moisture and soil properties), the quantity and quality of the dead material available to decomposers, and the nature of the microbial community itself. Temperature controls the rate of microbial respiration; the higher the temperature, the faster microbial decomposition occurs. It also affects soil moisture, which slows microbial growth and reduces leaching. Freeze-thaw cycles also affect decomposition—freezing temperatures kill soil microorganisms, which allow leaching to play a more important role in moving nutrients around. This can be especially important as the soil thaws in the Spring, creating a pulse of nutrients which become available.

Decomposition rates are low under very wet or very dry conditions.

Decomposition rates are highest in wet, moist conditions with adequate levels of oxygen. Wet soils tend to become deficient in oxygen (this is especially true Young Ji International School / College

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in wetlands), which slows microbial growth. In dry soils, decomposition slows as well, but bacteria continue to grow (albeit at a slower rate) even after soils become too dry to support plant growth. When the rains return and soils become wet, the osmotic gradient between the bacterial cells and the soil water causes the cells to gain water quickly. Under these conditions, many bacterial cells burst, releasing a pulse of nutrients. Decomposition rates also tend to be slower in acidic soils. Soils which are rich in clay minerals tend to have lower decomposition rates, and thus, higher levels of organic matter. The smaller particles of clay result in a larger surface area that can hold water. The higher the water contents of a soil, the lower the oxygen contented consequently, the lower the rate of decomposition. Clay minerals also bind particles of organic material to their surface, making them less accessibly to microbes.

The quality and quantity of the material available to decomposers is another major factor that influences the rate of decomposition. Substances like sugars and amino acids decompose readily and are considered "labile". Cellulose and hemicellulose, which are broken down more slowly, are "moderately labile".

Compounds which are more resistant to decay, like lignin or cutting, are considered "recalcitrant‖. Litter with a higher proportion of labile compounds decomposes much more rapidly than does litter with a higher proportion of recalcitrant material.

Consequently, dead animals decompose more rapidly than dead leaves, which themselves decompose more rapidly than fallen branches. As organic material in the soil ages, its quality decreases. The more labile compounds decompose quickly, leaving and increasing proportion of recalcitrant material. Microbial cell walls also contain a recalcitrant materials like chitin, and these also accumulate as the microbes die, further reducing the quality of older soil organic matter.

Nutrient cycling

Biological nitrogen cycling Ecosystems continually exchange energy and carbon with the wider environment; mineral nutrients, on the other hand, are mostly cycled back and forth between plants, animals, microbes and the soil. Most nitrogen enters ecosystems through biological nitrogen fixation, is deposited through precipitation, dust, gases or is applied as fertilizer.[15] Since most terrestrial ecosystems are nitrogen-limited, nitrogen cycling is an important control on ecosystem production.

Until modern times, nitrogen fixation was the major source of nitrogen for ecosystems. Nitrogen fixing bacteria either live symbiotically with plants, or live freely Young Ji International School / College

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in the soil. The energetic cost is high for plants which support nitrogen-fixing symbionts—as much as 25% of GPP when measured in controlled conditions. Many members of the legume plant family support nitrogen-fixing symbionts.

Some cyanobacteria are also capable of nitrogen fixation. These are phototrophs, which carry out photosynthesis. Like other nitrogen-fixing bacteria, they can either be free-living or have symbiotic relationships with plants. Other sources of nitrogen include acid deposition produced through the combustion of fossil fuels, ammonia gas which evaporates from agricultural fields which have had fertilizers applied to them, and dust. Anthropogenic nitrogen inputs account for about 80% of all nitrogen fluxes in ecosystems.

When plant tissues are shed or are eaten, the nitrogen in those tissues becomes available to animals and microbes. Microbial decomposition releases nitrogen compounds from dead organic matter in the soil, where plants, fungi and bacteria compete for it. Some soil bacteria use organic nitrogen-containing compounds as a source of carbon, and release ammonium ions into the soil. This process is known as nitrogen mineralization. Others convert ammonium to nitrite and nitrate ions, a process known as nitrification. Nitric oxide and nitrous oxide are also produced during nitrification. Under nitrogen-rich and oxygen-poor conditions, nitrates and nitrites are converted to nitrogen gas, a process known as gentrification.

Other important nutrients: Include phosphorus, sulfur, calcium, potassium, magnesium and manganese.  Phosphorus enters ecosystems through weathering. As ecosystems age this supply diminishes, making phosphorus-limitation more common in older landscapes (especially in the tropics). Calcium and sulfur are also produced by weathering, but acid deposition is an important source of sulfur in many ecosystems. Although magnesium and manganese are produced by weathering, exchanges between soil organic matter and living cells account for a significant portion of ecosystem fluxes. Potassium is primarily cycled between living cells and soil organic matter.

Function and biodiversity

Loch Lomond in Scotland forms a relatively isolated ecosystem. The fish community of this lake has remained stable over a long period until a number of introductions in the 1970s restructured its food web.

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Spiny forest at Ifaty, Madagascar, featuring various Adansonia (baobab) species, Alluaudiaprocera(Madagascar ocotillo) and other vegetation.

Ecosystem processes are broad generalizations that actually take place through the actions of individual organisms. The nature of the organisms—the species, functional and trophic levels to which they belong—dictates the sorts of actions these individuals are capable of carrying out, and the relative efficiency with which they do so. Thus, ecosystem processes are driven by the number of species in an ecosystem, the exact nature of each individual species, and the relative abundance organisms within these species. Biodiversity plays an important role in ecosystem functioning.

Ecological theory suggests that in order to coexist, species must have some level of limiting similarity—they must be different from one another in some fundamental way, otherwise one species would competitively exclude the other.

Despite this, the cumulative effect of additional species in an ecosystem is not linear—additional species may enhance nitrogen retention, for example, but beyond some level of species richness, additional species may have little additive effect. The addition (or loss) of species which are ecologically similar to those already present in an ecosystem tends to only have a small effect on ecosystem function. Ecologically distinct species, on the other hand, have a much larger effect. Similarly, dominant species have a large impact on ecosystem function, while rare species tend to have a small effect. Keystone species tend to have an effect on ecosystem function that is disproportionate to their abundance in an ecosystem.

Ecosystem goods and services Ecosystems provide a variety of goods and services upon which people depend. Ecosystem goods include the "tangible, material products" of ecosystem processes—food, construction material, medicinal plants—in addition to less tangible items like tourism and recreation, and genes from wild plants and animals that can be used to improve domestic species. Ecosystem services, on the other hand, are generally "improvements in the condition or location of things of value".These include things like the maintenance of hydrological cycles, cleaning air and water, the maintenance of oxygen in the atmosphere, crop pollination and even things like beauty, inspiration and opportunities for research. While ecosystem goods have traditionally been recognized as being the basis for things of economic value, ecosystem services tend to be taken for granted. While Gretchen Daily's original definition distinguished between ecosystem goods and ecosystem services, Robert Costanza and colleagues' later work and that of the Millennium Ecosystem Assessment lumped all of these together as ecosystem services.

Ecosystem management When natural resource management is applied to whole ecosystems, rather than single species, it is termed ecosystem management. A variety of definitions exist: F. Stuart Chapin and coauthors define it as "the application of ecological science to resource management to promote long-term sustainability of ecosystems and the delivery of essential ecosystem goods and services",while Norman Christensen and coauthors defined it as "management driven by explicit goals, executed by policies, protocols, and practices, and made adaptable by monitoring and research based on our best understanding of the ecological interactions and processes necessary to sustain ecosystem structure and function"and Peter Young Ji International School / College

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Brussard and colleagues defined it as "managing areas at various scales in such a way that ecosystem services and biological resources are preserved while appropriate human use and options for livelihood are sustained".

Although definitions of ecosystem management abound, there is a common set of principles which underlie these definitions. A fundamental principle is the longterm sustainability of the production of goods and services by the ecosystem; "intergenerational sustainability [is] a precondition for management, not an afterthought". It also requires clear goals with respect to future trajectories and behaviors of the system being managed. Other important requirements include a sound ecological understanding of the system, including connectedness, ecological dynamics and the context in which the system is embedded. Other important principles include an understanding of the role of humans as components of the ecosystems and the use of adaptive management. While ecosystem management can be used as part of a plan for wilderness conservation, it can also be used in intensively managed ecosystems.

Ecosystem dynamics

Temperate rainforest on the Olympic Peninsula in Washington State.

The High Peaks Wilderness Area in the 6,000,000-acre (2,400,000 ha)Adirondack Park is an example of a diverse ecosystem.

Ecosystems are dynamic entities—invariably, they are subject to periodic disturbances and are in the process of recovering from some past disturbance.

When an ecosystem is subject to some sort of perturbation, it responds by moving away from its initial state. The tendency of a system to remain close to its equilibrium state, despite that disturbance, is termed its resistance. On the other hand, the speed with which it returns to its initial state after disturbance is called its resilience.

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From one year to another, ecosystems experience variation in their biotic and abiotic environments. A drought, an especially cold winter and a pest outbreak all constitute short-term variability in environmental conditions. Animal populations vary from year to year, building up during resource-rich periods and crashing as they overshoot their food supply. These changes play out in changes in NPP, decomposition rates, and other ecosystem processes. Longer-term changes also shape ecosystem processes—the forests of eastern North America still show legacies of cultivation which ceased 200 years ago, while methane production in eastern Siberian lakes is controlled by organic matter which accumulated during the Pleistocene.

Disturbance also plays an important role in ecological processes. F. Stuart Chapin and coauthors define disturbance as "a relatively discrete event in time and space that alters the structure of populations, communities and ecosystems and causes changes in resources availability or the physical environment".This can range from tree falls and insect outbreaks to hurricanes and wildfires to volcanic eruptions and can cause large changes in plant, animal and microbe populations, as well soil organic matter content. Disturbance is followed by succession, a "directional change in ecosystem structure and functioning resulting from biotically driven changes in resources supply."

The frequency and severity of disturbance determines the way it impacts ecosystem function. Major disturbance like a volcanic eruption or glacial advance and retreat leave behind soils that lack plants, animals or organic matter.

Ecosystems that experience disturbances that undergo primary succession. Less severe disturbance like forest fires, hurricanes or cultivation result in secondary succession. More severe disturbance and more frequent disturbance result in longer recovery times. Ecosystems recover more quickly from less severe disturbance events.

The early stages of primary succession are dominated by species with small propagules (seed and spores) which can be dispersed long distances. The early colonizers—often algae, cyanobacteria and lichens—stabilize the substrate. Nitrogen supplies are limited in new soils, and nitrogen-fixing species tend to play an important role early in primary succession. Unlike in primary succession, the species that dominate secondary succession, are usually present from the start of the process, often in the soil seed bank. In some systems the successional pathways are fairly consistent, and thus, are easy to predict. In others, there are many possible pathways—for example, the introduced nitrogen-fixing legume, Myricafaya, alter successional trajectories in Hawaiian forests.

The theoretical ecologist Robert Ulanowicz has used information theory tools to describe the structure of ecosystems, emphasizing mutual information (correlations) in studied systems. Drawing on this methodology and prior observations of complex ecosystems, Ulanowicz depicts approaches to determining the stress levels on ecosystems and predicting system reactions to defined types of alteration in their settings (such as increased or reduced energy flow, and eutrophication.

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Ecosystem ecology

A hydrothermal vent is an ecosystem on the ocean floor. (The scale bar is 1 m.)

Ecosystem ecology studies "the flow of energy and materials through organisms and the physical environment". It seeks to understand the processes which govern the stocks of material and energy in ecosystems, and the flow of matter and energy through them. The study of ecosystems can cover 10 orders of magnitude, from the surface layers of rocks to the surface of the planet.

There is no single definition of what constitutes an ecosystem. German ecologist Ernst-Detlef Schulze and coauthors defined an ecosystem as an area which is "uniform regarding the biological turnover, and contains all the fluxes above and below the ground area under consideration." They explicitly reject Gene Likens' use of entire river catchments as "too wide a demarcation" to be a single ecosystem, given the level of heterogeneity within such an area. Other authors have suggested that an ecosystem can encompass a much larger area, even the whole planet. Schulze and coauthors also rejected the idea that a single rotting log could be studied as an ecosystem because the size of the flows between the log and its surroundings are too large, relative to the proportion cycles within the log.

Philosopher of science Mark Sagoff considers the failure to define "the kind of object it studies" to be an obstacle to the development of theory in ecosystem ecology.

Ecosystems can be studied through a variety of approaches—theoretical studies, studies monitoring specific ecosystems over long periods of time, those that look at differences between ecosystems to elucidate how they work and direct manipulative experimentation. Studies can be carried out at a variety of scales, from microcosms and mesocosms which serve as simplified representations of ecosystems, through whole-ecosystem studies. American ecologist Stephen R. Carpenter has argued that microcosm experiments can be "irrelevant and diversionary" if they are not carried out in conjunction with field studies carried out at the ecosystem scale, because microcosm experiments often fail to accurately predict ecosystem-level dynamics.

The Hubbard Brook Ecosystem Study, established in the White Mountains, New Hampshire in 1963, was the first successful attempt to study an entire watershed as an ecosystem. The study used stream chemistry as a means of monitoring ecosystem properties, and developed a detailed biogeochemical model of the ecosystem. Long-term research at the site led to the discovery of acid rain in North America in 1972, and was able to document the consequent depletion of soil cations(especially calcium) over the next several decades.

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Bailey outlined five different methods for identifying ecosystems: gestalt ("a whole that is not derived through considerable of its parts"), in which regions are recognized and boundaries drawn intuitively; a map overlay system where different layers like geology, landforms and soil types are overlain to identify ecosystems; multivariate of site attributes; digital image processing of remotely sensed data grouping areas based on their appearance or other spectral properties; or by a "controlling factors method" where a subset of factors (like soils, climate, vegetation physiognomy or the distribution of plant or animal species) are selected from a large array of possible ones are used to delineate ecosystems. In contrast with Bailey's methodology, Puerto Rico ecologist Ariel Lugo and coauthors identified ten characteristics of an effective classification system: that it be based on georeferenced, quantitative data; that it should minimize subjectivity and explicitly identify criteria and assumptions; that it should be structured around the factors that drive ecosystem processes; that it should reflect the hierarchical nature of ecosystems; that it should be flexible enough to conform to the various scales at which ecosystem management operates; that it should be tied to reliable measures of climate so that it can "anticipate [e] global climate change; that it be applicable worldwide; that it should be validated against independent data; that it take into account the sometimes complex relationship between climate, vegetation and ecosystem functioning; and that it should be able to adapt and improve as new data become available".

Types  Aquatic ecosystem  Marine ecosystem  Large marine ecosystem  Freshwater ecosystem  Lake ecosystem  River ecosystem  Wetland  Terrestrial ecosystem  Forest  Greater Yellowstone Ecosystem  Littoral zone  Riparian zone  Subsurface lithoautotrophic microbial ecosystem  Urban ecosystem  Movile Cave  Desert

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A freshwater ecosystem in Gran Canarias, an island of the Canary Islands.

Anthropogenic threats As human populations grow, so do the resource demands imposed on ecosystems and the impacts of the human ecological footprint. Natural resources are not invulnerable and infinitely available. The environmental impacts of anthropogenic actions, which are processes or materials derived from human activities, are becoming more apparent—air and water quality are increasingly compromised, oceans are being overfished, pests and diseases are extending beyond their historical boundaries, and deforestation is exacerbating flooding downstream. It has been reported that approximately 40–50% of Earth's ice-free land surface has been heavily transformed or degraded by anthropogenic activities, 66% of marine fisheries are either overexploited or at their limit, atmospheric CO2 has increased more than 30% since the advent of industrialization, and nearly 25% of Earth's bird species have gone extinct in the last two thousand years. Society is increasingly becoming aware that ecosystem services are not only limited, but also that they are threatened by human activities. The need to better consider long-term ecosystem health and its role in enabling human habitation and economic activity is urgent. To help inform decision-makers, many ecosystem services are being assigned economic values, often based on the cost of replacement with anthropogenic alternatives. The ongoing challenge of prescribing economic value to nature, for example through biodiversity banking, is prompting transdisciplinary shifts in how we recognize and manage the environment, social responsibility, business opportunities, and our future as a species.

Ecosystem Worksheet A. 1.

2.

3.

4.

Draw a model of your school ecosystem.

Identify the biotic and abiotic factors in your school ecosystem.

Describe how they interact with each other.

What is your role in your school ecosystem?

B. Imagine yourself to be part of a food chain.

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1. Make a list of all the food that you ate for dinner last night. ______________________________________________________________ ______________________________________________________________ ______________________________________________________________ 2. For every food, determine the food chain by using an energy pyramid so that it can represent your findings.

Questions: 1. Which are the producers? ______________________________________________________________ ______________________________________________________________ ______________________________________________________________ 2. Which are the consumers? ______________________________________________________________ ______________________________________________________________ ______________________________________________________________ 3. At what level are you considered a consumer? ______________________________________________________________ ______________________________________________________________ ______________________________________________________________

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Foreign Scientist

Significant Contribution in Biology

Gregor Mendel

father of heredity and the basic laws of inheritance; an Austrian monk

Louis Pasteur

father of bacteriology; developed vaccine against rabies; French chemist and microbiologist

Rudolf Virchow

father of modern pathology; contributed to the cell theory; German medical naturalist

Charles Darwin

worked on the theory of evolution and natural selection; British naturalist

Sir Alexander Flemming

discovered penicillin bacteriologist

William Harvey

discovered the mechanics of human blood circulation; English physician

Robert Koch

discovered bacteria causing anthrax, tuberculosis and cholera; German microbiologist

Carolus Linnaeus

father of taxonomy; Swedish naturalist and botanist

Joseph Lister

highlighted the importance of antiseptic in surgery; British medical doctor and surgeon

Edwar Jenner

worked on smallpox vaccine

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as

an

antibiotic;

Scottish

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Filipino Scientists in the Field of Biology Filipino Scientist

Area of Specialization

Eduardo A. Quisumbing, Botany Ph.D. Carmen Ph.D.

C.

Velasquez, Parasitology

Gregorio Ph.D.

T.

Velasquez, Phycology

Specific Contribution pioneered in the study of medicinal plants; Father of Philippine Orchidology identified numerous species and genus of parasitic organisms, particularly fish parasites produced 45 basic researches and 70 articles on algae

William G. Padolina Ph.D. Biotechnology

pioneered excellent researches in biotechnology and chemistry of natural products

Emerita V. Ph.D.

recognized for her research on propagation of mutant macapuno, and tissue culture techniques for rapid propagation of abaca and banana

De Guzman Biotechnology

Angel C. Alcala Ph.D

Ecology, Marine Biology

Ramon C. Barba Ph.D

Botany

Priscillano Ph.D

M.

Zamora Botany

Pedro B. EscuroPh.D

Geminiano OcampoPh.D

T.

known for conservation of coral reefs, mangroves, aquaculture studies in giant clams, mollusks and fishes known for mango flower induction technology, tissue culture of sugar cane, rattan and banana, and development of seedless kalamansi published articles on morphology and taxonomy of some crop plants, ferns gymnosperms

Botany Agriculture

gained international recognition for developing the dwarf high yielding C rice varieties

De Ophthalmology

pioneered in modern ophthalmology and led corneal transplantation in the country

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Activity Module (Lesson: Filipino and Foreign Scientist) Influential Scientists Crossword Puzzle Worksheet

ACROSS 1. A person who classifies animal and plant species.

4. Person who studies the sun, moon, stars, planets and other spatial bodies.

5. Someone who studies life in prehistoric times.

6. A person who learns about the layers of the earth and its history.

7. A person whose job is dealing with substances and the changes that happen when combined to make other substances.

13. Someone who studies the relationship between the earth's physical features and the forces that make or change them.

14. Someone who learns about things that are alive.

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DOWN 2. Person who explores people, life and customs of ancient times.

3. Someone who studies earthquakes and earth's crust's movements.

8. Someone who studies all the aspects of insects.

9. A person who studies the branch of zoology that is concerned with fish.

10. A person who studies the weather and the atmosphere.

11. Someone who learns about diseases and why we get sick or what makes us sick.

12. Someone who knows about oceans, seas, and all marine life.

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Module (Lesson: Microscope) A microscope is an instrument used to see objects that are too small for the naked eye. The science of investigating small objects using such an instrument is called microscopy.Microscopic means invisible to the eye unless aided by a microscope.

Different types of microscopes Optical Microscopes: These microscopes use visible light (or UV light in the case of fluorescence microscopy) to make an image. The light is refracted with optical lenses. The first microscopes that were invented belong to this category. The price of optical microscopes varies from very cheap to nearly unfordable (for the private person, at least). Optical microscopes can be further subdivided into several categories: Compound Microscope: These microscopes are composed of two lens systems, an objective and an ocular (eye piece). The maximum useful magnification of a compound microscope is about 1000x.

Stereo Microscope (dissecting microscope): These microscopes magnify up to about maximum 100x and supply a 3-dimensional view of the specimen. They are useful for observing opaque objects.

Confocal Laser scanning microscope: Unlike compound and stereo microscopes, these devices are reserved for research organizations. They are able to scan a sample also in depth. A computer is then able to assemble the data to make a 3D image.

X-ray Microscope: As the name suggests, these microscopes use a beam of x-rays to create an image. Due to the small wavelength, the image resolution is higher than in optical microscopes. The maximum useful magnification is therefore also higher and is between the optical microscopes and electron microscopes. One advantage of x-ray microscopes over electron microscopes is, that it is possible to observe living cells.

Scanning acoustic microscope (SAM): These devices use focused sound waves to generate an image. They are used in materials science to detect small cracks or tensions in materials. SAMs can also be used in biology where they help to uncover tensions, stress and elasticity inside biological structure.

Scanning Helium Ion Microscope (SHIM or HeIM): As the name suggests, these devices use a beam of Helium ions to generate an image. There are several advantages to electron microscopes, one being that the sample is left mostly intact (due to the low energy requirements) and that it provides a high resolution. It is a relatively new technology and the first commercial systems were released in 2007.

Neutron Microscope: These microscopes are still in an experimental stage. They have a high resolution and may offer better contrast than other forms of microscopy.

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Electron Microscopes: Modern electron microscopes can magnify up to 2 million times. This is possible, because the wavelength of high energy electrons is very small. At the same time, the high energy electrons are pretty tough on the sample being observed. It may take a long time to completely dehydrate and prepare the specimen. Some biological specimens also need to be coated with a very thin layer of a metal before they can be observed.

Transmission electron microscopy (TEM): In this case, the electron beam is passed through the sample. The result is a two dimensional image.

Scanning electron microscopy (SEM): Here the electron beam is projected on the sample. The electrons do not go through the sample but bounce off. This way it is possible to visualize the surface structure of the specimen. The image appears 3 dimensional.

Scanning Probe Microscopes: It is possible to visualize individual atoms with these microscopes. The image of the atom is computer-generated, however. A small tip measures the surface structure of the sample by rastering over the surface. If an atom projects out of the surface, then a higher electrical current will flow through the tip. The amount of current is proportional to the height of the structure. A computer will then assemble the position data of the tip and the current to generate an image.

Microscope Parts & Function Parts of the Microscope

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1. Eyepiece

Contains a magnifying lens that focuses the image from the objective into your eye.

2.

Course Adjust

For focusing under low magnification

3. Fine Adjust

For focusing under high magnification or low

4. Low Power Objective

For large specimens or overview

5. High Power Objective

For detailed viewing or small specimens

6.

Specimen on glass slide

What you want to look at

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7. Stage

Supports specimen in correct location to lens

8. Condenser

Focuses the light on specimen

9. Diaphragm (iris or disc)

Regulates amount light and contrast

10.

Source

Illuminates the specimen for viewing

Light

Activity Module (Lesson: Microscope)

Please use the words from this word list to identify When you can identify a part of the microscope place which points to that part of the microscope.

Arm Ocular Lens Objective lenses Base Course focus Knob Fine Focus Knob Projection Lens Stage

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the parts of the microscope. the matching word on the line Power Switch Revolving Nose Piece Iris Diaphragm Stage Clips

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of

Module (Lesson: Nutrient Cycling) A nutrient cycle (or ecological recycling) is the movement and exchange of organic and inorganic matter back into the production of living matter. The process is regulated by food web pathways that decompose matter into mineral nutrients.

Nutrient cycles occur within ecosystems. Ecosystems are interconnected systems where matter and energy flows and is exchanged as organisms feed, digest, and migrate about. Minerals and nutrients accumulate in varied densities and uneven configurations across the planet. Ecosystems recycle locally, converting mineral nutrients into the production of biomass, and on a larger scale they participate in a global system of inputs and outputs where matter is exchanged and transported through a larger system of biogeochemical cycles.

Mineral cycles include carbon cycle, nitrogen cycle, water cycle, phosphorus cycle, oxygen cycle, among others that continually recycle along with other mineral nutrients into productiveecological nutrition. Global biogeochemical cycles are the Young Ji International School / College

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sum product of localized ecological recycling regulated by the action of food webs moving particulate matter from one living generation onto the next. Earths ecosystems have recycled mineral nutrients sustainably for billions of years.

Carbon Cycle All living things are made of carbon. Carbon is also a part of the ocean, air, and even rocks. Because the Earth is a dynamic place, carbon does not stay still. It is on the move!

In the atmosphere, carbon is attached to some oxygen in a gas called carbon dioxide.

Plants use carbon dioxide and sunlight to make their own food and grow. The carbon becomes part of the plant. Plants that die and are buried may turn into fossil fuels made of carbon like coal and oil over millions of years. When humans burn fossil fuels, most of the carbon quickly enters the atmosphere as carbon dioxide.

Carbon dioxide is a greenhouse gas and traps heat in the atmosphere.

Without it and other greenhouse gases, Earth would be a frozen world. But humans have burned so much fuel that there is about 30% more carbon dioxide in the air today than there was about 150 years ago, and Earth is becoming a warmer place.

In fact, ice cores show us that there is now more carbon dioxide in the atmosphere than there has been in the last 420,000 years.

The Nitrogen Cycle Take a deep breath. Most of what you just inhaled is nitrogen. In fact, 80% of the air in our atmosphere is made of nitrogen. Your body does not use the nitrogen that you inhale with each breath. But, like all living things, your body needs nitrogen. Your body gets the nitrogen it needs to grow from food.

Most plants get the nitrogen they need from soil. Many farmers use fertilizers to add nitrogen to the soil to help plants grow larger and faster. Both nitrogen fertilizers and forest fires add huge amounts of nitrogen into the soil and nearby lakes and rivers.

Water full of nitrogen causes plants and algae to grow very fast and then die all at once when there are too many for the environment to support.

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Water Cycle The water cycle, also known as the hydrologic cycle or the H2O cycle, describes the continuous movement of water on, above and below the surface of the Earth.

The mass of water on Earth remains fairly constant over time but the partitioning of the water into the major reservoirs of ice, fresh water, saline water and atmospheric water is variable depending on a wide range of climatic variables. The water moves from one reservoir to another, such as from river to ocean, or from the ocean to the atmosphere, by the physical processes ofevaporation, condensation, precipitation, infiltration, runoff, and subsurface flow. In so doing, the water goes through different phases: liquid, solid (ice), and gas (vapor).

The water cycle involves the exchange of energy, which leads to temperature changes. For instance, when water evaporates, it takes up energy from its surroundings and cools the environment. When it condenses, it releases energy and warms the environment. These heat exchanges influence climate. The evaporative phase of the cycle purifies water which then replenishes the land with freshwater. The flow of liquid water and ice transports minerals across the globe. It is also involved in reshaping the geological features of the Earth, through processes including erosion and sedimentation. The water cycle is also essential for the maintenance of most life and ecosystems on the planet.

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The Oxygen Cycle Almost all living things need oxygen. They use this oxygen during the process of creating energy in living cells.

Just as water moves from the sky to the earth and back in the hydrologic cycle, oxygen is also cycled through the environment. Plants mark the beginning of the oxygen cycle. Plants are able to use the energy of sunlight to convert carbon dioxide and water into carbohydrates and oxygen in a process called photosynthesis.

This means that plants "breathe" in carbon dioxide and "breathe" out oxygen.

Animals form the other half of the oxygen cycle. We breathe in oxygen which we use to break carbohydrates down into energy in a process called respiration.

Carbon dioxide produced during respiration is breathed out by animals into the air.

So oxygen is created in plants and used up by animals, as is shown in the picture above. But the oxygen cycle is not actually quite that simple. Plants must break carbohydrates down into energy just as animals do. During the day, plants hold onto a bit of the oxygen which they produced in photosynthesis and use that oxygen to break down carbohydrates. But in order to maintain their metabolism and continue respiration at night, the plants must absorb oxygen from the air and give off carbon dioxide just as animals do. Even though plants produce approximately ten times as much oxygen during the day as they consume at night, the night-time consumption of oxygen by plants can create low oxygen conditions in some water habitats.

Phosphorus Cycle Phosphorus is an essential nutrient for plants and animals in the form of ions PO 43and HPO42-. It is a part of DNA-molecules, of molecules that store energy (ATP and ADP) and of fats of cell membranes. Phosphorus is also a building block of certain parts of the human and animal body, such as the bones and teeth.

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Phosphorus can be found on earth in water, soil and sediments. Unlike the compounds of other matter cycles phosphorus cannot be found in air in the gaseous state. This is because phosphorus is usually liquid at normal temperatures and pressures. It is mainly cycling through water, soil and sediments. In the atmosphere phosphorus can mainly be found as very small dust particles.

Phosphorus moves slowly from deposits on land and in sediments, to living organisms, and than much more slowly back into the soil and water sediment. The phosphorus cycle is the slowest one of the matter cycles that are described here.

Phosphorus is most commonly found in rock formations and ocean sediments as phosphate salts. Phosphate salts that are released from rocks through weathering usually dissolve in soil water and will be absorbed by plants. Because the quantities of phosphorus in soil are generally small, it is often the limiting factor for plant growth. That is why humans often apply phosphate fertilizers on farmland.

Phosphates are also limiting factors for plant-growth in marine ecosystems, because they are not very water-soluble. Animals absorb phosphates by eating plants or plant-eating animals.

Phosphorus cycles through plants and animals much faster than it does through rocks and sediments. When animals and plants die, phosphates will return to the soils or oceans again during decay. After that, phosphorus will end up in sediments or rock formations again, remaining there for millions of years. Eventually, phosphorus is released again through weathering and the cycle starts over.

Cycle’s worksheet Please answer the following using the words in the text box.

Carbon Cycle Coal

Oil

Photosynthesis Respiration

Natural Gas Ocean

burning of fossil Fuels Sugar Greenhouse

Volcanoes Decayed

1. Plants use CO2 in the process of ___________________ to make ___________ and oxygen.

2. Animals use oxygen in the process of _______________ and make more CO2.

3. The ____________ is the main regulator of CO2 in the atmosphere because CO2 dissolves easily in it.

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4. In the past, huge deposits of carbon were stored as dead plants and animals __________.

5. Today these deposits are burned as fossil fuels, which include _____________, _______________, and ______________.

6. More CO2 is released in the atmosphere today than in the past because of _________ ___________________ .

7. Another natural source for CO2 is __________________.

8. Too much CO2 in the atmosphere may be responsible for the _______________ effect.

9. Write the equation for photosynthesis.

10. Draw a simple diagram of the Carbon Cycle using the words in the text box above.

Oxygen Cycle Photosynthesis

Ozone

Waste

Crust

Oceans

Respiration

1. Plants release 430-470 billion tons of oxygen during process of _________________.

2. Atmospheric oxygen in the form of ___________ provides protection from harmful ultraviolet rays.

3. Oxygen is found everywhere on Earth, from Earth‘s _____________ (rocks) to the ______________ where it is dissolved.

4. Oxygen is vital for ________________ by animals, a process which produces CO2.and water.

5. Oxygen is also necessary for the decomposition of ______________ into other elements necessary for life.

6. Write the equation for respiration.

7. Draw a diagram of the Oxygen Cycle using the words in the text box.

Phosphorus Cycle Pollution

basins

rocks and minerals

waste DNA overgrowth

plants

1. Phosphorus in NOT found in the free state in Nature, but is contained mostly in _______ and ______________.

2. It is an essential nutrient for life, as it makes up important chemicals such as _______.

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3. In the Phosphorus Cycle, phosphorus moves between the soil and ___________, which are eaten by animals. The animals use phosphorus, and then their ___________ products help return the Sulfur for the next generation of phosphorus in the soil.

4. Some of the phosphorus in soils can be washed away into water ___________.

5. Another source of phosphorus in water comes from man-made _____________.

6. Too much phosphorus in water leads to plant ________________, strangling all other life forms in the water.

7. Why is the use of too much phosphorus-rich fertilizers bad for the environment?

Nitrogen Cycle Atmosphere 78% ammonia denitrificating Nitratenitrogen-fixing plants animalswaste plants

proteins

1. Our atmosphere is ______ nitrogen gas.

2. Animals and plants cannot directly use all the nitrogen found in our ________________.

3. Only special bacteria can directly use nitrogen in our atmosphere and ―fix‖ it so other organisms can benefit. These bacteria are called ____________-_________ bacteria.

4. Higher organisms use nitrogen to make their _____________.

5. Animal waste decay by the action of bacteria which create _____________and __________ products rich in nitrogen, and useful for plants to use again.

6. ______________ bacteria in the soil can break down the ammonia into the gaseous form of nitrogen, which is not available for use by plants or animals.

7. In another part of the cycle, animals eat ____________ containing nitrogen, which is again returned to the soil by animal _____________ or decaying ____________ and ___________.

8. Draw a diagram of the Nitrogen cycle using the words in the text box.

Module (Lesson: Pollution) Pollution is the introduction of contaminants into the natural environment that cause adverse change.

Pollution can take the form of chemical substances or energy, such as noise, heat or light. Pollutants, the components of pollution, can be either foreign substances/energies or naturally occurring contaminants. Pollution is often classed as point source or nonpoint source pollution.

Forms of pollution The major forms of pollution are listed below along with the particular contaminant relevant to each of them:  Air pollution: - the release of chemicals and particulates into the atmosphere.

Common gaseous pollutants include carbon monoxide, sulfur Young Ji International School / College

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   



 



dioxide, chlorofluorocarbons (CFCs) and nitrogen oxides produced byindustry and motor vehicles. Photochemical ozone and smog are created as nitrogen oxides and hydrocarbons react to sunlight. Particulate matter, or fine dust is characterized by their micrometre size PM10 to PM2.5.

Light pollution: includes light trespass, overillumination and astronomical interference.

Littering: - the criminal throwing of inappropriate man-made objects, unremoved, onto public and private properties.

Noise pollution: - which encompasses roadway noise, aircraft noise, industrial noise as well as high-intensity sonar.

Soil contamination occurs when chemicals are released by spill or underground leakage.

Among the most significant soil contaminants are hydrocarbons, heavy metals, MTBE, herbicides, pesticides and chlorinated hydrocarbons.

Radioactive contamination, resulting from 20th century activities in atomic physics, such as nuclear power generation and nuclear weapons research, manufacture and deployment. (See alpha emitters and actinides in the environment.)

Thermal pollution, is a temperature change in natural water bodies caused by human influence, such as use of water as coolant in a power plant.

Visual pollution, which can refer to the presence of overhead power lines, motorway billboards, scarred landforms (as from strip mining), open storage of trash, municipal solid waste or space debris.

Water pollution, by the discharge of wastewater from commercial and industrial waste (intentionally or through spills) into surface waters; discharges of untreated domestic sewage, and chemical contaminants, such as chlorine, from treated sewage; release of waste and contaminants into surface runoff flowing to surface waters (including urban runoff and agricultural runoff, which may contain chemical fertilizers and pesticides); waste disposal and leaching into groundwater; eutrophication and littering.

Effects Human health Adverse air quality can kill many organisms including humans. Ozone pollution can cause respiratory disease, cardiovascular disease, throat inflammation, chest pain, and congestion. Water pollution causes approximately 14,000 deaths per day, mostly due to contamination of drinking water by untreated sewage in developing countries. As of 2012, half the homes in India do not have a toilet; people defecate out in the open, in ditches or fields. Over ten million people in India fell ill with waterborne illnesses in 2013, and 1,535 people died, most of them children. Nearly 500 million Chinese lack access to safe drinking water. A 2010 analysis estimated that 1.2 million people died prematurely each year in China because of air pollution. The WHO estimated in 2007 that air pollution causes half a million deaths per year in India. Studies have estimated that the number of people killed annually in the US could be over 50,000.

Oil spills can cause skin irritations and rashes. Noise pollution induces hearing loss, high blood pressure, stress, and sleep disturbance. Mercury has been linked to developmental deficits in children and neurologic symptoms. Older people are majorly exposed to diseases induced by air pollution. Those with heart or lung Young Ji International School / College

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disorders are at additional risk. Children and infants are also at serious risk. Lead and other heavy metals have been shown to cause neurological problems.

Chemical and radioactive substances can cause cancer and as well as birth defects.

Environment Pollution has been found to be present widely in the environment. There are a number of effects of this:  Bio magnification describes situations where toxins (such as heavy metals) may pass through trophic levels, becoming exponentially more concentrated in the process.  Carbon dioxide emissions cause ocean acidification, the ongoing decrease in the pH of the Earth's oceans as CO 2 becomes dissolved.  The emission of greenhouse gases leads to global warming which affects ecosystems in many ways.  Invasive species can out compete native species and reduce biodiversity.

Invasive plants can contribute debris and biomolecules (allelopathy) that can alter soil and chemical compositions of an environment, often reducing native species competitiveness.  Nitrogen oxides are removed from the air by rain and fertilise land which can change the species composition of ecosystems.  Smog and haze can reduce the amount of sunlight received by plants to carry out photosynthesis and leads to the production of tropospheric ozone which damages plants.  Soil can become infertile and unsuitable for plants. This will affect other organisms in the food web.  Sulfur dioxide and nitrogen oxides can cause acid rain which lowers the pH value of soil.

Ways to Maintain Ecological Balance The Earth's organisms interact with their environment in a delicately balanced cycle.

Energy from the sun is used by plants which are in turn used as food by other creatures. The cycle continues as plant and animal life forms die and are consumed by microorganisms. This cycle of life is in jeopardy from humanity's overuse of natural resources and damage to the ecosystem from pollution.

Manage Natural Resources Carefully The expansion of civilization inflicts a growing burden on the ecosystem. Minerals, fossil fuels and other natural resources are being depleted at an alarming rate.

Overfishing and habitat destruction are causing a loss of biodiversity that will have long-term negative consequences on the ecosystem. Species needed to maintain a balanced ecology are threatened with extinction from overuse or destruction of their habitat. This can easily be seen in marine ecosystems where the loss of just a few species can threaten an entire ecosystem. A concerted effort to use natural resources in a sustainable manner will help to protect and maintain ecological balance, according to a webpage on the University of Michigan website.

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Control Population In nature, predators prevent species from over populating. Unfortunately, humans don't have any natural predators to control the population. It is necessary for action to be taken at the individual level and by governments to control population. This problem must be addressed despite emotional, cultural or religious sensitivity to the issue.

Just as too many fish in your aquarium fouls the water, too many humans on the planet can upset the ecological balance. Between 1927 and 1987, the Earth's population increased to 5 billion. By the year 1999 total population reached 6 billion and it is estimated that nearly 9 billion people will be living on the Earth in the year 2050, according to the University of Michigan webpage. Controlling the birth rate through contraception and family planning will reduce the strain on the ecosystem by reducing the rate at which people consume natural resources.

Protect the Water Contamination from sewage, and pollution from manufacturing and agricultural runoff threatens the balance of marine ecosystems. Sewer and agricultural runoff can cause a cascade of damaging effects on the ecosystem. Taking steps to reduce or eliminate pollution from nonpoint sources such as streets and farms will help to maintain the ecological balance.

Sewage and run-off of agricultural fertilizer can cause the rapid growth of algae in lakes and streams. The growth of algae blocks sunlight and depletes the oxygen in the water, according to a webpage on the University of South Alabama website. This causes a reduction in the amount of natural plant life in the marine ecosystem. The animals that feed on the plants die, which leads to the death of animals that prey on them. The decaying algae promote the growth of anaerobic organisms, which release compounds into the water that are toxic to marine animals.

What You Can Do Protecting the ecological balance is an issue that everybody can become involved in.

You have the power to have a positive effect, no matter how small, in maintaining the delicate balance of the Earth's ecosystem. Recycle to help prevent the overharvesting of natural resources. Conserve energy by choosing more energy efficient appliances and automobiles. If everybody uses less energy pollution is reduced and less coal will be needed to power the nation and the world. Encourage family and friends to be ecologically aware in the ways that they live day-to-day. Just as many hands make light work, many individuals working together can help protect and maintain the ecosystem.

Pollution Worksheet Select the proper terms listed below to match the statements that follow. Write the letter of the term in the blank. a. biomagnification b. fauna c. thermal d. recycling e. sulfuric f. ecology g. biodegradable h. ozone i. natural resources j. phosphates k. sulfur dioxide l. eutrophication m. smog n. biotic o. flora p. abiotic q. fossil r. pesticides 1. ______Process by which wastes are converted into new products and materials

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2. ______The earth's materials that are used by living things for such needs as food, shelter, and manufacturing 3. ______The toxic air-polluting gas that causes acid rain 4. ______The term used to denote increasing concentration of pesticides and other pollutants in the food chain 5. ______Term applied to wastes that break down into harmless substances when exposed to the environment 6. ______The layer of the atmosphere thought to be breaking down because of air pollution 7. ______A collective term for animals in the environment 8. ______The study of the interaction of living organisms with their environment 9. ______The nonliving factors of an organism's environment 10. ______Chemicals used to kill unwanted insects 11. ______Type of pollution in which water is heated 12. ______A collective term for plants in the environment 13. ______The acid in acid rain 14. ______The living factors of an organism's environment 15. ______Process that can lead to the death of a body of water from pollutants

Module (Lesson: Cell) The cell (from Latin cella, meaning "small room") is the basic structural, functional and biological unit of all known living organisms. Cells are the smallest unit of life that can replicate independently, and are often called the "building blocks of life". The study of cells is called cell biology.

Cells consist of a protoplasm enclosed within a membrane, which contains many biomolecules such as proteins and nucleic acids.Organisms can be classified as unicellular (consisting of a single cell; including most bacteria) or multicellular (including plants and animals). While the number of cells in plants and animals varies from species to species, humans contain about 100 trillion (1014) cells. Most plant and animal cells are visible only under the microscope, with dimensions between 1 and 100 micrometres.

The cell was discovered by Robert Hooke in 1665. The cell theory, first developed in 1839 by Matthias JakobSchleiden and Theodor Schwann, states that all organisms are composed of one or more cells, that all cells come from preexisting cells, that vital functions of an organism occur within cells, and that all cells contain the hereditary information necessary for regulating cell functions and for transmitting information to the next generation of cells. Cells emerged on Earth at least 3.5 billion years ago.

There are two types of cells, eukaryotes, which contain a nucleus, and prokaryotes, which do not. Prokaryotic cells are usually single-celled organisms, while eukaryotic cells can be either single-celled or part of multicellular organisms.

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Comparison of features of prokaryotic and eukaryotic cells Prokaryotes Eukaryotes Typical bacteria, arc organism protists, fungi, plants, animals haea s Typical size

~ 1–5 µm[9]

~ 10–100 µm[9]

nucleoid Type region; no true nucleus with double membrane of nucleus true nucleus DNA

circular (usually)

linear molecules (chromosomes) with histone proteins

RNA/prot coupled in RNA synthesis in ein the cytoplas protein synthesis in the cytoplasm synthesis m

the

nucleus

Ribosome 50S and 30S 60S and 40S s Cytoplas very few mic highly structured by endomembranes and a cytoskeleton structures structure flagella Cell flagella made and cilia containing microtubules; lamellipodia and filopodi movement of flagellin a containing actin Mitochond none ria

one to several thousand (though some lack mitochondria)

Chloropla none sts

in algae and plants

Organizat usually single single cells, colonies, higher multicellular organisms with ion cells specialized cells Cell division

Binary Mitosis (fission fission (simpl Meiosis e division)

or

budding)

Prokaryotic cells were the first form of life on Earth, as they have signaling and selfsustaining processes. They are simpler and smaller than eukaryotic cells, and lack membrane-bound organelles such as the nucleus. Prokaryotes include two of the domains of life, bacteria and archaea. The DNA of a prokaryotic cell consists of a single chromosome that is in direct contact with the cytoplasm. The nuclear region in the cytoplasm is called the nucleoid. Most of the prokaryotes are smallest of all organisms. Most prokaryotes range from 0.5 to 2.0 µm in diameter.

A prokaryotic cell has three architectural regions:

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





On the outside, flagella and pili project from the cell's surface. These are structures (not present in all prokaryotes) made of proteins that facilitate movement and communication between cells.

Enclosing the cell is the cell envelope – generally consisting of a cell wall covering a plasma membrane though some bacteria also have a further covering layer called a capsule. The envelope gives rigidity to the cell and separates the interior of the cell from its environment, serving as a protective filter. Though most prokaryotes have a cell wall, there are exceptions such as Mycoplasma (bacteria) and Thermoplasma (archaea). The cell wall consists of peptidoglycan in bacteria, and acts as an additional barrier against exterior forces. It also prevents the cell from expanding and bursting (cytolysis) from osmotic pressure due to a hypotonic environment. Some eukaryotic cells (plant cells and fungal cells) also have a cell wall.

Inside the cell is the cytoplasmic region that contains the genome (DNA), ribosomes and various sorts of inclusions. The prokaryotic chromosome is usually a circular molecule (an exception is that of the bacterium Borreliaburgdorferi, which causes Lyme disease). Though not forming a nucleus, the DNA is condensed in a nucleoid.

Prokaryotes can carry extrachromosomal DNA elements called plasmids, which are usually circular. Plasmids encode additional genes, such as antibiotic resistance genes.

Plants, animals, fungi, slime moulds, protozoa, and algae are all eukaryotic. These cells are about fifteen times wider than a typical prokaryote and can be as much as a thousand times greater in volume. The main distinguishing feature of eukaryotes as compared to prokaryotes is compartmentalization: the presence of membrane-bound compartments in which specific metabolic activities take place. Most important among these is a cell nucleus, a membrane-delineated compartment that houses the eukaryotic cell's DNA. This nucleus gives the eukaryote its name, which means "true nucleus". Other differences include:  The plasma membrane resembles that of prokaryotes in function, with minor differences in the setup. Cell walls may or may not be present.  The eukaryotic DNA is organized in one or more linear molecules, called chromosomes, which are associated with histone proteins. All chromosomal DNA is stored in the cell nucleus, separated from the cytoplasm by a membrane. Some eukaryotic organelles such as mitochondria also contain some DNA.  Many eukaryotic cells are ciliated with primary cilia. Primary cilia play important roles in chemosensation, mechanosensation, and thermosensation. Cilia may thus be "viewed as a sensory cellular antennae that coordinates a large number of cellular signaling pathways, sometimes coupling the signaling to ciliary motility or alternatively to cell division and differentiation."  Eukaryotes can move using motile cilia or flagella. Eukaryotic flagella are less complex than those of prokaryotes.

Cell Structure and Function Organelles and Their Functions In this lab you will look at the eukaryotic cells of plants and animals. Eukaryotic cells are distinguished from the more primitive prokaryotic cells by the presence of 1) cytoplasmic membranous organelles, 2) a nuclear membrane (i.e. a true nucleus), Young Ji International School / College

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and 3) chromosomal proteins. In this lab we will focus primarily on organelles, their functions within the cell and how they differ between plant and animal cells.

Think of the cell as a microscopic city. Like a real city it requires many services to keep it clean and running smoothly. Think of some of the services a real city needs: traffic control, waste disposal, and authority figure just to name a few. Like our imagined city a cell needs the same services. Organelles are the ―workers‖ that provide these services. The following is a list describing the various functions of some common organelles.

The NUCLEUS (―mayor of city hall‖) The nucleus houses the majority of genetic material of a cell. The nucleus is the ―brain‖ of the cell and controls all activity within the cell. Using DNA as a blueprint ( like the blueprints of a city) the nucleus directs the production of proteins. You will learn about this process in the DNA Transcription and Translation lab.

A nucleus with the DNA coiled into chromatin.

Electron microscope picture of a nucleus RIBOSOMES (―lumber or brick yard‖) The ribosomes carry out manual labor in the form of protein synthesis for the nucleus. They bring together all the raw ingredients such as RNA (copies of the original DNA blueprints) and amino acids to assemble proteins. The proteins created are essential to cell and organismal function. Think of proteins as machinery for cell functions much like electricity and plumbing are essential in a real city. For example, enzymes are a type of protein without which life could not exist.

The large and small subunits of ribosomal RNA translating an mRNA strand into a polypeptide chain.

Refer to DNA Transcription and Translation for further reading.

The ENDOPLASMIC RETICULUM (―highways and road systems‖) Young Ji International School / College

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There are two types of endoplasmic reticulum (ER) – Smooth ER and Rough ER. This extensive network makes up approximately one half of all membranous tissue of the cell and is the site of membrane and protein synthesis. The ER system is much like a road system along which industry can be found. Goods are manufactured and shipped to needed areas via the road system. Rough ER is named for the presence of ribosomes along its membrane and is the source of proteins. Smooth ER lacks ribosomes and is responsible for lipid synthesis and processes a variety of metabolic processes such as drug detoxification.

Can you tell the difference between the smooth and rough ER? CELL MEMBRANE (―City Border‖) and CELL WALL (―City Wall‖) Cell membranes are found in animal cells whereas cell walls are found in plant cells.

Cell walls and membranes have similar functions. Like a city perimeter, cell membranes surround the cell and have the ability to regulate entrance and exit of substances, thereby maintaining internal balance. These membranes also protect the inner cell from outside forces. Cell walls, as the city analogy implies, are much stronger than cell membranes and protect cells from lysing (exploding) in extremely hypotonic (diluted) solutions. You will learn more about these concepts in the Biological Membranes lab.

Artist rendition of an animal cell membrane. wall.

CYTOSKELETON (―steel girders‖)

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Artist rendition of a plant cell

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The cytoskeleton makes up the internal framework, like the steel girders that are the framework for buildings in a city that gives each cell its distinctive shape and high level of organization. It is important for cell movement and cell division (mitosis).

Picture of a cell‘s cytoskeleton- a complex network of tubules and filaments.

CYTOPLASM (―lawns and parks‖) Cytoplasm is a semi-fluid substance (think gelatin) found inside the cell. The cytoplasm encases, cushions and protects the internal organelles. It is the cell landscape found in any space where organelles are not and therefore is much like the lawns and parks of our city.

The cytoplasm is the substance surrounding the visible vacuoles in this cell.

GOLGI APPARATUS (―post office‖) Like a post office, the golgi apparatus is used for shipping those goods created by the ER and ribosomes to the rest of cell.

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EM picture of a golgi apparatus Artist rendition of the Golgi Complex CHLOROPLASTS (―solar energy plant‖) Chloroplasts are organelles found only in plant cells. Like a solar energy plant they use sunlight to create energy for the city. Chloroplasts are the site of photosynthesis a process in which the plant uses carbon dioxide, water and sunlight to create energy in the form of glucose for the plant cell as well as heterotrophs that consume the plant.

Artist rendition of a chloroplast- site of photosynthesis in plant cells.

MITOCHONDRIA (―energy plant‖) Mitochondria are found in both plant and animal cells and is the site of cellular respiration. Through this process that will be covered in the Photosynthesis and Respiration lab ATP is created which is used for energy by the cell.

Electron microscope picture of a mitochondria.

LYSOSOMES (―waste disposal and recycling‖) Young Ji International School / College

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The lysosomes are digestive sacs that can break down macromolecules in the cell using the process of hydrolysis. The digestion is carried out with lysosomal enzymes found in the lysosome. Like waste disposal in a city, lysosomes help keep excessive or bulky macromolecules from building up in the cell.

Electron microscope picture of a lysosome.

VACUOLES and VESICLES (―warehouses, water towers or garbage dumps‖) Think of these membrane sacs that have a variety of functions as containment units for anything in excess in a city. They can hold many substances from organic molecules to simple excess water. Plant cells have a central vacuole that is important in maintaining plant turgidity. You can read more about this phenomenon in the Biological Membranes Lab.

Central vacuole of a plant cell.

Plant versus Animal Cells Now that you know some important cell organelles let us identify those that distinguish plant cells from animal cells. From the descriptions above, we can identify three organelles unique to plant cells: 1) cell wall (versus a cell membrane in animal cells), 2) central vacuole (regular vacuoles are found in animal cells) and 3) chloroplasts animals do not perform photosynthesis. This is what makes plants autotrophs and animals heterotrophs.)

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Animal and Plant Cells Worksheet Direction: Identify the different parts.

Questions: 1. Which type of cell is this?

2. How do you know which type of cell it is?

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Questions: 1. Which type of cell is this?

2. How do you know which type of cell it is?

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Module (Lesson: Cellular Transport) Types of Transport There are 3 types of transport in cells: 1. Passive Transport: does not use the cell‘s energy in bringing materials in & out of the cell 2. Active Transport: does use the cell‘s energy in bringing materials in & out of the cell 3. Bulk Transport: involves the cell making membrane bound vesicles to bring materials in & out of the cell Passive Transport There are 3 types of passive transport: 1. Diffusion: involves small or uncharged molecules entering & leaving the cell 2. Osmosis: involves water entering & leaving the cell 3. Facilitated Diffusion: involves large or charged molecules that need a protein helper to get in & out of the cell Diffusion Diffusion is the net movement of a substance (liquid or gas) from an area of higher concentration to one of lower concentration. A drop of dye in water is concentrated but then begins to disperse throughout the water moving from an area of high to an area of low concentration.

Diffusion when the substance has fully dispersed throughout the container, it has reached equilibrium. Notice in the picture below how molecules A and B are evenly distributed throughout the container. When equilibrium has been reached, there is no longer a concentration gradient. A concentration gradient is the difference in concentration between two areas.

Diffusion Certain molecules can freely diffuse across the cell membrane. Look at the picture below-hydrophobic molecules and small uncharged molecules can diffuse through the membrane but large molecules or ions (atoms with a positive or negative charge) cannot move through the membrane.

Osmosis Osmosis is the diffusion of water from an area of high concentration to an area of low concentration across a membrane. Cell membranes are completely permeable to Young Ji International School / College

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water and the amount of water in the environment has a large effect on the survival of a cell. The picture shows a tube separated by a membrane and how the water moves from an area of high concentration to an area of low.

Osmosis There are 3 types of solutions that involve water and how they affect the cell. They are: 1.Hypertonic Solution: the solution the cell is placed in has less water than the cell 2. Hypotonic Solution: the solution the cell is placed in has more water then the cell 3. Isotonic Solution: the solution the cell is placed in has equal amount of water as the cell

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Hypertonic A hypertonic solution, there is a higher concentration of water inside the cell than outside the cell. A hypertonic solution has more solute (salt, sugar, etc.) than the cell and this causes there to be less water in the solution. Water flows from an area of high concentration to an area of low and leaves the cell. This loss of water causes the cell to shrivel. In animal cells, the shriveling is called crenating. The red blood cells in the picture to the left have crenated. In plant cells, plasmolysis occurs and the cell membrane shrinks away from the cell wall. Death will result in both cells.

Crenated red blood cells

Plasmolysis occurring in a plant cell

Hypotonic Solution In a hypotonic solution, the solution contains a higher percentage of water than the cell. A hypotonic solution has less solute than the cell and this causes the solution to have more water than the cell. When a cell is placed in a hypotonic solution, water flows from an area of high concentration to an area of low and rushes into the cell.

This causes the cell to expand and possibly burst. In animal cells, the cell bursts or will lyse, killing the cell. In plant cells, the cell membrane is pressed up against the cell wall but the cell wall does not allow the cell to expand anymore and the plant cell does not die.

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Plant cell in hypotonic solution

Red blood cells beginning to lyse

Isotonic Solution In an isotonic solution, there is the same percentage of water on the outside of the cell as the inside of the cell. An isotonic solution has the same amount of solute as the inside of the cell. Water moves at a constant rate in and out of the cell and the cell maintains its original shape.In animal and plant cells, the cell keeps its shape when in an isotonic solution. Most cells live in an isotonic environment and they are able to maintain their shape and survive.

Plant cells in an isotonic solution

Red blood cell in an isotonic solution Hypertonic and Hypotonic Solutions The plant cell to the left is placed in distilled water and salt solution. Notice what happens to the cell in the different types of solutions.

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The red blood cell to the right is placed in distilled water and salt solution. Notice what happens to the cell in the different types of solutions.

Facilitated Diffusion Some molecules are too large to pass through the cell membrane by diffusion and need help to cross. These molecules use facilitated diffusion. Facilitated diffusion is the flow of large molecules from an area of high concentration to an area of low using proteins in the cell membrane. Glucose is able to enter our cells from the blood stream by facilitated diffusion. A glucose molecule is too big to squeeze through the phospholipid bilayer and needs protein channels to help it pass into the cell. These protein ―helpers‖ are extremely important because they allow much needed molecules to enter our cells. Without them, our cells would not have glucose and our cells would not be able to make energy.

Active Transport The types of transport discussed so far are passive transport and do NOT require a cell to use its energy-the molecules flow withthe concentration gradient. There are times when the cell wants to pump againstthe gradient and to do so, it must use energy. The use of energy to pump molecules against the gradient is called active

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transport. A cell uses energy in the form of ATP (adenosine tri-phosphate). When energy is taken from ATP, it turns into ADP. The sodium-potassium pump in nerve cells is an example of active transport.

Sodium and potassium atoms are pumped against the gradient using ATP. By pumping against the gradient, the cell builds an even bigger gradient (difference between concentrations across the membrane) that helps nerve impulses.

Bulk Transport The last kind of cell transport is bulk transport. Bulk transport involves the cell membrane making vesicles to bring materials in and out of the cell. There are two kinds of bulk transport: 1. Exocytosis: moving materials OUT of the cell.

2. Endocytosis: moving materials INTO the cell.

There are 2 types of endocytosis: 1. Pinocytosis: bringing small molecules or liquids into the cell 2. Phagocytosis: bringing large molecules into the cell

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Exocytosis Exocytosis is the process of exporting materials out of the cell by forming a membrane bound vesicle around the materials. The cell uses exocytosis to get rid of cell waste or to export proteins made in the cell to give to other cells.

The proteins or waste are taken to the Golgi body where the materials are packaged into a membrane bound vesicle. The vesicle then merges with the cell membrane and the materials are released into the outside environment.

exocytosis

Micrograph of a vesicle expelling its contents

Endocytosis-Pinocytosis Endocytosis is the movement of materials into the cell through membrane bound vesicles. One type of endocytosis is called pinocytosis, or ―cell drinking‖. Pinocytosis is the movement of small molecules or liquids into the cell through bulk transport.

The small molecules make contact with the cell membrane and the cell membrane pinches off around the molecules. Pinocytosis is how animal cells make vacuoles (water filled sacs).

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Endocytosis-Phagocytosis The other type of endocytosis is phagocytosis, or ―cell eating‖. Phagocytosis is the movement of large molecules into the cell through bulk transport. The large molecules make contact with the cell membrane and the cell membrane pinches off around the molecules. The lysosomes then fuse with the vesicle and break down the large molecules into nutrients. Phagocytosis is how white blood cells engulf bacteria and break them down.

Micrograph of a white blood cell engulfing virus particles.

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a cell taking in a food particle and breaking it down.

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Endocytosis

Above are examples of endocytosis. Determine what type of endocytosis is shown in each situation. Notice the micrograph of actual cells performing the different types of endocytosis.

Activity Module (Lesson: Cellular Transport) Section A: Cell Membrane Structure 1. Label the cell membrane diagram. You‘ll need to draw lines to some of the structures. **Draw cholesterol molecules in the membrane. ** channel proteins integral proteins

phosphate hydrophilic head fatty acid hydrophobic tail

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carbohydrate chain peripheral proteins

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2. The cell membrane of the red blood cell will allow water, carbon dioxide, oxygen and glucose to pass through. Because other substances are blocked from entering, this membrane is called ______________________________.

3. How many layers are found in the cell membrane? ___________ 4. What are the molecules that make up the majority of the membrane? _______________________ 5. What do you call the phenomenon when you have a different concentration of materials on the inside and the outside of the cell? _______________________________ 6. Explain the concentration of molecules when a cell reaches dynamic equilibrium. ___________________________________________________________________ 7. The __ portion of the cell membrane functions as a barrier while the __ portion determines specific functions, including pumps, receptors, adhesion, etc. a. carbohydrate, nucleic acid b. lipid, carbohydrate

c. lipid, protein d. nucleic acid, lipid

8. What is the function of peripheral proteins? _________________________________________ 9. What is the function of integral proteins? ___________________________________________ 10. What factors can influence the rate of transport? ___________________________________________________________________ 11. What is homeostasis? __________________________________________________________

Section B: Graphic Organizer -- Fill in the missing information.

Passive transport

No _________________

_____ to ______ concentration

_________ the concentration gradient

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Active Transport

Needs ________________

_____ to _____ concentration

___________ the concentration gradient

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3rd Quarter Module (Lesson: The Diverse form of Organism)

Carl Linnaeus (1707-1778) also known as Carl von Linne or Carolus Linnaeus, is often called as the father of taxonomy. His system for naming, ranking, and classifying organisms is still use wide today (with many changes). His ideas on classification have influenced generations of biologists during and after his own lifetime, even those opposed to the philosophical and theological roots of his work.

Taxonomy is the part of science that focuses on naming and classifying or grouping organisms. A Swedish naturalist named Carolus Linnaeus is considered the 'father of taxonomy' because in the 1700s, he developed a way to name and organize species that we still use today. His two most important contributions to taxonomy were: 1. A hierarchical classification system 2. The system of binomial nomenclature (a 2-part naming method) 3. During his lifetime, Linnaeus collected around 40,000 specimens of plants, animals, and shells. He believed it was important to have a standard way of grouping and naming species. So in 1735, he published his first edition of SystemaNaturae (The System of Nature), which was a small pamphlet explaining his new system of the classification of nature.

4. He continued to publish more editions of SystemaNaturae that included more named species. In total, Linnaeus named 4,400 animal species and 7,700 plant species using his binomial nomenclature system. The tenth edition of SystemaEnglish is System of nature through the three kingdoms of

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nature, according to classes, orders, genera and species, with characters, differences, synonyms, places.

Living organisms exist in a large scale of sizes and various degrees of intricacy. The first form of life on Earth exists as cell or as colony of cells. Many of the living organisms on Earth are probably represented by unicellular organisms like bacteria and protists. And the rest of multicellular organisms through evolution this kind of organisms has resulted in highly visible forms that we commonly called plants, fungi and animals.

There are different species of organisms. Life scientists identify, group, and name these organisms to facilitate the study about them, they are called taxonomist. The science which deals with the branch of study is called taxonomy.

Scientist use one main system of grouping or classification. The classification of species is based on the organisms‘ evolutionary relationships.

These are the traits of organisms that they have inherited. These traits include the features such as the structure and chemical make-up of an organisms body and bodyparts.

Linnean System of Classification In SystemaNaturae, Linnaeus classified nature into a hierarchy. He proposed that there were three broad groups, called kingdoms, into which the whole of nature could fit. These kingdoms were animals, plants, and minerals. He divided each of these kingdoms into classes. Classes were divided into orders. These were further divided into genera (genus is singular) and then species. We still use this system today, but we have made some changes.

Today, we only use this system to classify living things. (Linnaeus included nonliving things in his mineral kingdom.) Also, we have added a few additional levels in the hierarchy. The broadest level of life is now a domain. All living things fit into only three domains: Archaea, Bacteria, and Eukarya. Within each of these domains there are kingdoms. For example, Eukarya includes the kingdoms Animalia, Fungi, Plantae, and more. Each kingdom contains phyla (singular is phylum), followed by class, order, family, genus, and species. Each level of classification is also called a taxon (plural istaxa).

Binomial Nomenclature Before Linnaeus came up with a standardized system of naming, there were often many names for a single species, and these names tended to be long and confusing. Linnaeus decided that all species names should be in Latin and should have two parts. Remember, this 2-part system is called binomial nomenclature. It is still used today and gives every species one unique 2-part scientific name.

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The formal system of naming species is called binomial nomenclature (especially in botany, but also used by zoologists), binominal nomenclature (since 1953, the technically correct form in zoology), or binary nomenclature.

The essence of this system of naming is this: each species name is formed out of (modern scientific) Latin (or is a Latinized version of other words), and has two parts, the genus name and the species name (also known as the specific epithet), for example, Homo sapiens, the name of the human species. The two-part name of a species is popularly known as the Latin name. However, biologists and philologists prefer to use the term scientific name rather than "Latin name", because the words used to create these names are not always from the Latin language, even if the words have been Latinized in order to make them suitable. Instead names are often derived from ancient Greek word roots, or words from numerous other languages.

Frequently species names are based on the surname of a person, such as a wellregarded scientist, or are a Latinized version of a relevant place name.

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Carl von LinnĂŠ (also known as Linnaeus) chose to use a two-word naming system, and did not use what over time came to be a full seven-category system (kingdom-phylum-class-order-family-genus-species.)

Linnaeus chose a binomial nomenclaturescheme, using only the genus name and the specific name or epithet which together form the whole name of the species. For example, humans belong to genus Homoand their specific name is sapiens. Humans as a species are thus classified as Homo sapiens. The first letter of the first name, the genus, is always capitalized, while that of the second is not, even when derived from a proper noun such as the name of a person or place. Conventionally, all names of genera and lower taxa are always italicized, while family names and higher taxa are printed in plain text. Species can be divided into a further rank, giving rise to a trinomial name for a subspecies (trinomen for animals, ternary name for plants).

Biologists, when using a name of a species, usually also give the authority and date of the species description. Thus zoologists will give the name of a particular sea snail species as: Patella vulgata Linnaeus, 1758. The name "Linnaeus" tells the reader who it was that described the species; 1758 is the date of the publication in which the original description can be found, in this case the book SystemaNaturae.

After almost 200 years of discovery and controversy over the classification of organism, the best compromise classification scheme was defined by R. H. Whittaker in 1963- the five kingdom classification scheme. This scheme places bacteria and blue- green algae (Cyanobacteria) under the most primitiveKingdom Monera, Protozoans and some types of algae are grouped in the Kingdom Protista. Molds, mushrooms and yeast are classified under Kingdom Fungi.

Multicellular algae and land plants make up the Kingdom Plantae, and multicellular animals form the Kingdom Animalia.

Relative Study of the Five Kingdom’s Characteristics Characteristics

Monera

Protista

1. Unicellul Most are Most are ar or unicellular unicellular Multicell ular 2. Presenc None Present e of Nuclear Membra ne Young Ji International School / College

Fungi

Plantae

Most are Multicellula multicellula r r Present

Present

Multicellula r Multicellula r

Present

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3. Type of Prokaryotic Cell 4. Presenc None e of Mitochon dria 5. Mode of Asexual reproduc tion

Eukaryotic

Eukaryotic

Eukaryotic

Eukaryotic

Present

Present

Present

Present

Sexual and Sexual and Sexual and Mostly asexual asexual asexual sexual, some asexual 6. Ability to Some Some Do not Perform Do not perform perform perform perform photosynth perform photosyn photosynth photosynth photosynth esis photosynth thesis esis esis esis esis 7. Mode of Heterotrop Heterotrop Heterotrop Autotrophs Heterotrop Nutrition h and h and h h autotrophs autotrophs 8. Motility Some Some Primarily Primarily Motile move, move, non-motile non-motile others do others do not not 9. Habitat Aquatic Aquatic Mostly Mostly Aquatic and and Terrestrial Terrestrial and terrestrial terrestrial terrestrial 10. Example Bacteria, Algae and Mushroom Mushroom All animals s blue green protozoans s, yeasts, s, yeasts, algae rusts, rusts, bread bread molds molds

Taxonomy worksheet Vocabulary Distinguish between the terms in each of the following pairs. a. Taxonomy and Binomial nomenclature b. K i n g d o m ,

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c. species

d. Phylum , genus

Complete the table for at least 2 organisms. common name Kingdom Phylum Class Order Family Genus Species Explain the why is giving scientific name very important.

Module (Lesson: Viruses and Monerans) Viruses: An organism is classified as living when it can reproduce, it responses to stimuli, they grow and can develop by itself.

The basic structure of a virus is that it is noncellular and it‘s made up of genetic material and protein that can invade other living cells. It has core of nucleic acid which is surrounded by protein coat called the protein capsid, it protects the nucleic acid core. It contains genes to several hundred genes. The nuecleic acid is either DNA or RNA, it‘s never both.

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The more complex structure is in the bacteriophages. They invade bacteria and they have a head region and a tail region. The head region is the capsid. Many bacteria‘s habe a membranous envelope that acts similarly to a cell. They vary from 10-400 nanometers.

The Host Cell: The host cell is where the viruses invade or infect so that they‘ll be able to reproduce and live.

LYTIC CYCLE AND LYSOGENIC CYCLE: The difference between the lytic cycle and the lysogenic cycle is that in the lytic cycle the host cell will lyse, the bacteriophage attaches itself to the bacterium using its tail fibres and the it injects its DNA in the cell and then the host cell is tricked into producing viral genes and the genes shut down and they take over the host cell while in the lysogenic cycle the virus does not reproduce and lyse the host cell. The virus just enters the host cell and is inserted to the DNA of the host cell and once the its inserted the Viral DNA, known as the prophage can block the entry of other viruses into the cell and it can even help the host cell ‗s DNA, but the virus will not stay as a prophage it will become active and remove itself from the host cell and then eventual enter the lytic cycle.

Viral Specify: Specific viruses infect specific organisms. A plant virus can‘t infect an animal. An example would be rabies where it infects all mammals and some birds. There‘s also the polio vaccine where it prevents or give a little chance for the humans to get polio.

Body’s Basic Lines of Defense: The primary line of defense are the earwax, pus, eyelids, stomach acid, tears, sweat, and many more. It is a nonspecific defense. Saliva, tears and swear are contained with lysozyme. Lysozyme breaks down the cells walls of bacteria.

The secondary line of defense would be when huge numbers of pathogens enter your body the second line of defense begins which is called the inflammatory response, The white blood cells start to leak from the blood vessels in the nearest tissue and the bacteria would be attacked by the phagocytes, which are white blood cells that destroy the bacteria and it would cause the area to be inflamed.

The third line of defense would be where the lymphocytes and antibodies come in.

The antibodies is a y shaped antigen and they will attach to the viral antigens and link the m in a large mass and destroy them. Some examples of antigens would be carbs, protein and lipids.

Some ways to reduce the spread of viral diseases would be to wash your hands properly and frequently, drink water and keep your mouth closed and stay away from sick people.

Kingdom Monera: The monerans are the most successful organism when it comes to how long they‘ve lived, their ability in reproducing, how they adapt and also how they survive. They have the simplest cell structure because they have prokaryotic cells, a prokaryotic cell means that there‘s no nucleus and other membrane bound organelles. The cell only have a cell membrane, cell wall, DNA, plasmids, ribosomes and cytoplasm and also thylakoids (for the photosynthetic prokaryotes). They are also the bottom of the Young Ji International School / College

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food chain which means that they are the ones who recycle. They are used to make yogurts, tan leather and treat sewage and industrial and manufacturing processes.

Classification: The classification of the monerans would be divided into 4 phyla and they are Eubacteria, Cyanobacteria, Archaebacteria and Prochlorobacteria.

Eubacteria is the largest phylum in the kingdom and it comes from the word ―true‖ in latin. They use their flagella to move. Inside the cell wall is a cell membrane. Some live in the soil, some live in the hosts as a parasite. Some make their own food through photosynthesis.

Cyanobacteria are also called ―blue-green ‖ bacteria. They are found all over the world. Only few of them have a blue-green colour and those are the ones with a phycocyanin (a blue pigment). They also have a green pigment which is the chlorophyll a. They produce a lot of the world‘s oxygen. They can be unicellular or grow together, often in filaments.

Archaebacteria and Prochlorobacteria - The archaebacteria live outrageously in harsh environments. Some of them don‘t need oxygen, in other words they are anaerobic and they can be found living deep within mud or inside the digestive tracts of animals.

- The prochlorobacteria are the newly discovered species of photosynthetic bacteria that are like the cyanobacteria but contains both chlorophyll a and chlorophyll b.

Cell Shape: There three kinds of shapes. shaped), cocci (sphere-shaped) and spirilla (spiral-shaped).

There‘s bacilli (rod-

Motility: They move by using their flagella, some by wriggling and others glide over a layer of a mucus-like slime and some don‘t move at all.

Ecological Role: They can be used to make antibiotics. They are also used in many kinds of production of food, beverages and consumer products. They are also used to produce vitamins, chemicals such as aceton and butanol, digest petroleum and remove waste from water. They we‘re also used for mining and synthesize drugs and chemicals in a wide variety of ways. They also recycle and decompose dead material.

Nutrition: Some monerans are heterotrophs which means that they can‘t make their own food, there are also other monerans that are chemotrophic autotrophs where they live in harsh environments and they get their energy from inorganic molecules like hydrogen, ammonia, sulfur and iron. There are also monerans that are phototrophic autotrophs where they make their own food and uses photosynthesis.

Lastly, there are phototrophic heterotrophs where they take in organic molecules and at the same can use photosynthesis.  Respiration: There are two kinds of respiration and they are aerobic respiration and fermentation. Aerobic respiration you need oxygen and fermentation are for the anaerobes and they don‘t require oxygen. There are obligate aerobes where they constantly need oxygen to live and there are obligate anaerobes where they can‘t live with oxygen around, if they get in

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the canned food they will produce toxins and cause botulism but there are also faculative anaerobes where they can live with or without oxygen.

Reproduction: They reproduce asexually by binary fission which means that when the bacterium has grown big enough it will replicate its DNA and divide in half and it will produce two identical ―daughter‖ cells. They reproduce every 15-20 minutes.

They also do conjugation where the ultimate is goal is genetic diversity and they exchange genetic formation with other bacteria. The donor (F+) sends parts of its DNA through a bridge made by protein to the recipient (F-).

Human Diseases: Some examples of bacterial disease: 1. Bubonic Plague 2. Chlamydia 3. Acne 4. Botulism 5. Salmonella 6. Gingivitis 7. Tetanus Beneficial Roles: They release carbon and nitrogen for recycling. They decompose dead and decaying matter as well.

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A virus reproduces itself by taking over a living cell and making it into a virus factory.

Viruses are tiny particles that cause disease in people, other animals, and plants.

Different viruses cause the common cold, influenza (flu), chicken pox, measles, AIDS, and many other diseases.

Monerans Moneranis a kingdom that contains unicellular organisms with a prokaryotic cell organization, (having no nuclear membrane), such as bacteria. The taxon Monera was first proposed as a phylum by Ernst Haeckel in 1866.

Subsequently, the phylum was elevated to the rank of kingdom in 1925 by ÉdouardChatton. The last commonly accepted mega-classification with the taxon Monera was the five-kingdom classification system established byRobert Whittaker in 1969.

Under the three-domain system of taxonomy, introduced by Carl Woese in 1977, which reflects the evolutionary history of life, the organisms found in kingdom Monera have been divided into two domains, Archaea and Bacteria (with Eukarya as the third domain). Furthermore the taxon Monera is paraphyletic (not all members descended from their most recent common ancestor), as Archaea and Eukarya are currently believed to be more closely related than either is to Bacteria. The term "moneran" is the informal name of members of this group and is still sometimes used (as is the term "prokaryote") to denote a member of either domain.[1] Most bacteria were classified under Monera however, Cyanobacteria (still often called the blue-green algae) were initially classified under Plantae due to their ability to photosynthesize.

Bacterial Cell The cell is the structural and functional unit of life. All living organisms on earth are made up of single or many cells.

Bacteria are single cellular microscopic organisms. The study of bacteria is known as bacteriology and it is a branch of microbiology. The singular world of bacteria is

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bacterium. Bacteria have been grouped into prokaryotic, which means absence of nucleus.

Structure of Bacteria

Characteristics of Bacteria → There are 3 types of bacteria based on their shapes such as: Bacteria grow in number not in size, but they make copies of themselves by dividing into half. There are three basic shapes of bacteria:  Rod shaped bacteria called as bacilli.  Spherical shaped bacteria called as cocci.  Curved shaped bacteria called as spirilla.

Some of the bacteria exist as single cells, others exist as cluster together.

Respiration in bacteria: Anaerobic bacteria: does not require oxygen for respiration.

Aerobic bacteria: require oxygen for respiration.

Gram staining bacteria are a method of differentiating bacterial species into two large groups, which are based on their chemical and physical properties of their cell wall.

Gram positive bacteria: Those bacteria when they are stained in gram stain results in purple colour.

Gram negative bacteria: Those bacteria when they are stained in gram stain results in pink colour.

Locomotion of bacteria: They move around by using their locomotion organs such as cilia and flagella.

Nutrition of bacteria: They exhibits different modes of nutrition level such as-

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 

 

Autotrophic bacteria: These bacteria are able to synthesize their own food.

For e.g.: Phototropic bacteria and chemosynthetic bacteria Heterotrophic bacteria: These bacteria are unable to synthesize their own food, hence they depends on other organic materials. For e.g.: saprophytic bacteria-these bacteria feeds on dead and decaying matter.

Symbiotic bacteria: These bacteria have a mutual benefit from other organisms. For e.g.: nitrogen fixing bacteria (or) rhizobium.

Parasitic bacteria: These bacteria are present in plants, animals and human beings. These bacteria feeds on host cells and causes harm to the host.

Reproduction in Bacteria: The reproduction in bacteria is mainly by cell division and binary fission. In some cases few bacteria also reproduce by budding.

Bacterial Cell Structures

Bacterial Shapes The most basic method used for identifying bacteria is based on the bacterium's shape and cell arrangement. This section will explain the three morphological categories which all bacteria fall into - cocci, bacilli, and spirilla. You should keep in mind that these categories are merely a way of describing the bacteria and do not necessarily refer to a taxonomic relationship. The most common shapes of bacteria include rod, cocci (round), and spiral forms. Cellular arrangements occur singularly, in chains, and in clusters. Some species have one to numerous projections called flagella enabling the bacteria to swim, making them motile organisms.

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Cocci (or coccus for a single cell) are round cells, sometimes slightly flattened when they are adjacent to one another. Cocci bacteria can exist singly, in pairs (as diplococci ), in groups of four (as tetrads ), in chains (as streptococci ), in clusters (as stapylococci ), or in cubes consisting of eight cells (as sarcinae .)

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Bacilli (or bacillus for a single cell) are rod-shaped bacteria. Since the length of a cell varies under the influence of age or environmental conditions, you should not use cell length as a method of classification for bacillus bacteria. Like coccus bacteria, bacilli can occur singly, in pairs, or in chains. Examples of bacillus bacteria include coliform bacteria, which are used as an indicator of wastewater pollution in water, as well as the bacteria responsible for typhoid fever.

Spirilla (or spirillum for a single cell) are curved bacteria which can range from a gently curved shape to a corkscrew-like spiral. Many spirilla are rigid and capable of movement. A special group of spirilla known as spirochetes are long, slender, and flexible.

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Bacteria Worksheet 1.) Label the following diagram of a typical bacterium

2.) Is the bacterium in the diagram a bacillus, coccus, or spirillum?

Explain. ______________________________________________________________ 3.) Suppose that this bacterium was a streptobacillus. What kind of colonies would you expect it to form?

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Explain. ______________________________________________________________ 4.) This bacterium is Gram -. What happens when it is subjected to Gram staining?

Explain. ______________________________________________________________ 5.) This bacterium is a facultative aerobe. What process or processes would you expect it to use to break down food?

Explain. ______________________________________________________________ ______________________________________________________________ ______________________________________________________________

Viruses Worksheet Fill in the blanks with appropriate term to have the sentence make sense.

1.) A virus is not considered to be a living organism by most scientists. It is not a cell, and therefore, is lacking in many of the cell parts. All viruses contain a protective ____________ and a core of _______________________. Since viruses cannot live outside a cell they are considered a(n) ______________.

2. Viruses are very specific in the types of organisms they infect. What are the 3 major groups (categories) of viruses, based on the organism they infect? a.) _________________ b.) _________________ c.) _________________ 3. Viruses can only reproduce in living cells. The ________ _________ is the reproductive cycle of most viruses. This cycle contains several steps. During the first step the virus is about to come in contact with the cell. After contact and binding to the cell markers, the virus__________________________________ into the cell. This DNA/RNA piece releases chemicals that deactivate or destroy the host‘s DNA. After a short period of time the viral DNA begins to make _____________. After this is completed, the DNA copies are translated to make viral _____________. Once all the viral pieces are completed being made the cell will assemble the _____________ ___________. The viral DNA will produce an enzyme that will lead to ___________ in the cellular membrane. This will allow water to rush in and ______________ the cell, allowing the _______________ to escape.

4. Some examples of human pathogenic viruses are: _______________, _______________, _________________, and _________________.

5.) The ________________ _____________ is the alternative reproductive form of viral reproduction. During this process the viral DNA attaches itself to the cell‘s DNA and hides. It is not active and is called a ______________. In most cases the cell will continue functioning, growing, and dividing into new cells that alsocontain the prophage. If something happens to the cell (stress) and activates the phage DNA, the cell will undergo the _________________________, eventually killing the cell.

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Module (Lesson: Protist and Fungi)

Antoni van Leeuwenhoek(1632-1723)

The first detailed descriptions of protists were made in 1676 by the inventor of the microscope, naturalists Antoni van Leeuwenhoek, who observed microscopic organisms that he called animalcules.

Kingdom Protista Protists Protists belong to the Kingdom Protista, which include mostly unicellular organisms that do not fit into the other kingdoms.

Characteristics of Protists  mostly unicellular, some are multicellular (algae)  can be heterotrophic or autotrophic  most live in water (though some live in moist soil or even the human body)  ALL are eukaryotic (have a nucleus)  A protist is any organism that is not a plant, animal or fungus Protista = the very first Classification of Protists  how they obtain nutrition  how they move

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AnimallikeProtists – also called protozoa (means ―first animal‖) – heterotrophs Plantlike Protists – also called algae – autotrophs FunguslikeProtists – heterotrophs, decomposers, external digestion Animal-like Protists: Protozoans Four Phyla of Animal-like Protists – Classified by how they move  Zooflagellates – flagella  Sarcodines – extensions of cytoplasm (pseudopodia)  Ciliates – cilia  Sporozoans – do not move Zooflagellates move using one or two flagella absorb food across membrane Ex. Leishmania

Sarcodines Ameba See Ameba Coloring Sheet moves using pseudopodia ( ―false feet‖ ), which are like extensions of the cytoplasm –ameboid movement ingests food by surrounding and engulfing food (endocytosis), creating a food vacuole reproducing by binary fission (mitosis) contractile vacuole – removes excess water can cause amebic dysentery in humans – diarrhea and stomach upset from drinking contaminated water Other sarcodines: Foraminferans, Heliozoans

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Ciliates Paramecium move using cilia has two nuclei: macronucleus, micronucleus food is gathered through the :mouth pore, moved into a gullet, forms a food vacuole anal pore is used for removing waste contractile vacuole removes excess water exhibits avoidance behavior reproduces asexually (binary fission) or sexually (conjugation) outer membrane -pellicle- is rigid and paramecia are always the same shape, like a shoe

Sporozoans do not move on their own parasitic Malaria is caused by a sporozoan (Plasmodium), which infects the liver and blood; transmitted by mosquitos.

Protists Worksheet

EUGLENA Euglena are unicellular organisms classified into the Kingdom Protista, and the Phylum Euglenophyta. All euglena have chloroplasts and can make their own food by photosynthesis. They are not completely autotrophic though, euglena can also absorb food from their environment. Euglena usually live in quiet ponds or puddles. Euglena move by a flagellum (plural ‚ flagella), which is a long whip-like structure that acts like a little motor. The flagellum is located on the anterior (front) end, and rotates in such a way as to pull the cell through the water. It is attached at an inward pocket called the reservoir.

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(must consume food) and autotrophic (can make its own food). Chloroplasts within the euglena trap sunlight that is used for photosynthesis, and can be seen as several rod-like structures though out the cell. Euglena also have an eyespot at the anterior end that detects light, it can be seen near the reservoir. This helps the euglena find bright areas to gather sunlight to make their food. Euglena can also gain nutrients by absorbing them across their cell membrane, hence they become heterotrophic when light is not available, and they cannot photosynthesize. The euglena has a stiff pellicle outside the cell membrane that helps it keep its shape, though the pellicle is somewhat flexible and some euglena can be observed scrunching up and moving in an inchworm type fashion.

In the center of the cell is the nucleus, which contains the cell's DNA and controls the cell's activities. The nucleolus can be seen within the nucleus. The interior of the cell contains a jelly-like fluid substance called cytoplasm. Toward the posterior of the cell is a star-like structure, the contractile vacuole. This organelle helps the cell remove excess water, and without it, the euglena could take in some much water due to osmosis that the cell would explode.

1. Are euglena unicellular or multicellular?

2. What Kingdom do euglena belong to? What Phylum?

3. What organelle carries out photosynthesis?

4. On which end is the flagellum located?

5. Define autotrophic.

6. Define heterotrophic.

7. Describe the two ways in which the euglena get their nutrients.

8. What is the eyespot used for?

9. What is the function of the nucleus?

10. What is the function of the contractile vacuole? What would happen if the cell did not have this organelle.

AMOEBA The amoeba is a protozoan that belongs to the Kingdom Protista. The name ameba comes from the Greek word "amoibe", which means change.

Amoeba is also spelled ameba. Protists are microscopic unicellular organisms that don't fit into the other kingdoms.

Some protists are considered plant-like while others are considered animal-like.

The animal-like protists are known as protozoans. The amoeba is considered an animal-like protist because it moves and consumes its food. Protists are classified by how they move, some have cilia or flagella, but the amoeba has an unusual way of creeping along by stretching its cytoplasm into fingerlike extensions called pseudopodia.

The word "pseudopodia" means "false foot". When looking at amoeba under a microscope, an observer will note that no amoebas looks the same as any other, the cell membrane is very flexible and allows for the amoeba to change shape. Amoebas live in ponds or puddles, and can even live inside people.

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There are two types of cytoplasm in the amoeba, the darker cytoplasm toward the interior of the protozoan is called endoplasm, and the clearer cytoplasm that is found near the cell membrane is called ectoplasm. By pushing the endoplasm toward the cell membrane, the amoeba causes its body to extend and creep along. The amoeba also uses this method to consume its food. The pseudopodia extend out and wrap around a food particle in a process call phagocytosis. The food is then engulfed into the amoeba and digested by the enzymes contained in the amoeba's lysosomes. As the food is digested it exists in a structure called a food vacuole.

Also visible in the amoeba is the nucleus, which contains the amoeba's DNA. In order to reproduce the ameba goes through mitotic division, where the nucleus duplicates its genetic material and the cytoplasm splits into two new daughter cells, each identical to the original parent. This method of reproduction is called binary fission. Another structure easily seen in the amoeba is the contractile vacuole.

This organellepumps out excess water so that the amoeba does not burst or lyse.

During unfavorable conditions, the ameba can create a cyst, this hard walled body can exist for a long period of time until conditions become favorable again. At this point it opens up and the amoeba emerges. Often cysts are created during cold or dry periods where the ameba could not survive in its normal condition. Amoebas can cause disease. A common disease caused by the ameba is called Amebic Dysentery. A person becomes infected by drinking contaminated water. The ameba then upsets the person's digestive system and causes cramps and diarrhea. A person is most likely to be infected in countries where the water is not filtered or purified.

1. How does an ameba move?

2. What structure contains the ameba's DNA? 3. How does an ameba reproduce?

4. During unfavorable conditions, an ameba forms a ... ?

5. Fingerlike extensions of the ameba's cytoplasm are called ...?

6. What disease is caused by the ameba?

7. To what Kingdom does the ameba belong?

8. How are protists classified?

PARAMECIA The Genus Paramecium is commonly found throughout the world, in fresh and marine water containing bacteria and decaying organic matter. Paramecium is a small unicellular organism. It is elongated and ranges in size from 120 to 300 microns. The outside of the cell is covered with a tough pellicle. Label the pellicle. The posterior half is slightly wider than the anterior half and is bluntly pointed, while the anterior end is rounded. On its underside there is a large and long groove running about half the length of its body. The outer surface of the organism is covered with many hundreds of minute hair-like projections called cilia. Label the cilia. This large ciliate protozoan that lives in stagnant freshwater has an oral groove on one side that leads inward to the gullet and Young Ji International School / College

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eventually the mouth. Paramecia have two nuclei --- a larger macronucleus and a smaller micronucleus. The macronucleus, which is relatively large and located near the center of the organism, and controls most of the metabolic functions of the cell. The micronucleus, which lies partly within a depression on the oral side of the macronucleus, is involved primarily in reproductive and hereditary functions Because paramecia live in water, they require an organelle to pump out excess water so they do not lyse (burst). These organelles are the contractile vacuoles, usually one at each end, each surrounded by several radiating canals which collect water from the surrounding cytoplasm. The contractile vacuoles serve a critical function of osmoregulation, as water tends to accumulate inside the cytoplasm due to osmotic pressure. These structures are absent in marine Paramecium. Food vacuoles, which are round in shape, contain enzymes to digest the other smaller protozoans that the paramecium feeds on. These vacuoles can be seen at the mouth where the food is loaded into them for digestion.

Undigested food leaves through the anal pore. At the base of the cilia are defensive structures called trichocysts. These structures can discharge their contents as long threads.

1. What is the funnel like depression on the pellicle called?

2. How do paramecia regulate their water content?

3. Paramecia are heterotrophs. Explain this statement.

4. How do paramecia move?

5. What is the function of the macronucleus?

6. What is the function of the micronucleus?

7. What do paramecia use for defense?

8. Where can you find paramecia?

9. What do paramecia eat?

10. Where does digestion occur in a paramecium?

Module (Lesson: The Diverse form of Organism) Kingdom Fungi The organisms in kingdom fungi include mushrooms, yeasts, molds, rusts, smuts, puffballs, truffles, morels, and molds. More than 70,000 species of fungi have been identified. The fungi constitute and independent group to that of plants and animals.

They live everywhere in air, in water, on land, in soil, and on or in plants and animals. Some fungi are microscopic and other extend for more than a thousand acres. Mycology is a discipline of biology which deals with the study of fungi. Fungi appear like plants but are closely related to animals. Fungi are not capable of producing their own food,so they get their nourishment from other sources. Fungi are in a wide variety of sizes and forms and have great economic importance.

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Fungi show a great diversity in morphology and habitat. Fungi are heterotrophic organisms, they obtain their nutrients by absorption. The cell wall of fungi are mostly made up of carbohydrate chitin, while the cell wall in plants is made of cellulose. The carbohydrates stored in fungi is in the form of glycogen. The 'fruit' body of fungus is only seen, while the living body of the fungus is a mycelium, it is made of tiny filaments called hyphae. The mycelium is hidden.Nutrition in fungi is by absorbing nutrients from the organic material in which they live. Fungi do not have stomachs, they digest their food before it pass through the cell wall into the hyphae. The hyphae secrets enzymes and acids that break down the organic material into simple compounds.

Kingdom Fungi Characteristics General characteristics of fungi are as follows:  Fungi are eukaryotic organisms.  They are non-vascular organisms.  They reproduce by means of spores.  Depending on the species and conditions both sexual and asexual spores may be produced.  They are typically non-motile.  Fungi exhibit the phenomenon of alteration of generation.  The vegetative body of the fungi may be unicellular or composed of microscopic threads called hyphae.  The structure of cell wall is similar to plants but chemically the fungi cell wall are composed of chitin.  Fungi are heterotrophic organisms.  They fungi digest the food first and then ingest the food, to accomplish this the fungi produce exoenzymes.

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     

Fungi store their food as starch.

Biosynthesis of chitin occurs in fungi.

The nuclei of the fungi is very small.

During mitosis the nuclear envelope is not dissolved.

Nutrition in fungi - they are saprophytes, or parasites or symbionts.

Reproduction in fungi is both by sexual and asexual means. Sexual state is referred to as teleomorph, asexual state is referred to as anamorph.

Kingdom Fungi Classification Based on the spore case in which the spores are produced fungi are classified into four divisions.

Division Ascomycota: Sac Fungi The sac-fungi produce spores in small cup-shaped sacs called asci, hence the name ascomycota. The mature sac fungi spores are known as ascospores, they are released at the tip of the ascus breaks open. Yeast is the most common one-celled fungi. Yeast reproduces through asexual process called budding. The buds form at the side of the parent cell, they pinch-off and grow into new yeast cell which is identical to the parent cell. Examples of sac-fungi are morels, truffles, cup fungi and powdery mildews. Example: Aspergillus, Claviceps, Neurospora.

Division Basidiomycota: Club Fungi Basidiomycota includes the mushrooms, puff-balls, smuts, rusts and toadstools. The spores are borne on a club-shaped spore case called basidium. In mushrooms the basidia are lined at the gills under the cap. Huge numbers of spores are produced by the club fungi. In fact, an average sized mushroom produces over 16 billion spores.

These spores rarely germinate or mature.

Example: Agaricus(mushroom), Ustilago(smut), and Puccinia(rust fungus).

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Division Zygomycota: Zygote forming Fungi These fungi are usually found on cheese, bread, and other decaying food. They are zygote forming fungi, hence the name zygomycota. The spores are produced in round-shaped case called sporangium. The grayish fuzz seen on bread and decaying food is actually mass of mature sporangia mold. Under the microscope they are seen as pinheads. When the sporangium breaks open hundreds of spores are released. Example: Mucor,Rhizopus (the bread mould) and Albugo.

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Division Deuteromycota: Imperfect Fungi These organisms are known as imperfect fungi because they lack sexual reproduction. They reproduce by asexual spores known as conidia. Most of the fungi causes diseases to humans like ringworm, athlete's foot. Economically important imperfect fungi are Penicillium and Aspergillus. Other examples are Alternaria, Colletotrichum and Trichoderma.

Kingdom Fungi Examples Some of the examples of kingdom fungi are as follows: Sac-fungi : Agaricus (mushroom), Ustilago (smut), and Puccinia (rust fungus).

Zygote-forming fungi : Mucor, Rhizopus (the bread mould) and Albugo.

Club fungi: Agaricus (mushroom), Ustilago (smut), and Puccinia (rust fungus).

Imperfect fungi: Alternaria, Colletotrichum and Trichoderma.

Members of the Kingdom Fungi Mycorrhizae - More than 90% of the plants are symbionts of mycorrhizae. Myco means fungus and rhiza means root. Mycorrhizae are of two typesectomycorrhizae and endomycorrhizae.

Ectomycorrhizae - These are fungus forms sheath outside the root.

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Endomycorrhizae - They are also known as vesicular-arbuscular-mycorrhizae (VAM). Fungus does not form sheath around the roots.

Lichens - They are symbionts. They have a symbiotic relationship between a fungus and a alga. Neither of the organisms can survive on their own.

Economic Importance of Fungi Fungi are important in a variety of ways: Recycling - Together with bacteria the fungi form a major role in recycling the dead and decayed matter.

Food - Many mushrooms are used as food by humans. Mushrooms species are edible and are cultured in many parts of the world for sale.

Medicines - Penicillin antibiotic is derived from a common fungi Penicillium. Many other fungi also produces antibiotics, which are used to control diseases in humans and animals.

Bio-control Agents - Fungi are used to parasitise insects which help control pests.

Spores of fungi are sprayed on crops, this method is cheaper and environmentally friendly.

Plant and Animal Diseases - Many fungi live on and in plants and animals causing diseases. They also co-exist harmoniously with plants and animals.

Food spoilage - Fungi play a major role in recycling organic material. Fungal damage is responsible for large losses of stored food usually when the food contains moisture.

Fungi Worksheet Write true if the statement is true or false if the statement is false. _____ 1. Fungi are a kingdom in the domain Prokarya. _____ 2. Mushrooms are fungi. _____ 3. Yeasts are fungi. _____ 4. Amoeba are fungi. _____ 5. Fungi spend most of their life cycle in the diploid state. _____ 6. Fungi have cell walls made of cellulose, just like plants do. _____ 7. Many fungi grow as hyphae. _____ 8. Most fungi reproduce only by sexual reproduction. _____ 9. A fungal spore is a diploid cell produced by meiosis of the parent cell. _____ 10. Fungal spores can be transported by wind, water, and even by traveling on other organisms. _____ 11. A yeast cell produced by budding off of a parent cell is genetically identical to the parent cell. _____ 12. Mating of two haploid fungal hyphae produces a diploid zygospore. _____ 13. Fungi first colonized land at about the same time as plants did. _____ 14. In general, fungi are able to move themselves around. _____ 15. Baker‘s yeast is a fungus.

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Read these passages from the text and answer the questions that follow.

Reproduction of Fungi The majority of fungi can reproduce both asexually and sexually. This allows them to adjust to conditions in the environment. They can spread quickly through asexual reproduction when conditions are stable.They can increase their genetic variation through sexual reproduction when conditions are changing and variation may help them survive.

Asexual Reproduction Almost all fungi reproduce asexually by producing spores. A fungi spore is a haploid cell produced by mitosis from a haploid parent cell. It is genetically identical to the parent cell. Fungi spores can develop into new haploid individuals without being fertilized.

Spores may be dispersed by moving water, wind, or other organisms. Some fungi even have ―cannons‖ that ―shoot‖ the spores far from the parent organism. This helps to ensure that the offspring will not have to compete with the parents for space or other resources. You are probably familiar with puffballs. They release a cloud of spores when knocked or stepped on. Wherever the spores happen to land, they do not germinate until conditions are favorable for growth. Then they develop into new hyphae. Yeasts do not produce spores. Instead, they reproduce asexually by budding. Budding is the pinching off of an offspring from the parent cell. The offspring cell is genetically identical to the parent.

Sexual Reproduction Sexual reproduction also occurs in virtually all fungi. This involves mating between two haploid hyphae. During mating, two haploid parent cells fuse, forming a diploid spore called a zygospore. The zygospore is genetically different from the parents.

After the zygospore germinates, it can undergo meiosis, forming haploid cells that develop into new hyphae.

Questions 1. How do fungi benefit from being able to reproduce both asexually and sexually?

2. What are fungal spores? How are they made?

3. Why have fungi evolved mechanisms for dispersal of their spores? Name a few of these mechanisms.

4. How do many yeast reproduce asexually? What is this process called?

5. How do fungi mate?

Module (Lesson: Plant Kingdom) Plant Kingdom (or Plantae ) Virtually all other living creatures depend on plants to survive.

Through photosynthesis, plants convert energy from sunlight into food stored as carbohydrates. Because animals cannot get energy directly from the sun, they must eat plants (or other animals that have had a vegetarian meal) to survive. Plants also provide the oxygen humans and animals breathe, because plants use carbon dioxide for photosynthesis and release oxygen into the atmosphere.

Plants are found on land, in oceans, and in fresh water. They have been on Earth for millions of years. Plants were on Earth before animals and currently number about 260,000 species. Three features distinguish plants from animals:  Plants have chlorophyll, a green pigment necessary for photosynthesis;  Their cell walls are made sturdy by a material called cellulose; and Young Ji International School / College

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

They are fixed in one place (they don‘t move).

Plant Classification In order to study the billions of different organisms living on earth, biologists have sorted and classified them based on their similarities and differences. This system of classification is also called a taxonomy and usually features both English and Latin names for the different divisions.

All plants are included in one so-called kingdom (Kingdom Plantae), which is then broken down into smaller and smaller divisions based on several characteristics, including:  Whether they can circulate fluids (like rainwater) through their bodies or need to absorb them from the moisture that surrounds them;  How they reproduce (e.g., by spores or different kinds of seeds); and  Their size or stature.

The majority of the 260,000 plant species are flowering herbs. To describe all plant species, the following divisions (or phyla) are most commonly used to sort them. The first grouping is made up of plants that are non-vascular; they cannot circulate rainwater through their stems and leaves but must absorb it from the environment that surrounds them. The remaining plant species are all vascular (they have a system for circulating fluids). This larger group is then split into two groups: one that reproduces from spores rather than seeds, and the other that reproduces from seeds.

Non-Vascular Plants Mosses and “allies,” or related species (Bryophyta and allies) Mosses or bryophyta are non-vascular. They are an important foundation plant for the forest ecosystem and they help prevent erosion by carpeting the forest floor. All bryophyte species reproduce by spores not seeds, never have flowers, and are found growing on the ground, on rocks, and on other plants.

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Originally grouped as a single division or phylum, the 24,000 bryophyte species are now grouped in three divisions: Mosses(Bryophyta), Liverworts (Hepatophyta), and Hornworts (Anthocerotophyta). Also included among the non-vascular plants isChlorophyta , a kind of fresh-water algae.

Vascular Plants with Spores Ferns and allies (Pteridophyta and allies) Unlike mosses, ferns and related species have a vascular system, but like mosses, they reproduce from spores rather than seeds. The ferns are the most plentiful plant division in this group, with 12,000 species. Other divisions (the fern allies) include Club mosses or Lycopods (Lycopodiophyta) with 1,000 species, Horsetails (Equisetophyta) with 40 species, and Whisk ferns (Psilophyta) with 3 species.

Vascular Plants with Seeds Conifers and allies (Coniferophyta and allies) Conifers and allies (Coniferophyta and allies) Conifers reproduce from seeds, but unlike plants like blueberry bushes or flowers where the fruit or flower surrounds the seed, conifer seeds (usually cones) are ―naked.‖ In addition to having cones, conifers are trees or shrubs that never have flowers and that have needle-like leaves.

Included among conifers are about 600 species including pines, firs, spruces, cedars, junipers, and yew. The conifer allies include three small divisions with fewer than 200 species all together: Ginko (Ginkophyta) made up of a single species, the maidenhair tree; the palm-likeCycads (Cycadophyta), and herb-like plants that bear cones (Gnetophyta) such as Mormon tea.

Flowering Plants (Magnoliophyta) The vast majority of plants (around 230,000) belong to this category, including most trees, shrubs, vines, flowers, fruits, vegetables, and legumes. Plants in this category are also called angiosperms. They differ from conifers because they grow their seeds inside an ovary, which is embedded in a flower or fruit.

Structures of Flowering Plants 

Pistil – Central female organ of the flower. It is generally bowling-pin shaped and located in the center of the flower.       



Stigma – Receives pollen, typically flattened and sticky Style – Connective tissues between stigma and ovary Ovary – Contains ovules or embryo sacs Ovules – Unfertilized, immature seeds Stamen – Male flower organ Anthers – Pollen-producing organs Filament – Stalk supporting anthers

Petals – Usually colorful petal-like structures making up the ―flower‖, collectively called the corolla. They may contain perfume and nectar glands.

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

Sepals – Protective leaf-like enclosures for the flower buds, usually green, collectively called calyx. Sometimes highly colored like the petal as in iris.



Receptacle – Base of the flower

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Pedicel – Flower inflorescence

stalk

of

an

individual

flower

in

an

Figure 1. Parts of a flower Monocot or Dicot Flower The number of sepals and petals is used in plant identification.

Dicots typically have sepals and petals in fours, fives, or multiples thereof. Monocots typically have flower parts in threes or multiples of three.

Figure 2. Monocot and dicot flowers.

Terms Defining Flower Parts  Terms referring to flowers 

Complete – Flower containing sepals, petals, stamens, and pistil

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





Incomplete – Flower stamens, and/or pistils

 

Perfect – Flowers containing male and female parts Imperfect – Flowers that lack either male or female parts

 

Pistillate – Flowers containing only female parts Staminate – Flowers containing only male parts

lacking

sepals,

petals,

Terms referring to plants  Hermaphroditic – Plants with perfect flowers (apples, tulips)  Monoecious – Plants with separate male flowers and female flowers on the same plant (corn, squash, and pine)  Dioecious – Plants with male flowers and female flowers on separate plants (maple, holly, and salt brush)  Gynoecious – Plants with only female flowers  Andromonoecious – Plants with only male flowers Inflorescence (flower arrangement on a stem) Catkin – A spike with only pistillate or staminate flowers (alder, poplar, walnut, and willows)



Composite or Head – A daisy-type flower composed of ray flowers (usually sterile with attractive, colored petals) around the edge and disc flowers that develop into seed in center of the flat head (sunflower and aster) On some composites, the ray and disc flowers are similar (chrysanthemums and dahlias)



Corymb – Stemlets (pedicels) arranged along main stem.

Outer florets have longer pedicals than inner florets giving the display a flat top. (yarrow, crabapple)

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Cyme – A determinate, flat or convex flower, with inner floret opening first.

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Panicle – An indeterminate flower with repeated branching. It can be made up of racemes, spikes, corymbs, or umbels. (begonia)

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Raceme – A modification of a spike with flowers attached to a main stem (peduncle) by stemlets (pedicel). (snapdragon, bleeding heart, Canterbury bells)

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Solitary (or single) – One flower per stem (tulip, crocus)

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Spadix – Showy part is a bract or spathe, partially surrounding the male and female flowers inside. (calla, caladium)

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Spike – Flowers attached to main stem, without stemlets, bottom florets open first. (gladiolus, ajuga and gayfeather)

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Umbel – Florets with stemlets attached to main stem at one central point, forming a flat or rounded top. Outer florets open first. (dill, onion)



Symmetrical – Symmetrical flowers (lily)



Asymmetrical – Asymmetrical flowers (snapdragon)

Figure 3. Types of inflorescence (flower arrangement on stem) Specialized or Modified Stems A stem is one of two main structural axes of a vascular plant, the other being the root. The stem is normally divided into nodes and internodes. The nodes holdbuds which grow into one or more leaves, conifer cones, roots, other stems, or flowers (inflorescences); the internodes distance one node from another. The term "shoots" is often confused with "stems"; "shoots" generally refers to new fresh plant growth including both stems and other structures like leaves or flowers. In most plants stems are located above the soil surface but some plants have underground stems. A stem develops buds and shoots and usually grows above the ground.

Inside the stem, materials move up and down the tissues of the transport system.Stems are often green.Stems have thin pipes to carry water around the plant.Stem consists of xylem and phloem tissue. Stems and roots hold the plant upright. Xylem tissue carries water around the plant, while phloem tissue carries food around the plant.The leaves make food for the plant, the Pallisade tissue helps it.

Stems have four main functions which are:  Support for and the elevation of leaves, flowers and fruits. The stems keep the leaves in the light and provide a place for the plant to keep its flowers and fruits.  Transport of fluids between the roots and the shoots in the xylem and phloem.  Storage of nutrients.

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

Production of new living tissue. The normal life span of plant cells is one to three years. Stems have cells called meristems that annually generate new living tissue.

Stems are often specialized for storage, asexual reproduction, protection or photosynthesis, including the following:  Acaulescent – used to describe stems in plants that appear to be stemless.

Actually these stems are just extremely short, the leaves appearing to rise directly out of the ground, e.g. some Violaspecies.  Arborescent – tree like with woody stems normally with a single trunk.  Branched - aerial stems are described as being branched or unbranched  Bud – an embryonic shoot with immature stem tip.  Bulb – a short vertical underground stem with fleshy storage leaves attached, e.g. onion, daffodil, tulip. Bulbs often function in reproduction by splitting to form new bulbs or producing small new bulbs termed bulblets. Bulbs are a combination of stem and leaves so may better be considered as leaves because the leaves make up the greater part.  Caespitose – when stems grow in a tangled mass or clump or in low growing mats.  Cladode (including phylloclade) – a flattened stem that appears more-or-less leaf like and is specialized for photosynthesis,[2] e.g. cactus pads.  Climbing – stems that cling or wrap around other plants or structures.  Corm – a short enlarged underground, storage stem, e.g. taro, crocus, gladiolus.  Decumbent – stems that lie flat on the ground and turn upwards at the ends.  Fruticose – stems that grow shrub like with woody like habit.  Herbaceous – non woody, they die at the end of the growing season.  Pedicel – stems that serve as the stalk of an individual flower in an inflorescence or in frutescence.  Peduncle – a stem that supports an inflorescence  Prickle – a sharpened extension of the stem's outer layers, e.g. roses.  Pseudostem – a false stem made of the rolled bases of leaves, which may be 2 or 3 m tall as in banana  Rhizome – a horizontal underground stem that functions mainly in reproduction but also in storage, e.g. most ferns, iris  Runner (plant part) – a type of stolon, horizontally growing on top of the ground and rooting at the nodes, aids in reproduction. e.g. garden strawberry, Chlorophytumcomosum.  Scape – a stem that holds flowers that comes out of the ground and has no normal leaves. Hosta, Lily, Iris, Garlic.  Stolon – a horizontal stem that produces rooted plantlets at its nodes and ends, forming near the surface of the ground.  Thorn – a modified stem with a sharpened point.  Tuber – a swollen, underground storage stem adapted for storage and reproduction, e.g. potato.  Woody – hard textured stems with secondary xylem.

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Leaves and Leaf Anatomy

Leaf Function: Leaves are the powerhouse of plants. In most plants, leaves are the major site of food production for the plant. Structures within a leaf convert the energy in sunlight into chemical energy that the plant can use as food. Chlorophyll is the molecule in leaves that uses the energy in sunlight to turn water (H2O) and carbon dioxide gas (CO2) into sugar and oxygen gas (O2). This process is called photosynthesis.

Leaf Structure: A leaf is made of many layers that are sandwiched between two layers of tough skin cells (called the epidermis). The epidermis also secretes a waxy substance called the cuticle. These layers protect the leaf from insects, bacteria, and other pests.

Among the epidermal cells are pairs of sausage-shaped guard cells. Each pair of guard cells forms a pore (called stoma; the plural is stomata). Gases enter and exit the leaf through the stomata.

Most food production takes place in elongated cells called palisade mesophyll. Gas exchange occurs in the air spaces between the oddly-shaped cells of the spongy mesophyll.

Veins support the leaf and are filled with vessels that transport food, water, and minerals to the plant.

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Leaf Margins Leaf Margins: Leaves come in many sizes and shapes; they are often used to help identify plants.

Some leaves are flat and wide; others are spiky and thin. Plant spines (like cactus spines) are actually modified leaves.

Leaf Glossary: air space - intercellular gaps within the spongy mesophyll. These gaps are filled with gas that the plant uses (carbon dioxide - CO2 ) and gases that the plant is expelling (oxygen - O2, and water vapor). axil - the angle between the upper side of the stem and a leaf or petiole. chlorophyll - a molecule in leaves that can use light energy from sunlight to turn water and carbon dioxide gas into sugar and oxygen (this process is called photosynthesis). Chlorophyll is magnesium-based and is green. compound leaf - a leaf that is divided into many separate parts (leaflets) along a midrib (the rachis). All the leaflets of a compound leaf are oriented in the same plane. crenate - having rounded teeth. cuticle - the waxy, water-repelling layer on the outer surface of a leaf that helps keep it from dying out (and protect it from invading bacteria, insects, and fungi). The cuticle is secreted by the epidermis (including the guard cells) and is often thinner on the underside of leaves. The cuticle is generally thicker on plants that live in dry environments. entire - having a smooth edge with neither teeth nor lobes. epidermis - the protective, outler layer of cells on the surface of a leaf. The guard cells (and stoma) are part of the epidermis. The surface of many leaves is coated with a waxy cuticle which is secreted by the epidermis. guard cell - one of a pair of sausage-shaped cells that surround a stoma (a pore in a leaf). Guard cells change shape (as light and humidity change), causing the stoma to open and close. lamina - the blade of a leaf. leaf apex - the outer end of a leaf; the end that is opposite the petiole. lobed - divided into rounded or pointed sections and the incisions (cuts) go less than halfway to the midrib. mesophyll - the chlorophyll-containing leaf tissue located between the upper and lower epidermis. These cells convert sunlight into usable chemical energy for the plant. midrib - the central rib of a leaf - it is usually continuous with the petiole. palisade mesophyll - a layer of elongated cells located under the upper epidermis.

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These cells contain most of the leaf's chlorophyll, converting sunlight into usable chemical energy for the plant. parted (or cleft) - the margins between the irregular teeth go more than halfway to the midrib. petiole - a leaf stalk; it attaches the leaf to the plant. photosynthesis - the process in which plants convert sunlight, water, and carbon dioxide into food energy (sugars and starches), oxygen and water. Chlorophyll or closely-related pigments (substances that color the plant) are essential to the photosynthetic process. pinnate - a compound leaf that is made up of many small leaflets arranged in pairs on either side of a long central midrib (the rachis). There is often a single terminal leaflet at the end of the midrib. serrate (or toothed) - having small, pointy teeth that point toward the tip of the leaf. spongy mesophyll - the layer below the palisade mesophyll; it has irregularlyshaped cells with many air spaces between the cells. These cells contain some chlorophyll. The spongy mesophyll cells communicate with the guard cells (stomata), causing them to open or close, depending on the concentration of gases. stem - (also called the axis) the main support of the plant. stipule - the small, paired appendages (sometimes leaf-life) that are found at the base of the petiole of leaves of many flowering plants. stoma - (plural stomata) a pore (or opening) in a plant's leaves where water vapor and other gases leave and enter the plant. Stomata are formed by two guard cells that regulate the opening and closing of the pore. Generally, many more stomata are on the bottom of a leaf than on the top. vein (vascular bundle) - Veins provide support for the leaf and transport both water and minerals (via xylem) and food energy (via phloem) through the leaf and on to the rest of the plant.

Plant Roots The root system of a plant constantly provides the stems and leaves with water and dissolved minerals. In order to accomplish this the roots must grow into new regions of the soil. The growth and metabolism of the plant root system is supported by the process of photosynthesis occurring in the leaves.

Photosynthate from the leaves is transported via the phloem to the root system.

Root structure aids in this process. This section will review the different kinds of root systems an look at some specialized roots, as well as describe the anatomy of the roots in monocots and dicots.

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Root Systems: Taproot System: Characterized by having one main root (the taproot) from which smaller branch roots emerge. When a seed germinates, the first root to emerge is the radicle, or primary root. In conifers and most dicots, this radicle develops into the taproot.

Taproots can be modified for use in storage (usually carbohydrates) such as those found in sugar beet or carrot. Taproots are also important adaptations for searching for water, as those long taproots found in mesquite and poison ivy.

Fibrous Root System: Characterized by having a mass of similarly sized roots. In this case the radicle from a germinating seed is short lived and is replaced by adventitious roots.

Adventitious roots are roots that form on plant organs other than roots. Most monocots have fibrous root systems. Some fibrous roots are used as storage; for example sweet potatoes form on fibrous roots. Plants with fibrous roots systems are excellent for erosioncontrol, because the mass of roots cling to soil particles.

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Root Structures and Their Functions: Root Tip: the end 1 cm of a root contains young tissues that are divided into the root cap, quiescent center, and the subapical region.

Root Cap: root tips are covered and protected by the root cap. The root cap cells are derived from the rootcap meristem that pushes cells forward into the cap region. Root cap cells differentiate first into columellacells.Columella cells contain amylopasts that are responsible for gravity detection.

These cells can also respond to light and pressure from soil particles. Once columella cells are pushed to the periphery of the root cap, they differentiate into peripheral cells. These cells secrete mucigel, a hydrated polysaccharide formed in the dictyosomes that contains sugars, organic acids, vitamins, enzymes, and amino acids. Mucigel aids in protection of the root by preventing desiccation. In some plants the mucigel contains inhibitors that prevent the growth of roots from competing plants. Mucigel also lubricates the root so that it can easily penetrate the soil. Mucigel also aids in water and nutrient absorption by increasing soil:root contact. Mucigel can act as a chelator, freeing up ions to be absorbed by the root. Nutrients in mucigel can aid in the establishment of mycorrhizae and symbiotic bacteria.

Quiescent Center: behind the root cap is the quiescent center, a region of inactive cells. They function to replace the meristematic cells of the rootcap meristem. The quiescent center is also important in organizing the patterns of primary growth in the root.

Subapical Region: this region, behind the quiescent center is divided into three zones. Zone of Cell Division - this is the location of the apical meristem (~0.5 -1.5 mm behind the root tip). Cells derived from the apical meristem add to the primary growth of the root. Zone of Cellular Elongation - the cells derived from the apical meristem increase in length in this region. Elongation occurs through water uptake into the vacuoles. This elongation process shoves the root tip into the soil. Zone of Cellular Maturation - the cells begin differentiation. In this region one finds root hairs which function to increase water and nutrient absorption. In this region the xylem cells are the first of the vascular tissues to differentiate.Mature Root: the primary tissues of the root begin to form within or just behind the Zone of Cellular Maturation in the root tip. The root apical meristem gives rise to three primary meristems: protoderm, ground meristem, and procambium.

Epidermis: the epidermis is derived from the protoderm and surrounds the young root one cell layer thick. Epidermal cells are not covered by cuticle so that they can absorb water and mineral nutrients. As roots mature the epidermis is replaced by the periderm.

Cortex: interior to the epidermis is the cortex which is derived from the ground meristem. The cortex is divided into three layers: the hypodermis, storage parenchyma cells, and the endodermis. The hypodermis is the suberinized protective layer of cells just below the epidermis. The suberin in these cells aids in water retention. Storage parenchyma cells are thin-walled and often store starch.

The endodermis is the innermost layer of the cortex. Endodermal cells are closely

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packed and lack intercellular spaces. Their radial and transverse walls are impregnated with lignin ansuberin to form the structure called the Casparian Strip.

The Casparian Strip forces water and dissolved nutrients to pass through the symplast (living portion of the cell), thus allowing the cell membrane to control absorption by the root.

Stele: all tissues inside the endodermis compose the stele. The stele includes the outer most layer, pericycle, and the vascular tissues.

The pericycle is a meristematic layer important in production of branch roots. The vascular tissues are made up of the xylem and phloem. In dicots the xylem is found as a star shape in the center of the root with the phloem located between the arms of the xylem star. New xylem and phloem is added by the vascular cambium located between the xylem and phloem.

Kingdom Plantae Worksheet 1. For each of the following, place a checkmark(s) in the correct columns.

Mosses Ferns

Gymnosperms Angiosperms

The simplest type of land plant The most advanced type of land plant Usually found in moist environments Have xylem and phloem Reproduce by spores Are eukaryotic Tend to be very short to stay near the water Can do photosynthesis Are nonvascular (no xylem nor phloem) Have a waxy cuticle to prevent water loss Have cell walls made of cellulose Have protected seeds Produce flowers Have ―naked‖ (unprotected) seeds 2. Explain the difference between xylem and phloem in your own words. __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ 3. How do ferns get their food? __________________________________________________________________ __________________________________________________________________ Young Ji International School / College

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Module (Lesson: Animal Kingdom) There are many different types of animals in the world. Many animals are quite similar to each other. Others are quite different. Animals can be classified based on their similarities. Continue on, and learn more about your fellow Earth inhabitants.

Here are some of the animals you can investigate in our Science Reference Library. The first name you read is the common name for the animal. The name in parentheses ( ) is the Latin word for the group (the phylum or subphylum or class or group or order) that scientists sometimes use to refer to animals.

Invertebrates Animals without a Backbone or Spinal Column:

Vertebrates Animals with a Backbone or Spinal Column: (All these animals are in the phyla Chordata and the subphyla Vertebrata.)

PROTOZOA Protozoa are simple, single-celled animals. They are the smallest of all animals.

Most protozoa are microscopic in size, and can only be seen under a microscope.

However, they do breathe, move and reproduce like multicelled animals.

There are several types of protozoa. The amoebas are clear, shapeless cells.

Flagellates have a body shape looking like a hair.

Although we can't see them, protozoa do a lot for us. Protozoa play a useful role in the food chain as a source of food for fish and other animals. Some protozoa are helpful to humans by eating dangerous bacteria. Unfortunately, other protozoa are parasites and can be harmful to humans by transmitting disease.

Protozoa eat tiny algae and bacteria. Some protozoa absorb food through their cell membrane. Others surround and engulf their food or have openings to collect food. They digest their food in stomach-like compartments called vacuoles.

Protozoa take in oxygen and give off carbon dioxide through the cell membrane.

Protozoa reproduces by splitting in half.

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ECHINODERMS Echinoderms are marine animals that live in the ocean. Common echinoderms include the sea star sea urchin, sand dollar and sea cucumber. Most echinoderms have arms or spines that radiate from the center of their body. The central body contains their organs, and their mouth for feeding.

Sea stars, commonly known as the starfish, have 5 or more arms attached to their body.

On the bottom of the Starfish are small tube feet to help with movement and feeding. The starfish's mouth is underneath, and is capable of eating other sea life such as clams and mussels.

Another type of echinoderm is the sea urchin. Sea urchins have many spines connected to their body. These spines help to protect them from predators.

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ANNELIDS There are about 9,000 species of Annelids known today, including worms and leeches.

They can be found almost anywhere in the world. Annelids have existed on Earth for over 120 million years. Annelids have bodies that are divided into segments. They have very well-developed internal organs. One common characteristic of annelids is that they don't have any limbs.

Some annelids may have long bristles. Others have shorter bristles and seem smooth, like the earthworm shown here.

There are many types of worms. Commonly known worms include earthworms, roundworms and flatworms. Most worms are small, measuring fractions of an inch to several inches long. Other worms, such as the ribbon worm, can grow up to 100 feet in length.

Some worms are considered parasites, in that they live inside the human body.

MOLLUSKS Mollusks were among the first inhabitants of the Earth. Fossils of mollusks have been found in rocks and date back over 500 million years. Mollusk fossils are usually well preserved because of their hard shell.Most mollusks have a soft, skin-like organ covered with a hard outside shell.

Some mollusks live on land, such as the snail and slug. Other mollusks live in water, such as the oyster, mussel, clam, squid and octopus.

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Land living mollusks, like the snail, move slowly on a flat sole called a foot.

Ocean living mollusks move or swim by jet propulsion. They propel themselves by ejecting water from their body. For example, the squid ejects water from a cavity within its body, and the scallop ejects water to move by clamping its shell closed.

Other ocean living mollusks, like the oyster, attach themselves to rocks or other surfaces, and can't move. They feed by filtering small food particles from water that flows through them.

ARTHROPODS Arthropods make up over 75% of the world's animal species. Arthropods include animals such as insects, crustaceans and arachnids. The largest group of Arthropods are the insects. The next largest group are the crustaceans, including lobsters and crabs.

The arachnids include spiders and ticks. Other Arthropods include centipedes and millipedes.

Arthropods have limbs with joints that allow them to move. They also have an exoskeleton, which is a hard, external skeleton. Their body cavity contains the nervous system, circulatory system, reproductive system and digestive system.

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Examples:

Crustaceans

Arachnids

Insects

CRUSTACEANS

Crustaceans are a type of Arthropod. The name may not sound familiar, but you probably know them. You may even have eaten one.Crustaceans live mostly in the ocean or other waters.

Most commonly known crustaceans are the crab, lobster and barnacle.

Crustaceans have a hard, external shell which protects their body. Crustaceans have a head and abdomen. The head has antennae which are part of their sensory system. The abdomen includes the heart, digestive system and reproductive system.

The abdomen also has appendages, such as legs, for crawling and swimming. Many crustaceans also have claws that help with crawling and eating.

ARACHNIDS Arachnids are a type of arthropod. You know many of them as spiders.

Common arachnids are spiders, scorpions, ticks and mites.

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appendages for walking.

Most arachnids have 4 pairs of legs. In some, the first pair of legs may be used for holding their prey and feeding. Unlike other arthropods, arachnids do not have antennae.

Spiders are easily recognized with their 8 legs. All legs are used for walking.

The first pair of legs is also used for holding prey and feeding. The second pair of legs may also be used for holding and killing their prey. Most spiders have 8 eyes. Spiders have fangs that are used to inject poison to paralyze or kill their prey. Many spiders can produce silk threads to spin webs for catching prey, and for building an egg sack to hold and protect their eggs.

Scorpions are large arachnids, some reaching over 8 inches in length. They have 4 pairs of legs, and a pair of pincers for catching and holding their prey. Scorpions also have a sharp stinger at the end of their tail that is used to paralyze or kill insects and small animals.

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Mites and ticks are small arachnids that are parasites living on the blood and tissue fluid of other animals. They can occasionally transmit disease.

INSECTS Insects are the largest group of arthropods. There are over 800,000 different types of insects.

Insects are very adaptable, living almost everywhere in the world. Common insects include the fly, beetle, butterfly, moth, dragonfly, bee, wasp and praying mantis.

Insects have an exoskeleton that covers their entire body. An insect's body consists of 3 parts:

the head, thorax and abdomen.

The insect's head has a pair of antennae, and a pair of compound eyes.

Compound eyes are different from human eyes which have a single lens for each eye.

Compound eyes have many lenses for each eye. For example, the fly has about 4,000 lenses in a single eye.

This provides them with very good eyesight.

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The thorax contains the legs for walking, swimming, jumping or digging. The thorax may also have wings for flying. The abdomen contains many body organs, such as the heart, respiratory system, digestive system and reproductive system.

The insect's hard, exoskeleton makes it difficult for the insect to grow and get larger.

This is because the exoskeleton can't grow and get larger. Many insects must molt in order to grow. Molting is the process where an insect sheds it outer skeleton. It wriggles out of this old skin, and a new, larger exoskeleton develops.

FISH Almost three-fourths of the world's surface is covered in water. This water is home to over 20,000 different species of fish. The earliest fossils of fish date back over 400 million years.

There are a wide variety of fish — from the goby which is less than one half an inch long, to the whale shark which can be over 60 feet long.

Most fish breathe through gills. Gills perform the gas exchange between the water and the fish's blood. They allow the fish to breathe oxygen in the water.

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Fishes are vertebrates that have a skeleton made of either bone or cartilage.

About 95% of fishes have skeletons made of bone. These bony fishes have a swim bladder, a gas-filled sac, that they can inflate or deflate allowing them to float in the water even when not swimming.

Fishes with a cartilage skeleton tend to be heavier than water and sink. They must swim to keep afloat.

Cartilaginous (cartilage) fish include the ray and the shark.

Most fish swim using a tail fin. Muscles in the tail fin move it from side to side, forcing water backward, and propeling the fish forward. Other fins help the fish change direction and stop. Pectoral fins on their side help them swim up and down. Dorsal and anal fins on the top and bottom keep the fish upright. Pelvic fins on the underside help steer left and right.

Many fish eat plants, while others such as the shark, eat other fish.

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AMPHIBIANS

Amphibians lay their eggs in water, and young amphibians tend to resemble small fish. The tadpole, or newborn frog, is born and lives in water. It has a tail that allows it to swim like a fish. It also has gills so that it can breathe under water.

As the tadpole grow into a frog, it loses its gills and tail, and develops legs for Moving on land. Most amphibians can both walk and swim in water. on the species of amphibian, breathing can take place in gills, lungs, the lining of the mouth, the skin, or some combination of these.

Amphibians body temperature changes with its environment. In cold climates, amphibians hibernate during the winter.

REPTILES Reptiles have been around for 300 million years, even during the dinosaur age. The most common reptiles include alligators, crocodiles, lizards, snakes, tortoises and turtles. Reptiles are air-breathing animals, although many live not only on land but in water. The most noticeable feature of reptiles are the scales that cover their body. The majority of reptiles lay eggs to give birth to their young. Although reptiles breathe through lungs, some reptiles can also absorb oxygen in water through membranes in their mouth.

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Reptiles are often called cold-blooded because they can't regulate their own body temperature. Their body temperature depends on the external temperature. They will lay in the sun to heat their body, or hide in the ground, under a rock or in water to cool their body.

Crocodiles and alligators are large reptiles that spend much of their time on land and in water. They can walk on land using their webbed feet. They can also use their long tail to swim in water. Crocodiles feed on large animals they catch on land or in water. They have powerful jaws and teeth to tear apart their prey.

Lizards and snakes are the largest group of reptiles. Lizards are four legged animals with a long tail. Many lizards can shed their tail to escape from predators. They can then grow a new tail. Some lizards, such as the chameleon, can change colors to blend into their environment.

This camouflage helps to protect them from predators.

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Snakes don't have limbs. They move by slithering along the ground.

Some snakes are poisonous, or venomous, such as the rattle snake, cobra, and eastern green Mamba. They have fangs which bite into their prey and inject poison into the victim.

Other snakes, such as the boa constrictor and the python kill their prey by crushing it.

Most snakes can dislocate their jaw, allowing them to swallow prey much larger than themselves.

BIRDS

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There are over 8,000 species of birds. Birds have 3 major differentiating characteristics: wings for flight, feathers, and a beak rather than teeth.

Birds have adapted their vertebrate skeleton for flight. Their bones and skull are very thin, making their bodies extremely light.

To support flight also required other changes to their skeleton. Obvious changes are the addition of wings.

Other changes are less obvious. The claws and muscles of a bird's foot are designed to lock and hold onto a perch even while the bird is sleeping.

A bird's respiratory system is also adapted to make it easier to breathe at high elevations, where air is thinner.

MAMMALS Mammals have several unique characteristics that differentiate them from other animals.

Most mammals have hair, or fur, covering their body. They are also capable of regulating their body temperature. The mammals metabolism controls heat production, and the sweat glands help cool the body. These allow the mammal to maintain a constant body temperature, regardless of the environmental temperature. One other difference is that mammals give birth to fully formed babies, and the female mammals produce milk to feed their young.

Most mammals walk on 4 legs, with only the humans walking upright on 2 legs.

Aquatic mammals have flippers, or fins, for swimming rather than legs. Common mammals include: primates, such humans and monkeys; marsupials; rodents; whales; dolphins; and, seals.

Examples:

Rodents

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Marsupials

Whales and dolphins

Primates

Seal

MARSUPIALS Marsupials are best known for the Australian members of the family, the kangaroo, wallaby and the koala. The only marsupial native to North America is the Virginia opossum. There are also some marsupials native to Central America and South America.

Marsupials are members of the mammal family. However, they are different from other mammals because they have an abdominal pouch to carry their young. The marsupial female gives birth very early and the baby animal climbs from the mother's birth canal to her pouch. Here the baby marsupial continues to develop for weeks, or even months, depending on the species.

At birth, marsupial babies are not fully developed. The baby's hind legs are just nubs. The baby lives and continues to develop in the mother's pouch. The pouch, or marsupium, also has the mother's mammary glands for feeding the baby. A baby kangaroo may live in its mother's pouch for 6 months.

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Koalas and wombats are a little different from Kangaroos. While a kangaroo pouch opens upwards at the top, the opening of the koala and wombat pouch is lower and more downward facing toward the hind legs. The pouch has a strong muscle around the opening to prevent the baby from falling out.

PRIMATES Humans are part of the primate family. Other common primates include the monkey, baboon, orangutan, chimpanzee and gorilla. While humans inhabit much of the world, most other primates live in tropical or subtropical regions of the Americas, Africa and Asia.

Primates have several distinctive features that separate them from other mammals.

Primates have well developed hands and feet, with fingers and toes. Their opposable thumb makes it easy for them to grab things.

Primate eyes are forward in the head giving them stereoscopic vision. This allows them to judge distance.

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Primates also have large, highly developed brains. Their intelligence allows them to control and manipulate their environment.

The highly developed visual center of the brain helps primates distinguish colors.

Their large brain also allows them to develop complex language and communication skills.

Monkeys and apes walk on all four limbs, but they may run upright using only their hind legs.

Although primates are born fully formed, they tend to have a long gestation period in their mother's womb.

Parents also care for and educate their young much longer than other animals. This results in a strong bond between a baby and the mother.

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Primates are very social animals, and tend to form strong bonds with family and friends.

While humans are similar to monkeys in many ways, there are also several significant differences. The human brain is more than twice the size of other primates. This makes humans the most intelligent primate, with the most developed communication, language and reasoning skills.

Humans are able to make and use complex tools to help control their environment.

Humans also walk upright on two legs.

Although primates are born fully formed, they tend to have a long gestation period in their mother's womb.

RODENTS The largest family of mammals are the rodents. These mammals are named rodent, which means "gnawing animal," because of their large incisor teeth and the way they eat.

The two long pairs of incisors are used like chisels to gnaw on hard foods like nuts and wood.

These incisors must grow continuously since they are worn down by gnawing.

There are 3 major types of rodents, represented by squirrels, mice and porcupines.

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Squirrel-like rodents such as the squirrel and gopher, have bushy long tails and large eyes.

They can live in trees or underground in tunnels. They may hibernate during the winter.

Mouse-like rodents include the mouse, rat and hamster. Some have a long, thin tail with short legs. Others have a short tail. They mostly live above ground, although some burrow under ground. They may also hibernate during the winter. Rats and mice often live near humans, sometimes in their buildings, so they can live off human food and garbage.

Porcupines differ from other mammals because they have long, sharp quills on their backs for protection.

WHALES and DOLPHINS Although they live in the water -- whales, dolphins and porpoises are mammals.

Since whales and dolphins are mammals, they cannot breathe under water.

They must come to the surface to breathe air. They breathe through a blowhole, or nostrils, on the top of their head. Babies are born under water and must be pushed to the surface, by the mother, so that they can take a breath.

Whales and dolphins also look different from many other mammals because they don't have fur. Although, they do have a sparse covering of hair.

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Orca The circulatory and respiratory systems have adapted to living in water. Whales and dolphins can dive deep in the water on a single breath.

Whales and dolphins also have a highly developed brain. They are consider to be very intelligent.

Dolphins, and some whales, can use echolocation to find food and identify objects around them.

They make loud clicking and squeaking sounds that bounce off objects and echo back to the dolphin. This echo tells the dolphin about the nearby object.

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SEALS

Seals also spend considerable time lying around on rocky islands and beaches. But they are clumsy and move slowly on land using their flippers.

Baby seals are born on land after a long, 12 month gestation period. The pups develop rapidly, with some able to swim within a few hours of birth.

Walruses differ from seals in that they are larger and have large tusks. They can be over 10 feet long and over 3,000 pounds.

Kingdom Animalia Worksheet 1.

2.

3.

4.

5.

6.

What is an animal?

How do invertebrates differ from vertebrates?

Explain the different types of symmetry, Distinguish between acoelomates, pseudo coelomates, and coelomates.

List and give symptoms of several diseases caused by animals.

Account for the fact that MOST invertebrates are aquatic and MOST vertebrates are terrestrial.

7. What is the most diverse group of animals? Explain.

8. Compare and contrast the different classes of Annelida (segmented worms).

9. What is it about arthropods that make them so diverse?

10. Compare and contrast the similarities and differences among major groups of arthropods.

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11. Compare the similarities among the different classes of echinoderms.

12. What evidence do Biologists have for determining that echinoderms are close relatives of chordates?

13. Explain how invertebrate chordates are related to vertebrates.

14. Distinguish between sea squirts and lancelets.

15. Compare and contrast the characteristics of the different classes of fishes.

16. Relate the evolution of the three-chambered heart to the amphibian life style.

17. Compare and contrast the different orders of amphibians.

18. Compare the characteristics of different orders of reptiles.

19. Relate bird adaptations to their ability to fly.

20. Compare the characteristics of the different order of birds.

21. Which came first, the chicken or the egg? Defend your answer.

22. Explain how the characteristics of mammals enable them to adapt to most habitats on Earth.

23. Compare the reproduction of the three different groups of living mammals.

Describe any other differences.

Module (Lesson: Theories of Evolution)

Charles Robert Darwin, FRS (12 February 1809 – 19 April 1882) was an English naturalist and geologist, best known for his contributions to evolutionary theory. He established that all species of life have descended over time from common ancestors, and in a joint publication with Alfred Russel Wallace introduced his scientific theory that this branching pattern of evolution resulted from a process that he called natural selection, in which the struggle for existence has a similar effect to the artificial selection involved in selective breeding.

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Darwin published his theory of evolution with compelling evidence in his 1859 book On the Origin of Species, overcoming scientific rejection of earlier concepts of transmutation of species. By the 1870s the scientific community and much of the general public had accepted evolution as a fact. However, many favored competing explanations and it was not until the emergence of the modern evolutionary synthesis from the 1930s to the 1950s that a broad consensus developed in which natural selection was the basic mechanism of evolution. In modified form, Darwin's scientific discovery is the unifying theory of the life sciences, explaining the diversity of life.

Darwin's early interest in nature led him to neglect his medical education at the University of Edinburgh; instead, he helped to investigate marine invertebrates.

Studies at the University of Cambridge (Christ's College) encouraged his passion for natural science. His five-year voyage on HMS Beagle established him as an eminent geologist whose observations and theories supported Charles Lyell's uniformitarian ideas, and publication of his journal of the voyage made him famous as a popular author.

Puzzled by the geographical distribution of wildlife and fossils he collected on the voyage, Darwin began detailed investigations and in 1838 conceived his theory of natural selection. Although he discussed his ideas with several naturalists, he needed time for extensive research and his geological work had priority. He was writing up his theory in 1858 when Alfred Russel Wallace sent him an essay which described the same idea, prompting immediate joint publication of both of their theories. Darwin's work established evolutionary descent with modification as the dominant scientific explanation of diversification in nature. In 1871 he examined human evolution and sexual selection in The Descent of Man, and Selection in Relation to Sex, followed by The Expression of the Emotions in Man and Animals. His research on plants was published in a series of books, and in his final book, he examined earthworms and their effect on soil.

Darwin became internationally famous, and his pre-eminence as a scientist was honoured by burial in Westminster Abbey. Darwin has been described as one of the most influential figures in human history.

Lamarck's theory

The long neck of the giraffe is often used as an example in explanations of Lamarckism.

The identification of Lamarckism with the inheritance of acquired characteristics is regarded by some as an artifact of the subsequent history of evolutionary thought, repeated in textbooks without analysis. Stephen Jay Gould wrote that late 19th Young Ji International School / College

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century evolutionists "re-read Lamarck, cast aside the guts of it ... and elevated one aspect of the mechanics - inheritance of acquired characters - to a central focus it never had for Lamarck himself." He argued that "the restriction of "Lamarckism" to this relatively small and non-distinctive corner of Lamarck's thought must be labelled as more than a misnomer, and truly a discredit to the memory of a man and his much more comprehensive system". Gould advocated defining "Lamarckism" more broadly, in line with Lamarck's overall evolutionary theory.

Lamarck incorporated two ideas into his theory of evolution, in his day considered to be generally true: 1. Use and disuse – Individuals lose characteristics they do not require (or use) and develop characteristics that are useful.

2. Inheritance of acquired traits – Individuals inherit the traits of their ancestors.

Examples of what is traditionally called "Lamarckism" would include:  Giraffes stretching their necks to reach leaves high in trees (especially Acacias), strengthen and gradually lengthen their necks. These giraffes have offspring with slightly longer necks (also known as "soft inheritance").  A blacksmith, through his work, strengthens the muscles in his arms. His sons will have similar muscular development when they mature.

Lamarck stated the following two laws: 1. Première Loi. Dans tout animal qui n' a point dépassé le terme de sesdéveloppements, l' emploi plus fréquentestsoutenu d' un organequelconque, fortifiépeu à peu, cetorgane le développe, l' agrandit, et luidonneune puissance proportionnée à la durée de cetemploi ;tandisque le défaut constant d' usage de telorgane, l'affaiblitinsensiblement, le détériore, diminueprogressivementsesfacultés, et finit par le faire disparaître.

2. DeuxièmeLoi. Tout ceque la nature a fait acquérirouperdre aux individuspar l' influence des circonstancesoùleur race se trouvedepuis long-temps exposée, et, par conséquent, par l' influence de l' emploiprédominant de telorgane, ou par celle d' un défaut constant d' usage de tellepartie ;elle le conserve par la génération aux nouveaux individus qui en proviennent, pourvuque les changementsacquissoientcommuns aux deux sexes, ou à ceux qui ontproduitces nouveaux individus.

English translation: 1. First Law. In every animal which has not passed the limit of its development, a more frequent and continuous use of any organ gradually strengthens, develops and enlarges that organ, and gives it a power proportional to the length of time it has been so used; while the permanent disuse of any organ imperceptibly weakens and deteriorates it, and progressively diminishes its functional capacity, until it finally disappears.

2. Second Law. All the acquisitions or losses wrought by nature on individuals, through the influence of the environment in which their race has long been placed, and hence through the influence of the predominant use or permanent disuse of any organ; all these are preserved by reproduction to the new individuals which arise, provided that the acquired modifications are common to both sexes, or at least to the individuals which produce the young.[ In essence, a change in the environment brings about change in "needs" (besoins), resulting in change in behavior, bringing change in organ usage and development, bringing change in form over time — and thus the gradual transmutation of the species.

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However, as historians of science such as Michael Ghiselin and Stephen Jay Gould have pointed out, none of these views were original to Lamarck. On the contrary, Lamarck's contribution was a systematic theoretical framework for understanding evolution. He saw evolution as comprising two processes; 1. Le pouvoir de la vie (a complexifying force) - in which the natural, alchemical movements of fluids would etch out organs from tissues, leading to ever more complex construction regardless of the organ's use or disuse. This would drive organisms from simple to complex forms.

2. L'influence des circonstances (an adaptive force) - in which the use and disuse of characters led organisms to become more adapted to their environment. This would take organisms sideways off the path from simple to complex, specialising them for their environment.

Darwin's Theory of Evolution - The Premise Darwin's Theory of Evolution is the widely held notion that all life is related and has descended from a common ancestor: the birds and the bananas, the fishes and the flowers -- all related. Darwin's general theory presumes the development of life from non-life and stresses a purely naturalistic (undirected) "descent with modification".

That is, complex creatures evolve from more simplistic ancestors naturally over time.

In a nutshell, as random genetic mutations occur within an organism's genetic code, the beneficial mutations are preserved because they aid survival -- a process known as "natural selection." These beneficial mutations are passed on to the next generation. Over time, beneficial mutations accumulate and the result is an entirely different organism (not just a variation of the original, but an entirely different creature).

Darwin's Theory of Evolution - Natural Selection While Darwin's Theory of Evolution is a relatively young archetype, the evolutionary worldview itself is as old as antiquity. Ancient Greek philosophers such as Anaximander postulated the development of life from non-life and the evolutionary descent of man from animal. Charles Darwin simply brought something new to the old philosophy -- a plausible mechanism called "natural selection." Natural selection acts to preserve and accumulate minor advantageous genetic mutations. Suppose a member of a species developed a functional advantage (it grew wings and learned to fly). Its offspring would inherit that advantage and pass it on to their offspring. The inferior (disadvantaged) members of the same species would gradually die out, leaving only the superior (advantaged) members of the species. Natural selection is the preservation of a functional advantage that enables a species to compete better in the wild. Natural selection is the naturalistic equivalent to domestic breeding. Over the centuries, human breeders have produced dramatic changes in domestic animal populations by selecting individuals to breed. Breeders eliminate undesirable traits gradually over time. Similarly, natural selection eliminates inferior species gradually over time.

Darwin's Theory of Evolution - Slowly But Surely...

Darwin's Theory of Evolution is a slow gradual process. Darwin wrote, "‌Natural selection acts only by taking advantage of slight successive variations; she can never take a great and sudden leap, but must advance by short and sure, though slow steps." Thus, Darwin conceded that, "If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down." Such a Young Ji International School / College

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complex organ would be known as an "irreducibly complex system". An irreducibly complex system is one composed of multiple parts, all of which are necessary for the system to function. If even one part is missing, the entire system will fail to function.

Every individual part is integral. Thus, such a system could not have evolved slowly, piece by piece. The common mousetrap is an everyday non-biological example of irreducible complexity. It is composed of five basic parts: a catch (to hold the bait), a powerful spring, a thin rod called "the hammer," a holding bar to secure the hammer in place, and a platform to mount the trap. If any one of these parts is missing, the mechanism will not work. Each individual part is integral. The mousetrap is irreducibly complex.

Darwin's Theory of Evolution - A Theory In Crisis Darwin's Theory of Evolution is a theory in crisis in light of the tremendous advances we've made in molecular biology, biochemistry and genetics over the past fifty years.

We now know that there are in fact tens of thousands of irreducibly complex systems on the cellular level. Specified complexity pervades the microscopic biological world.

Molecular biologist Michael Denton wrote, "Although the tiniest bacterial cells are incredibly small, weighing less than 10-12 grams, each is in effect a veritable microminiaturized factory containing thousands of exquisitely designed pieces of intricate molecular machinery, made up altogether of one hundred thousand million atoms, far more complicated than any machinery built by man and absolutely without parallel in the non-living world."

And we don't need a microscope to observe irreducible complexity. The eye, the ear and the heart are all examples of irreducible complexity, though they were not recognized as such in Darwin's day. Nevertheless, Darwin confessed, "To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree."

Comparison Between Lamark’s and Darwin’s Theory

Jean Baptist de Lamarck

Charles Darwin

Conception of species:

Population of individuals all of the same kind (identical characteristics in all members).

Individuals capable of transformation.

Population of interbreeding individuals with similar characteristics, though variation is common among all of them at all times.

Individuals fixed and unchanging.

Population capable of transformation.

Mechanism

Internal drive toward greater

Natural selection. Variation

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of new species production:

complexity modified by the inheritance of acquired characteristics.

Change directed to meet organism needs.

exists regardless of organism's needs not directed toward any purpose.

Example of this type of explanation:

The giraffe's neck: ―At some point in the past, giraffes must have found themselves in an environment where they had difficulty reaching food present on the tops of trees.

In order to eat, they must have had to stretch their necks and in doing so physically elongated them some. This longer neck was passed on to the offspring in the next generation, who in turn stretched their necks even further, thus resulting in the giraffe species having very long necks."

Keen eyesight of the hawk: ―In a population of hawks, individual variation existed in the power of their vision, just as variation exists in the color of their feathers. In their competition for food, the individuals with keener eyesight could more easily spot their prey (small voles and mice) and thus were successful in securing food to eat. The hawks with poor eyesight had difficulty spotting prey and died for lack of food. The hawks with the keen eyesight passed on this trait to their offspring.

The hawks that died were not able to produce any offspring. Over a number of generations, the population of hawks all came to possess extremely powerful vision."

Phenomena the model can account for:

• • Fossil record

• Adaptation • Fossil record • Homologous structures • Biogeographical diversity patterns

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Theory of Evolution Worksheet

Write true if the statement is true or false if the statement is false. _____ 1. As recently as 200 years ago, many people believed that Earth was only 6,000 years old. _____ 2. Artificial selection occurs when nature selects for beneficial traits. _____ 3. The individual Galápagos Islands are all similar to each other. _____ 4. Malthus argued that human populations grow faster than their resources. _____ 5. Lamarck was one of the first scientists to propose that species evolve by natural selection. _____ 6. Lyell was one of the first to say that Earth must be far older than most people believed. _____ 7. Lamarck‘s inheritance of acquired characteristics is has become a widely accepted scientific theory. _____ 8. Fossils proved to Darwin that species can evolve. _____ 9. The term fitness to refer to an organism‘s ability to outrun its hunters. _____ 10. Darwin published his findings soon after returning to England from the voyage of the Beagle. _____ 11. According to Darwin, natural selection is what occurs, and evolution is how it happens. _____ 12. During his journey aboard the Beagle, Darwin found fossils from the seas in the mountains. _____ 13. Galápagos tortoises have differently shaped shells depending on where they live. _____ 14. Darwin‘s book changed science forever.

4th Quarter Module (Lesson: Evidence of Evolution) The Evolution of Theory The theory of evolution is one of the great intellectual revolutions of human history, drastically changing our perception of the world and of our place in it. Charles Darwin put forth a coherent theory of evolution and amassed a great body of evidence in support of this theory. In Darwin's time, most scientists fully believed that each organism and each adaptation was the work of the creator. Linneaus established the system of biological classification that we use today, and did so in the spirit of cataloguing God's creations.

In other words, all of the similarities and dissimilarities among groups of organisms that are the result of the branching process creating the great tree of life (see Figure 1), were viewed by early 19th century philosophers and scientists as a consequence of omnipotent design.

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Figure 1: A phylogenetic "tree of life" constructed by computer analysis of cyochrome c molecules in the organisms shown; there are as many different trees of life as there are methods of analysis for constructing them.

However, by the 19th Century, a number of natural historians were beginning to think of evolutionary change as an explanation for patterns observed in nature. The following ideas were part of the intellectual climate of Darwin's time.  No one knew how old the earth was, but geologists were beginning to make estimates that the earth was considerably older than explained by biblical creation. Geologists were learning more about strata, or layers formed by successive periods of the deposition of sediments. This suggested a time sequence, with younger strata overlying older strata.  A concept called uniformitarianism, due largely to the influential geologist Charles Lyell, undertook to decipher earth history under the working hypothesis that present conditions and processes are the key to the past, by investigating ongoing, observable processes such as erosion and the deposition of sediments.  Discoveries of fossils were accumulating during the 18th and 19th centuries.

At first naturalists thought they were finding remains of unknown but still living species. As fossil finds continued, however, it became apparent that nothing like giant dinosaurs was known from anywhere on the planet. Furthermore, as early as 1800, Cuvier pointed out that the deeper the strata, the less similar fossils were to existing species.  Similarities among groups of organisms were considered evidence of relatedness, which in turn suggested evolutionary change. Darwin's intellectual predecessors accepted the idea of evolutionary relationships Young Ji International School / College

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among organisms, but they could not provide a satisfactory explanation for how evolution occurred.  Lamarck is the most famous of these. In 1801, he proposed organic evolution as the explanation for the physical similarity among groups of organisms, and proposed a mechanism for adaptive change based on the inheritance of acquired characteristics. He wrote of the giraffe: "We know that this animal, the tallest of mammals, dwells in the interior of Africa, in places where the soil, almost always arid and without herbage, obliges it to browse on trees and to strain itself continuously to reach them. This habit sustained for long, has had the result in all members of its race that the forelegs have grown longer than the hind legs and that its neck has become so stretched, that the giraffe, without standing on its hind legs, lifts its head to a height of six meters."

In essence, this says that the necks of Giraffes became long as a result of continually stretching to reach high foliage. Larmarck was incorrect in the hypothesized mechanism, of course, but his example makes clear that naturalists were thinking about the possibility of evolutionary change in the early 1800's.  Darwin was influenced by observations made during his youthful voyage as naturalist on the survey ship Beagle. On the Galapagos Islands he noticed the slight variations that made tortoises from different islands recognizably distinct. He also observed a whole array of unique finches, the famous "Darwin's finches," that exhibited slight differences from island to island. In addition, they all appeared to resemble, but differ from, the common finch on the mainland of Ecuador, 600 miles to the east. Patterns in the distribution and similarity of organisms had an important influence of Darwin's thinking.

The picture at the top of this page is of Darwin's own sketches of finches in his Journal of Researches.  In 1859, Darwin published his famous On the Origin of Species by Means of Natural Selection, a tome of over 500 pages that marshalled extensive evidence for his theory. Publication of the book caused a furor - every copy of the book was sold the day that it was released. Members of the religious community, as well as some scientific peers, were outraged by Darwin's ideas and protested. Most scientists, however, recognized the power of Darwin's arguments. Today, school boards still debate the validity and suitability of Darwin's theory in science curricula, and a whole body of debate has grown up around the controversy (see the WWW site Talk.Origins for an ongoing dialogue). We do not have time to cover all of Darwin's evidence and arguments, but we can examine the core ideas. What does this theory of evolution say?

Darwin's Theory Darwin‘s theory of evolution entails the following fundamental ideas. The first three ideas were already under discussion among earlier and contemporaneous naturalists working on the ―species problem‖ as Darwin began his research.

Darwin‘s original contributions were the mechanism of natural selection and copious amounts of evidence for evolutionary change from many sources. He also provided thoughtful explanations of the consequences of evolution for our understanding of the history of life and modern biological diversity.  Species (populations of interbreeding organisms) change over time and space. The representatives of species living today differ from those that lived in the recent past, and populations in different geographic regions today differ Young Ji International School / College

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slightly in form or behavior. These differences extend into the fossil record, which provides ample support for this claim.  All organisms share common ancestors with other organisms. Over time, populations may divide into different species, which share a common ancestral population. Far enough back in time, any pair of organisms shares a common ancestor. For example, humans shared a common ancestor with chimpanzees about eight million years ago, with whales about 60 million years ago, and with kangaroos over 100 million years ago. Shared ancestry explains the similarities of organisms that are classified together: their similarities reflect the inheritance of traits from a common ancestor.  Evolutionary change is gradual and slow in Darwin‘s view. This claim was supported by the long episodes of gradual change in organisms in the fossil record and the fact that no naturalist had observed the sudden appearance of a new species in Darwin‘s time. Since then, biologists and paleontologists have documented a broad spectrum of slow to rapid rates of evolutionary change within lineages.

The primary mechanism of change over time is natural selection, elaborated below.

This mechanism causes changes in the properties (traits) of organisms within lineages from generation to generation.

The Process of Natural Selection Darwin‘s process of natural selection has four components.

1. Variation. Organisms (within populations) exhibit individual variation in appearance and behavior. These variations may involve body size, hair color, facial markings, voice properties, or number of offspring. On the other hand, some traits show little to no variation among individuals—for example, number of eyes in vertebrates.

2. Inheritance. Some traits are consistently passed on from parent to offspring.

Such traits are heritable, whereas other traits are strongly influenced by environmental conditions and show weak heritability.

3. High rate of population growth. Most populations have more offspring each year than local resources can support leading to a struggle for resources.

Each generation experiences substantial mortality.

4. Differential survival and reproduction. Individuals possessing traits well suited for the struggle for local resources will contribute more offspring to the next generation.

From one generation to the next, the struggle for resources (what Darwin called the ―struggle for existence‖) will favor individuals with some variations over others and thereby change the frequency of traits within the population. This process is natural selection. The traits that confer an advantage to those individuals who leave more offspring are called adaptations.

In order for natural selection to operate on a trait, the trait must possess heritable variation and must confer an advantage in the competition for resources. If one of these requirements does not occur, then the trait does not experience natural selection. (We now know that such traits may change by other evolutionary mechanisms that have been discovered since Darwin‘s time.)

Natural selection operates by comparative advantage, not an absolute standard of design. ―…as natural selection acts by competition for resources, it adapts the inhabitants of each country only in relation to the degree of perfection of their associates‖ (Charles Darwin, On the Origin of Species, 1859).

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During the twentieth century, genetics was integrated with Darwin‘s mechanism, allowing us to evaluate natural selection as the differential survival and reproduction of genotypes, corresponding to particular phenotypes. Natural selection can only work on existing variation within a population. Such variations arise by mutation, a change in some part of the genetic code for a trait. Mutations arise by chance and without foresight for the potential advantage or disadvantage of the mutation. In other words, variations do not arise because they are needed.

Evidence of Natural Selection Let's look at an example to help make natural selection clear.

Industrial melanism is a phenomenon that affected over 70 species of moths in England. It has been best studied in the peppered moth, Bistonbetularia.

Prior to 1800, the typical moth of the species had a light pattern (see Figure 2). Dark colored or melanic moths were rare and were therefore collectors' items.

During the Industrial Revolution, soot and other industrial wastes darkened tree trunks and killed off lichens. The light-colored morph of the moth became rare and the dark morph became abundant. In 1819, the first melanic morph was seen; by 1886, it was far more common -illustrating rapid evolutionary change.

Figure 2. Image of Peppered Moth Eventually light morphs were common in only a few locales, far from industrial areas. The cause of this change was thought to be selective predation by birds, which favored camouflage coloration in the moth.

In the 1950's, the biologist Kettlewell did releaserecapture experiments using both morphs. A brief summary of his results are shown below. By observing bird predation from blinds, he could confirm that conspicuousness of moth greatly influenced the chance it would be eaten.

Recapture Success light moth dark moth non-industrial woods 14.6 %

4.7 %

industrial woods 13 % 27.5 % Local Adaptation - More Examples So far in today's lecture we have emphasized that natural selection is the cornerstone of evolutionary theory. It provides the mechanism for adaptive change. Any change in the environment (such as a change in the background color of the tree trunk that you roost on) is likely to lead to local adaptation.

Any widespread population is likely to experience different environmental conditions in different parts of its range. As a consequence it will soon consist of a number of sub-populations that differ slightly, or even considerably.

The following are examples that illustrate the adaptation of populations to local conditions. o The rat snake, Elapheobsoleta, has recognizably different populations in different locales of eastern North America (see Figure 3). Whether Young Ji International School / College

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these should be called geographic "races" or subspecies is debatable.

These populations all comprise one species, because mating can occur between adjacent populations, causing the species to share a common gene pool.

Figure 3: Subspecies of the rat snake Elapheobsoleta, which interbreed where their ranges meet. o Galapagos finches are the famous example from Darwin's voyage.

Each island of the Galapagos that Darwin visited had its own kind of finch (14 in all), found nowhere else in the world. Some had beaks adapted for eating large seeds, others for small seeds, some had parrot-like beaks for feeding on buds and fruits, and some had slender beaks for feeding on small insects (see Figure 4). One used a thorn to probe for insect larvae in wood, like some woodpeckers do. (Six were ground-dwellers, and eight were tree finches.) (This diversification into different ecological roles, or niches, is thought to be necessary to permit the coexistence of multiple species, a topic we will examined in a later lecture.) To Darwin, it appeared that each was slightly modified from an original colonist, probably the finch on the mainland of South America, some 600 miles to the east. It is probable that adaptive radiation led to the formation of so many species because other birds were few or absent, leaving empty niches to fill; and because the numerous islands of the Galapagos provided ample opportunity for geographic isolation.

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Figure 4 Stabilizing, Directional, and Diversifying Selection Finally, we will look at a statistical way of thinking about selection. Suppose that each population can be portrayed as a frequency distribution for some trait -- beak size, for instance. Note again that variation in a trait is the critical raw material for evolution to occur.

What will the frequency distribution look like in the next generation?

First, the proportion of individuals with each value of the trait (size of beak, or body weight) might be exactly the same. Second, there may be directional change in just one direction. Third (and with such rarity that its existence is debatable), there might be simultaneous change in both directions (e.g. both larger and smaller beaks are favored, at the expense of those of intermediate size). Figures 5a-c capture these three major categories of natural selection.

Figures 5a-c

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Under stabilizing selection, extreme varieties from both ends of the frequency distribution are eliminated.

The frequency distribution looks exactly as it did in the generation before (see Figure 5a). Probably this is the most common form of natural selection, and we often mistake it for no selection. A real-life example is that Figure 6 of birth weight of human babies (see Figure 6).

Under directional selection, individuals at one end of the distribution of beak sizes do especially well, and so the frequency distribution of the trait in the subsequent generation is shifted from where it was in the parental generation (see Figure 5b). This is what we usually think of as natural selection. Industrial melanism was such an example.

The fossil lineage of the horse provides a remarkable demonstration of directional succession. The full lineage is quite complicated and is not just a simple line from the tiny dawn horse Hyracotheriumof the early Eocene, to today's familiar Equus. Overall, though, the horse has evolved from a small-bodied ancestor built for moving through woodlands and thickets to its long- legged descendent built for speed on the open grassland.

This evolution has involved welldocumented changes in teeth, leg length, and toe structure (see Figure 7).

Under diversifying (disruptive) selection, both extremes are favored at the expense of intermediate varieties (see Figure 7 Figure 5c). This is uncommon, but of theoretical interest because it suggests a mechanism for species formation without geographic isolation.

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Evolution and Natural Selection Worksheet Define evolution and natural selection _____________________________ is the process in which changes in an environment pressure a species to change. _____________________________ is the process in which traits caused by mutations slowly accumulate in a population over time.

I. Evolution Practice Worksheet Directions: Circle the correct answer in questions 1 – 17.

1.

The process in which the environment puts pressure on a species to change: (natural selection or evolution) 2.

Slow change in a species over time describes Darwin‘s theory of (natural selection or evolution).

3.

According to Darwin, evolution occurs as a result of (artificial selection or natural selection).

4.

The (population or individual) evolves.

5.

Giant tortoises are only found on the Galapagos Islands. Each island had a different species of tortoises. This would suggest that all tortoises evolved from ( different ancestors common ancestor).

6.

The source of variation in a species is (lack of change or mutation) in DNA.

7.

Mutations can be harmful or helpful. A helpful mutation will (decrease or increase) the fitness of an individual in its environment.

8.

According to the theory of natural selection, a good mutation will probably (decrease or increase) in frequency in a population.

9.

Members of (the same or different) species share the same group of alleles called a gene frequency.

10.

Fossils in the lowest sedimentary rock layers are (younger or older) than fossils found in higher layers of rock.

11.

The whale‘s flipper and the arms of a human are examples of (homologous structure or vestigial organs) because they have the same bones but use them for different functions.

12.

The hip bones in whales and snakes serve no function, so they are examples of (homologous structures or vestigial organs).

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13.

(Homologous structures or Vestigial organs) how that two species evolved from a common ancestor.

14.

All vertebrate embryos are (not alike or alike) in that they all have similar patterns of development.

15.

An ancestral flock of finches flew from South America to the Galapagos Islands. They spread out and adapted to all the different environments on the islands. This is an example of (artificial selection or evolution) due to (geographic or behavioral) isolation.

16.

Mountains, volcanic eruptions, and large bodies of water are examples of (reproductive or geographic) barriers that can isolate populations.

17.

Two groups that are geographically isolated for long periods of time tend to become reproductively isolated due to (mutations or choice).

18.

Number (1 to 5) the following sentences in the order in which they occur during speciation. ___ As food sources become scarce the population of mice migrates around the sides of a mountain. ___ Over thousands of years, mutations slowly start to accumulate in the separated mice populations. ___ Gene sharing in a mice population is not interrupted because they have the same habitat gene pool. ___ The mice population becomes reproductively isolated and two new species evolve. ___ Members of the mice population become geographically isolated on either side of the mountain and members no longer share a common gene pool.

Module (Lesson: Photosynthesis) Photosynthesis is a process used by plants and other organisms to convert light energy, normally from the Sun, into chemical energy that can be later released to fuel the organisms' activities. This chemical energy is stored in carbohydrate molecules, such as sugars, which are synthesized from carbon dioxide and water – hence the name photosynthesis, from the Greek phĹ?s, "light", and synthesis, "putting together". In most cases, oxygen is also released as a waste product. Most plants, most algae, and cyanobacteria perform photosynthesis, and such organisms are called photoautotrophs. Photosynthesis maintains atmospheric oxygen levels and supplies all of the organic compounds and most of the energy necessary for life on Earth.

Although photosynthesis is performed differently by different species, the process always begins when energy from light is absorbed by proteins called reaction centers that contain green chlorophyll pigments. In plants, these proteins are held inside organelles called chloroplasts, which are most abundant in leaf cells, while in bacteria they are embedded in the plasma membrane. In these light-dependent reactions, some energy is used to strip electrons from suitable substances such as water, producing oxygen gas. Furthermore, two further compounds are generated: Young Ji International School / College

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reduced nicotinamide adenine dinucleotide phosphate (NADPH) and adenosine triphosphate (ATP), the "energy currency" of cells.

In plants, algae and cyanobacteria, sugars are produced by a subsequent sequence of light-independent reactions called the Calvin cycle, but some bacteria use different mechanisms, such as the reverse Krebs cycle. In the Calvin cycle, atmospheric carbon dioxide is incorporated into already existing organic carbon compounds, such as ribulosebisphosphate (RuBP). Using the ATP and NADPH produced by the lightdependent reactions, the resulting compounds are then reduced and removed to form further carbohydrates such as glucose.

The first photosynthetic organisms probably evolved early in the evolutionary history of life and most likely used reducing agents such as hydrogen or hydrogen sulfide as sources of electrons, rather than water. Cyanobacteria appeared later, and the excess oxygen they produced contributed to the oxygen catastrophe which rendered the evolution of complex life possible. Today, the average rate of energy capture by photosynthesis globally is approximately 130 terawatts, which is about six times larger than the current power consumption of human civilization. Photosynthetic organisms also convert around 100–115 thousand million metric tons of carbon into biomass per year.

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Photosynthetic organisms are photoautotrophs, which means that they are able to synthesize food directly from carbon dioxide and water using energy from light.

However, not all organisms that use light as a source of energy carry out photosynthesis, since photoheterotrophs use organic compounds, rather than carbon dioxide, as a source of carbon. In plants, algae and cyanobacteria, photosynthesis releases oxygen. This is called oxygenic photosynthesis. Although there are some differences between oxygenic photosynthesis in plants, algae, and cyanobacteria, the overall process is quite similar in these organisms. However, there are some types of bacteria that carry out an oxygenic photosynthesis, which consumes carbon dioxide but does not release oxygen.

Carbon dioxide is converted into sugars in a process called carbon fixation. Carbon fixation is an endothermic redox reaction, so photosynthesis needs to supply both a source of energy to drive this process, and the electrons needed to convert carbon dioxide into a carbohydrate. This addition of the electrons is a reduction reaction. In general outline and in effect, photosynthesis is the opposite of cellular respiration, in which glucose and other compounds are oxidized to produce carbon dioxide and water, and to release exothermic chemical energy to drive the organism's metabolism. However, the two processes take place through a different sequence of chemical reactions and in different cellular compartments.

The general equation for photosynthesis is therefore: 2n CO2 + 2n DH2 + photons → 2(CH2O)n + 2n DO Carbon dioxide + electron donor + light energy → carbohydrate + oxidized electron donor In oxygenic photosynthesis water is the electron donor and, since its hydrolysis releases oxygen, the equation for this process is: 2n CO2 + 4n H2O + photons → 2(CH2O)n + 2n O2 + 2n H2O carbon dioxide + water + light energy → carbohydrate + oxygen + water Often 2n water molecules are cancelled on both sides, yielding: 2n CO2 + 2n H2O + photons → 2(CH2O)n + 2n O2 carbon dioxide + water + light energy → carbohydrate + oxygen Other processes substitute other compounds (such as arsenite) for water in the electron-supply role; for example some microbes use sunlight to oxidize arsenite to arsenate: The equation for this reaction is: CO2 + (AsO33–) + photons → (AsO43–) + CO carbon dioxide + arsenite + light energy → arsenate + carbon monoxide (used to build other compounds in subsequent reactions) Photosynthesis occurs in two stages. In the first stage, light-dependent reactions or light reactions capture the energy of light and use it to make the energystorage molecules ATP and NADPH. During the second stage, the light-independent reactions use these products to capture and reduce carbon dioxide.

Most organisms that utilize photosynthesis to produce oxygen use visible light to do so, although at least three use shortwave infrared or, more specifically, far-red radiation.

Archaeobacteria use a simpler method using a pigment similar to the pigments used for vision. The archaearhodopsin changes its configuration in response to sunlight, acting as a proton pump. This produces a proton gradient more directly which is then converted to chemical energy. The process does not involve carbon dioxide fixation and does not release oxygen. It seems to have evolved separately.

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In the light reactions, one molecule of the pigment chlorophyll absorbs one photon and loses one electron. This electron is passed to a modified form of chlorophyll called pheophytin, which passes the electron to a quinone molecule, allowing the start of a flow of electrons down an electron transport chain that leads to the ultimate reduction of NADP to NADPH. In addition, this creates a proton gradient across the chloroplast membrane; its dissipation is used by ATP synthase for the concomitant synthesis of ATP. The chlorophyll molecule regains the lost electron from a water molecule through a process called photolysis, which releases a dioxygen (O2) molecule. The overall equation for the light-dependent reactions under the conditions of non-cyclic electron flow in green plants is: 2 H2O + 2 NADP+ + 3 ADP + 3 Pi + light → 2 NADPH + 2 H+ + 3 ATP + O2 Not all wavelengths of light can support photosynthesis. The photosynthetic action spectrum depends on the type of accessory pigments present. For example, in green plants, the action spectrum resembles the absorption spectrum for chlorophylls and carotenoids with peaks for violet-blue and red light. In red algae, the action spectrum overlaps with the absorption spectrum of phycobilins for red blue-green light, which allows these algae to grow in deeper waters that filter out the longer wavelengths used by green plants. The non-absorbed part of the light spectrum is what gives photosynthetic organisms their color (e.g., green plants, red algae, purple bacteria) and is the least effective for photosynthesis in the respective organisms.

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Calvin cycle In the light-independent (or "dark") reactions, the enzyme RuBisCO captures CO2 from the atmosphere and in a process that requires the newly formed NADPH, called the Calvin-Benson Cycle, releases threecarbon sugars, which are later combined to form sucrose and starch. The overall equation for the light-independent reactions in green plants is: 3 CO2 + 9 ATP + 6 NADPH + 6 H+ → C3H6O3-phosphate + 9 ADP + 8 Pi + 6 NADP+ + 3 H2O

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To be more specific, carbon fixation produces an intermediate product, which is then converted to the final carbohydrate products. The carbon skeletons produced by photosynthesis are then variously used to form other organic compounds, such as the building material cellulose, as precursors for lipid and amino acid biosynthesis, or as a fuel in cellular respiration. The latter occurs not only in plants but also in animals when the energy from plants gets passed through a food chain.

The fixation or reduction of carbon dioxide is a process in which carbon dioxide combines with a five-carbon sugar,ribulose 1,5-bisphosphate (RuBP), to yield two molecules of a three-carbon compound, glycerate 3-phosphate (GP), also known as 3-phosphoglycerate (PGA). GP, in the presence of ATP and NADPH from the light-dependent stages, is reduced to glyceraldehyde 3-phosphate (G3P). This product is also referred to as 3-phosphoglyceraldehyde (PGAL) or even as triose phosphate. Triose is a 3-carbon sugar. Most (5 out of 6 molecules) of the G3P produced is used to regenerate RuBP so the process can continue The 1 out of 6 molecules of the triose phosphates not "recycled" often condense to form hexose phosphates, which ultimately yield sucrose, starch and cellulose. The sugars produced during carbon metabolism yield carbon skeletons that can be used for other metabolic reactions like the production of amino acids and lipids.

Carbon concentrating mechanisms On land

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In hot and dry conditions, plants close their stomata to prevent the loss of water.

Under these conditions, CO2 will decrease, and oxygen gas, produced by the light reactions of photosynthesis, will decrease in the stem, not leaves, causing an increase of photorespiration by the oxygenase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase and decrease in carbon fixation. Some plants have evolved mechanisms to increase the CO2 concentration in the leaves under these conditions.

C4 plants chemically fix carbon dioxide in the cells of the mesophyll by adding it to the three-carbon molecule phosphoenolpyruvate (PEP), a reaction catalyzed by an enzyme called PEP carboxylase, creating the four-carbon organic acid oxaloacetic acid. Oxaloacetic acid or malate synthesized by this process is then translocated to specialized bundle sheath cells where the enzyme RuBisCO and other Calvin cycle enzymes are located, and where CO2 released by decarboxylation of the fourcarbon acids is then fixed by RuBisCO activity to the three-carbon sugar 3phosphoglyceric acids. The physical separation of RuBisCO from the oxygengenerating light reactions reduces photorespiration and increases CO 2 fixation and, thus, photosynthetic capacity of the leaf. C4 plants can produce more sugar than C3 plants in conditions of high light and temperature. Many important crop plants are C4 plants, including maize, sorghum, sugarcane, and millet. Plants that do not use PEP-carboxylase in carbon fixation are called C3 plants because the primary carboxylation reaction, catalyzed by RuBisCO, produces the three-carbon sugar 3phosphoglyceric acids directly in the Calvin-Benson cycle. Over 90% of plants use C3 carbon fixation, compared to 3% that use C4 carbon fixation.; however, the fact that C4 has evolved in over 60 plant lineages makes it a striking example of convergent evolution.

Xerophytes, such as cacti and most succulents, also use PEP carboxylase to capture carbon dioxide in a process calledCrassulacean acid metabolism (CAM). In contrast to C4 metabolism, which physically separates the CO2 fixation to PEP from the Calvin cycle, CAM temporally separates these two processes. CAM plants have a different leaf anatomy from C3plants, and fix the CO2 at night, when their stomata are open. CAM plants store the CO2 mostly in the form of malic acidvia carboxylation of phosphoenolpyruvate to oxaloacetate, which is then reduced to malate. Decarboxylation of malate during the day releases CO2 inside the leaves, thus allowing carbon fixation to 3-phosphoglycerate by RuBisCO. Sixteen thousand species of plants use CAM. In water Cyanobacteria possess carboxysomes, which increase the concentration of CO 2 around RuBisCO to increase the rate of photosynthesis. An enzyme, carbonic anhydrase, located within the carboxysome releases CO2 from the dissolved hydrocarbonate ions (HCO3–). Before the CO2 diffuses out it is quickly sponged up

by RuBisCO, which is concentrated within the carboxysomes. HCO3– ions are made from CO2 outside the cell by another carbonic anhydrase and are actively pumped into the cell by a membrane protein. They cannot cross the membrane as they are charged, and within the cytosol they turn back into CO2 very slowly without the help of carbonic anhydrase. This causes the HCO3– ions to accumulate within the cell from where they diffuse into the carboxysomes.

Pyrenoids in algae and hornworts also act to concentrate CO2 around rubisco.

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CELLULAR RESPIRATION We all need energy to function and we get this energy from the foods we eat. The most efficient way for cells to harvest energy stored in food is through cellular respiration, a catabolic pathway for the production of adenosine triphosphate (ATP). ATP, a high energy molecule, is expended by working cells. Cellular respiration occurs in both eukaryotic and prokaryotic cells. There are three main stages of cellular respiration: glycolysis, the citric acid cycle, and electron transport.

Glycolysis Glycolysis literally means "splitting sugars." Glucose, a six carbon sugar, is split into two molecules of a three carbon sugar. In the process, two molecules of ATP, two molecules of pyruvic acid and two "high energy" electron carrying molecules of NADH are produced. Glycolysis can occur with or without oxygen. In the presence of oxygen, glycolysis is the first stage of cellular respiration. Without oxygen, glycolysis allows cells to make small amounts of ATP. This process is called fermentation .

The Citric Acid Cycle The Citric Acid Cycle or Krebs Cycle begins after the two molecules of the three carbon sugar produced in glycolysis are converted to a slightly different compound (acetyl CoA). Through a series of intermediate steps, several compounds capable of storing "high energy" electrons are produced along with two ATP molecules. These compounds, known as nicotinamide adenine dinucleotide (NAD) and flavin adenine dinucleotide (FAD), are reduced in the process. These reduced forms carry the "high energy" electrons to the next stage. The Citric Acid Cycle occurs only when oxygen is present but it doesn't use oxygen directly.

Electron Transport Electron Transport requires oxygen directly. The electron transport "chain" is a series of electron carriers in the membrane of the mitochondria in eukaryotic cells. Through a series of reactions, the "high energy" electrons are passed to oxygen. In the process, a gradient is formed, and ultimately ATP is produced.

Maximum ATP Yields In summary , prokaryotic cells can yield a maximum of 38 ATP molecules while eukaryotic cells can yield a maximum of 36. In eukaryotic cells, the NADH molecules produced in glycolysis pass through the mitochondrial membrane, which "costs" two ATP molecules.

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Cellular Respiration Worksheet 1. What are the 3 phases of the cellular respiration process?

2. Where in the cell does the glycolysis part of cellular respiration occur?

3. Where in the cell does the Krebs (Citric Acid) cycle part of cellular respiration occur?

4. Where in the cell does the electron transport part of cellular respiration occur?

5. How many ATP (net)are made in the glycolysis part of cellular respiration?

6. How many ATP are made in the Kreb‘s cycle part of cellular respiration?

7. How many ATP are made in the electron transport part of cellular respiration?

8. In which phase of cellular respiration is carbon dioxide made?

9. In which phase of cellular respiration is water made?

10. In which phase of cellular respiration is oxygen a substrate?

11. In which phase of cellular respiration is glucose a substrate?

12. On average, how many ATP can be made from each NADH during the electron transport process?

13. On average, how many ATP can be made from each FADH 2 during the electron transport process?

14. What would happen to the cellular respiration process if the enzyme for one step of the process were missing or defective?

15. What happens to the high-energy electrons (and hydrogen) held by NADH if there is no O2 present?

Module (Lesson: Organ System) Nervous System The nervous system is the part of an animal's body that coordinates its voluntary and involuntary actions and transmits signals between different parts of its body. Nervous tissue first arose in wormlike organisms about 550 to 600 million years ago. In most animal species it consists of two main parts, the central nervous system (CNS) and the peripheral nervous system (PNS). The CNS contains the brain and spinal cord. The PNS consists mainly of nerves, which are enclosed bundles of the long fibers or axons, that connect the CNS to every other part of the body. The PNS includes motor, mediating voluntary movement; the autonomic nervous system, comprising the sympathetic nervous system and Young Ji International School / College

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the parasympathetic nervous system, which regulate involuntary functions, and the enteric nervous system, which functions to control the gastrointestinal system.

At the cellular level, the nervous system is defined by the presence of a special type of cell, called the neuron, also known as a "nerve cell". Neurons have special structures that allow them to send signals rapidly and precisely to other cells. They send these signals in the form of electrochemical waves traveling along thin fibers called axons, which cause chemicals called neurotransmitters to be released at junctions called synapses. A cell that receives a synaptic signal from a neuron may be excited, inhibited, or otherwise modulated. The connections between neurons can form neural circuits and also neural networks that generate an organism's perception of the world and determine its behavior. Along with neurons, the nervous system contains other specialized cells called glial cells (or simply glia), which provide structural and metabolic support.

Nervous systems are found in most multicellular animals, but vary greatly in complexity.[1] The only multicellular animals that have no nervous system at all are sponges, placozoans and mesozoans, which have very simple body plans. The nervous systems of the radially symmetric organisms the ctenophores (comb jellies) and cnidarians (which include anemones, hydras, corals and jellyfish) consist of a diffuse nerve net. All other animal species, with the exception of a few types of worm, have a nervous system containing a brain, a central cord (or two cords running in parallel), and nerves radiating from the brain and central cord. The size of the nervous system ranges from a few hundred cells in the simplest worms, to around 100 billion cells in humans.

The central nervous system functions to send signals from one cell to others, or from one part of the body to others and to receive feedback. Malfunction of the nervous system can occur as a result of genetic defects, physical damage due to trauma or toxicity, infection or simply of ageing. The medical specialty of neurology studies disorders of the nervous system and looks for interventions that can prevent or treat them. In the peripheral nervous system, the most common problem is the failure of nerve conduction, which can be due to different causes including diabetic neuropathy and demyelinating disorders such as multiple

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sclerosis and amyotrophic lateral sclerosis.

Neuroscience is the field of science that focuses on the study of the nervous system.

Skeletal System The human skeleton is the internal framework of the body. It is composed of 270 bones at birth – this total decreases to 206 bones by adulthood after some bones have fused together. The bone mass in the skeleton reaches maximum density around age 30. The human skeleton can be divided into the axial skeleton and the appendicular skeleton. The axial skeleton is formed by the vertebral column, the rib cage and the skull. The appendicular skeleton, which is attached to the axial skeleton, is formed by the pectoral girdle, the pelvic girdle and the bones of the upper and lower limbs.

The human skeleton serves six major functions; support, movement, protection, production of blood cells, storage of ions and endocrine regulation.

The human skeleton is not as sexually dimorphic as that of many other primate species, but subtle differences between sexes in themorphology of the skull, dentition, long bones, and pelves exist. In general, female skeletal elements tend to be smaller and less robust than corresponding male elements within a given population. The pelvis in female skeletons is also different from that of males in order to facilitate child birth.

Axial skeleton The axial skeleton (80 bones) is formed by the vertebral column (32–34 bones; the number of the vertebrae differs from human to human as the lower 2 parts, sacral and coccygeal bone may vary in length), the rib cage (12 pairs of ribs and the sternum), and the skull (22 bones and 7 associated bones).

The upright posture of humans is maintained by the axial skeleton, which transmits the weight from the head, the trunk, and the upper extremities down to the lower extremities at the hip joints.

The bones of the spine are supported by many ligaments. The erectors spinae muscles are also supporting and are useful for balance.

A human is able to survive with just the axial portion of their skeleton.

Appendicular skeleton The appendicular skeleton (126 bones) is formed by the pectoral girdles, the upper limbs, the pelvic girdle or pelvis, and the lower limbs. Their functions are to make locomotion possible and to protect the major organs of digestion, excretion and reproduction.

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Muscular System The muscular system is an organ system consisting of skeletal, smooth and cardiac muscles. It permits movement of the body, maintains posture, and circulates blood throughout the body. The muscular system in vertebrates is controlled through the nervous system, although some muscles (such as the cardiac muscle) can be completely autonomous. Together with the skeletal system it forms the musculoskeletal system, which is responsible for movement of the human body

There are three distinct types of muscles: skeletal muscles, cardiac or heart muscles, and smooth (non-striated) muscles. Muscles provide strength, balance, posture, movement and heat for the body to keep warm.

Upon stimulation by an action potential, skeletal muscles perform a coordinated contraction by shortening each sarcomere. The best proposed model for understanding contraction is the sliding filament model of muscle contraction. Actin Young Ji International School / College

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and myosin fibers overlap in a contractile motion towards each other. Myosin filaments have club-shaped heads that project toward the actin filaments.

Larger structures along the myosin filament called myosin heads are used to provide attachment points on binding sites for the actin filaments. The myosin heads move in a coordinated style, they swivel toward the center of the sarcomere, detach and then reattach to the nearest active site of the actin filament. This is called a rachet type drive system. This process consumes large amounts of adenosine triphosphate (ATP).

Energy for this comes from ATP, the energy source of the cell. ATP binds to the cross bridges between myosin heads and actin filaments. The release of energy powers the swiveling of the myosin head. Muscles store little ATP and so must continuously recycle the discharged adenosine diphosphate molecule (ADP) into ATP rapidly. Muscle tissue also contains a stored supply of a fast acting recharge chemical, creatinephosphatewhich can assist initially producing the rapid regeneration of ADP into ATP. Calcium ions are required for each cycle of the sarcomere. Calcium is released from the sarcoplasmic reticulum into the sarcomere when a muscle is stimulated to contract. This calcium uncovers the actin binding sites. When the muscle no longer needs to contract, the calcium ions are pumped from the sarcomere and back into storage in the sarcoplasmic reticulum.

Digestive System In the human digestive system, the process of digestion has many stages, the first of which starts in the mouth (oral cavity).

Digestion involves the breakdown of food into smaller and smaller components which can be absorbed and assimilated into the body. The secretion of saliva helps to produce a bolus which can be swallowed in the oesophagus to pass down into the stomach.

Saliva also contains a catalytic enzyme called amylase which starts to act on food in the mouth. Digestion is helped by the mastication of food by the teeth and also

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by the muscular contractions of peristalsis. Gastric juice in the stomach is essential for the continuation of digestion as is the production of mucus in the stomach.

Peristalsis is the rhythmic contraction of muscles that begins in the oesophagus and continues along the wall of the stomach and the rest of the gastrointestinal tract. This initially results in the production of chyme which when fully broken down in the small intestine is absorbed into the blood. Most of the digestion of food takes place in the small intestine. Water and some minerals are reabsorbed back into the blood, in the colon of the large intestine. The waste products of digestion are defecated from the anus via the rectum.

Circulatory System The circulatory system also called the cardiovascular system, is an organ system that permits blood to circulate and transport nutrients (such as amino acids and electrolytes), oxygen, carbon dioxide, hormones, and blood cells to and from cells in the body to nourish it and help to fight diseases, stabilize body temperature and pH, and to maintain homeostasis.

The circulatory system is often seen to be composed of both the cardiovascular system, which distributes blood, and the lymphatic system, which circulates lymph.

These are two separate systems. The passage of lymph for example takes a lot longer than that of blood. Blood is a fluid consisting of plasma, red blood cells, white blood cells, and platelets that is circulated by the heart through the vertebrate vascular system, carrying oxygen and nutrients to and waste materials away from all body tissues. Lymph is essentially recycled excess blood plasma after it has been filtered from the interstitial fluid (between cells) and returned to the lymphatic system.

The cardiovascular (from Latin words meaning 'heart''vessel') system comprises the blood, heart, and blood vessels. The lymph, lymph nodes, and lymph vessels form the lymphatic system, which returns filtered blood plasma from the interstitial fluid (between cells) as lymph.

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and capillaries), some invertebrate groups have an open cardiovascular system. The lymphatic system, on the other hand, is an open system providing an accessory route for excess interstitial fluid to get returned to the blood. The more primitive, diploblastic animal phyla lack circulatory systems.

Respiratory System The respiratory system (or ventilatory system) is a biological system consisting of specific organs and structures used for the process of respiration in an organism.

The respiratory system is involved in the intake and exchange of oxygen and carbon dioxide between an organism and the environment.

In air-breathing vertebrates like human beings, respiration takes place in the respiratory organs called lungs. The passage of air into the lungs to supply the body with oxygen is known as inhalation, and the passage of air out of the lungs to expel carbon dioxide is known as exhalation; this process is collectively called breathing or ventilation. In humans and other mammals, the anatomical features of the respiratory system include trachea, bronchi, bronchioles, lungs, and diaphragm. Molecules of oxygen and carbon dioxide are passively exchanged, by diffusion, between the gaseous external environment and the blood. This exchange process occurs in the alveoli air sacs in the lungs.

In fish and many invertebrates, respiration takes place through the gills. Other animals, such as insects, have respiratory systems with very simple anatomical features, and in amphibians even the skin plays a vital role in gas exchange. Plants also have respiratory systems but the directionality of gas exchange can be opposite to that in animals. The respiratory system in plants also includes anatomical features such as holes on the undersides of leaves known as stomata.

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Reproductive System The female reproductive system is designed to carry out several functions. It produces the female egg cells necessary for reproduction, called the ova or oocytes.

The system is designed to transport the ova to the site of fertilization. Conception, the fertilization of an egg by a sperm, normally occurs in the fallopian tubes. The next step for the fertilized egg is to implant into the walls of the uterus, beginning the initial stages of pregnancy. If fertilization and/or implantation does not take place, the system is designed to menstruate (the monthly shedding of the uterine lining). In addition, the female reproductive system produces female sex hormones that maintain the reproductive cycle.

What Parts make up the Female Anatomy?

The female reproductive anatomy includes parts inside and outside the body.

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The function of the external female reproductive structures (the genitals) is twofold: To enable sperm to enter the body and to protect the internal genital organs from infectious organisms. The main external structures of the female reproductive system include: Labia majora: The labia majora enclose and protect the other external reproductive organs. Literally translated as "large lips," the labia majora are relatively large and fleshy, and are comparable to the scrotum in males. The labia majora contain sweat and oil-secreting glands. After puberty, the labia majora are covered with hair.

Labia minora: Literally translated as "small lips," the labia minora can be very small or up to 2 inches wide. They lie just inside the labia majora, and surround the openings to the vagina (the canal that joins the lower part of the uterus to the outside of the body) and urethra (the tube that carries urine from the bladder to the outside of the body).

Bartholin's glands: These glands are located beside the vaginal opening and produce a fluid (mucus) secretion.

Clitoris: The two labia minora meet at the clitoris, a small, sensitive protrusion that is comparable to the penis in males. The clitoris is covered by a fold of skin, called the prepuce, which is similar to the foreskin at the end of the penis. Like the penis, the clitoris is very sensitive to stimulation and can become erect.

The internal reproductive organs in the female include: Vagina: The vagina is a canal that joins the cervix (the lower part of uterus) to the outside of the body. It also is known as the birth canal.

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Uterus (womb): The uterus is a hollow, pear-shaped organ that is the home to a developing fetus. The uterus is divided into two parts: the cervix, which is the lower part that opens into the vagina, and the main body of the uterus, called the corpus.

The corpus can easily expand to hold a developing baby. A channel through the cervix allows sperm to enter and menstrual blood to exit.

Ovaries: The ovaries are small, oval-shaped glands that are located on either side of the uterus. The ovaries produce eggs and hormones.

Fallopian tubes: These are narrow tubes that are attached to the upper part of the uterus and serve as tunnels for the ova (egg cells) to travel from the ovaries to the uterus. Conception, the fertilization of an egg by a sperm, normally occurs in the fallopian tubes. The fertilized egg then moves to the uterus, where it implants into the lining of the uterine wall.

Male Reproductive System The purpose of the organs of the male reproductive system is to perform the following functions: To produce, maintain, and transport sperm (the male reproductive cells) and protective fluid (semen) To discharge sperm within the female reproductive tract during sex To produce and secrete male sex hormones responsible for maintaining the male reproductive system

Unlike the female reproductive system, most of the male reproductive system is located outside of the body. These external structures include the penis, scrotum, and testicles.

Penis: This is the male organ used in sexual intercourse. It has three parts: the root, which attaches to the wall of the abdomen; the body, or shaft; and the glans, which is the cone-shaped part at the end of the penis. The glans, also called the head of the penis, is covered with a loose layer of skin called foreskin. This skin is sometimes removed in a procedure called circumcision. The opening of the urethra, the tube that transports semen and urine, is at the tip of the penis. The glans of the penis also contains a number of sensitive nerve endings.

The body of the penis is cylindrical in shape and consists of three circular shaped chambers. These chambers are made up of special, sponge-like tissue. This tissue contains thousands of large spaces that fill with blood when the man is sexually aroused. As the penis fills with blood, it becomes rigid and erect, which allows for Young Ji International School / College

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penetration during sexual intercourse. The skin of the penis is loose and elastic to accommodate changes in penis size during an erection.

Semen, which contains sperm (reproductive cells), is expelled (ejaculated) through the end of the penis when the man reaches sexual climax (orgasm). When the penis is erect, the flow of urine is blocked from the urethra, allowing only semen to be ejaculated at orgasm.

Scrotum: This is the loose pouch-like sac of skin that hangs behind and below the penis. It contains the testicles (also called testes), as well as many nerves and blood vessels. The scrotum acts as a "climate control system" for the testes. For normal sperm development, the testes must be at a temperature slightly cooler than body temperature. Special muscles in the wall of the scrotum allow it to contract and relax, moving the testicles closer to the body for warmth or farther away from the body to cool the temperature.

Testicles (testes): These are oval organs about the size of large olives that lie in the scrotum, secured at either end by a structure called the spermatic cord. Most men have two testes. The testes are responsible for making testosterone, the primary male sex hormone, and for generating sperm. Within the testes are coiled masses of tubes called seminiferous tubules. These tubes are responsible for producing sperm cells.

Excretory System The excretory system is a passive biological system that removes excess, unnecessary materials from an organism, so as to help maintain homeostasis within the organism and prevent damage to the body. It is responsible for the elimination of the waste products of metabolism as well as other liquid and gaseous wastes, as urine and as a component of sweat and exhalation. As most healthy functioning organs produce metabolic and other wastes, the entire organism depends on the function of the system; however, only the organs specifically for the excretion process are considered a part of the excretory system.

As it involves several functions that are only superficially related, it is not usually used in more formal classifications of anatomy or function.

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Endocrine System The endocrine system refers to the collection of glands of an organism that secrete hormones directly into the circulatory system to be carried towards a distant target organ. The major endocrine glands include the pineal gland, pituitary gland, pancreas, ovaries, testes, thyroid gland, parathyroid gland, hypothalamus, gastrointestinal tract and adrenal glands. The endocrine system is in contrast to the exocrine system, which secretes its hormones using ducts. The endocrine system is an information signal system like the nervous system, yet its effects and mechanism are classifiably different. The endocrine system's effects are slow to initiate, and prolonged in their response, lasting from a few hours up to weeks. The nervous system sends information very quickly, and responses are generally short lived. In vertebrates, the hypothalamus is the neural control center for all endocrine systems. The field of study dealing with the endocrine system and its disorders is endocrinology, a branch of internal medicine.

Special features of endocrine glands are, in general, their ductless nature, their vascularity, and commonly the presence of intracellular vacuoles or granules that store their hormones. In contrast, exocrine glands, such as salivary glands, sweat glands, and glands within the gastrointestinal tract, tend to be much less vascular and have ducts or a hollow lumen.

In addition to the specialized endocrine organs mentioned above, many other organs that are part of other body systems, such as bone, kidney, liver, heart and gonads, have secondary endocrine functions. For example the kidney secretes endocrine hormones such as erythropoietin and renin.

A number of glands that signal each other in sequence are usually referred to as an axis, for example, the hypothalamic-pituitary-adrenal axis.

As opposed to endocrine factors that travel considerably longer distances via the circulatory system, other signaling molecules, such as paracrine factors involved in paracrine signalling diffuse over a relatively short distance.

The word endocrine derives from the Greek words endo- "inside, within," and krinein "to separate, distinguish".

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ORGAN SYSTEM WORKSHEET Match column A with column B. Write the letter of the correct match on the blank. Use CAPITAL letter. ____1. digestive system materials from our body ____2. skeletal system parts of our body ____3. respiratory system our body ____4. circulatory system out of our body ____5. nervous system our body can use ____6. muscular system substances to all parts of our body ____7. urinary system

A. removes extra water and waste B. allows us to move different C. protects the delicate organs in D. takes air into and removes air E. breaks down food into substances F. made up of parts that help move

G. the control center of our brain

Name one major function of the organ systems listed below.

1. Skeletal System 2. Muscular System 3. Digestive System 4. Respiratory System 5. Circulatory System 6. Nervous System 7. Urinary System Name the organ system where the body part belongs. Write the beginning letter of the correct organ system on the blank.

M muscular D digestive C circulatory U urinary S skeletal

R respiratory N nervous

____1. rib ____2. bladder ____3. brain ____4. muscles ____5. nerves ____6. skull ____7. heart Young Ji International School / College

____11. large& small intestine ____12. ureters ____13. anus ____14. spinal cord ____15. stomach ____16. blood vessels ____17. mouth Page 158

____8. kidneys ____9. gullet ____10. lungs

____18. backbone ____19. Windpipe ____20. Nose

Indicate which organ system will be primarily used in the following situation. Write the beginning letter of correct organ system on the blank.

M muscular D digestive S skeletal

C circulatory U urinary

R respiratory N nervous

_____1. Prepare for a 5km run and eat lots of carbohydrates like rice to give you more energy. _____2. You lift your feet and move your legs as fast as you can. _____3. But you have to go to the bathroom because you drank too much water before the run. _____4. Your breathing is getting faster and faster. _____5. Ouch! You accidentally tripped and scraped your knee. _____6. Good thing you have strong bones to protect you. _____7. The heart is pumping fast as you sprint for the final 1km.

Module (Lesson: Genetics) Genetics is the study of genes, heredity, and variation in living organisms. It is generally considered a field of biology, but it intersects frequently with many of the life sciences and is strongly linked with the study of information systems.

The father of genetics is Gregor Mendel, a scientist and Augustinian friar. Mendel studied 'trait inheritance,' patterns in the way traits were handed down from parents to offspring. He observed that organisms (pea plants) inherit traits by way of discrete "units of inheritance". This term, still used today, is a somewhat ambiguous definition of what is referred to as a gene.

Trait inheritance and molecular inheritance mechanisms of genes are still a primary principle of genetics in the 21st century, but modern genetics has expanded beyond inheritance to studying the function and behavior of genes. Gene structure and function, variation, and distribution are studied within the context of the cell, the organism (e.g. dominance) and within the context of a population. Genetics has given rise to a number of sub-fields including epigenetics and population genetics.

Organisms studied within the broad field span the domain of life, including bacteria, plants, animals, and humans.

Genetic processes work in combination with an organism's environment and experiences to influence development and behavior, often referred to as Nature versus nurture. The intra- or extra-cellular environment of a cell or organism may switch gene transcription on or off. A classic example is two seeds of genetically identical corn, one placed in a temperate climate and one in an arid climate. While the average height of the two corn stalks may be genetically determined to be equal, the one in the arid climate only grows to half the height of the one in the temperate climate, due to lack of water and nutrients in its environment.

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Etymology The word genetics stems from the Ancient Greek genetikos meaning "genitive"/"generative", which in turn derives from genesis meaning "origin".

The Gene The modern working definition of a gene is a portion (or sequence) of DNA that codes for a known cellular function or process (i.e. the function "make melanin molecules"). A single 'gene' is most similar to a single 'word' in the English language.

The nucleotides (molecules) that make up genes can be seen as 'letters' in the English language. A single gene may have a small number of nucleotides or a large number of nucleotides, in the same way that a word may be small or large (e.g. 'cell' vs. 'electrophysiology'). A single gene often interacts with neighboring genes to produce a cellular function and can even be ineffectual without those neighboring genes. This can be seen in the same way that a 'word' may have meaning only in the context of a 'sentence.' A series of nucleotides can be put together without forming a gene (non coding regions of DNA), like a string of letters can be put together without forming a word (e.g. udkslk). Nonetheless, all words have letters, like all genes must have nucleotides.

A quick heuristic that is often used (but not always true) is "one gene, one protein" meaning a singular gene codes for a singular protein type in a cell (enzyme, transcription factor, etc.)

The sequence of nucleotides in a gene is read and translated by a cell to produce a chain of amino acids which in turn folds into a protein. The order of amino acids in a protein corresponds to the order of nucleotides in the gene. This relationship between nucleotide sequence and amino acid sequence is known as the genetic code. The amino acids in a protein determine how it folds into its unique threedimensional shape, a structure that is ultimately responsible for the protein's function. Proteins carry out many of the functions needed for cells to live. A change to the DNA in a gene can change a protein's amino acid sequence, thereby changing its shape and function and rendering the protein ineffective or even malignant (e.g. sickle cell anemia). Changes to genes are called mutations.

History of genetics

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DNA, the molecular basis for biological inheritance. Each strand of DNA is a chain ofnucleotides, matching each other in the center to form what look like rungs on a twisted ladder.

The observation that living things inherit traits from their parents has been used since prehistoric times to improve crop plants and animals through selective breeding. The modern science of genetics, seeking to understand this process, began with the work of Gregor Mendel in the mid-19th century.

Although the science of genetics began with the applied and theoretical work of Gregor Mendel in the mid-19th century, other theories of inheritance preceded Mendel. A popular theory during Mendel's time was the concept of blending inheritance: the idea that individuals inherit a smooth blend of traits from their parents.[8] Mendel's work provided examples where traits were definitely not blended after hybridization, showing that traits are produced by combinations of distinct genes rather than a continuous blend. Blending of traits in the progeny is now explained by the action of multiple genes with quantitative effects. Another theory that had some support at that time was the inheritance of acquired characteristics: the belief that individuals inherit traits strengthened by their parents. This theory (commonly associated with Jean-Baptiste Lamarck) is now known to be wrong—the experiences of individuals do not affect the genes they pass to their children, although evidence in the field of epigenetics has revived some aspects of Lamarck's theory. Other theories included the pangenesis of Charles Darwin (which had both acquired and inherited aspects) and Francis Galton's reformulation of pangenesis as both particulate and inherited.

Mendelian and classical genetics Modern genetics started with Gregor Johann Mendel, a scientist and Augustinian friar who studied the nature of inheritance in plants. In his paper "Versuche über Pflanzenhybriden" ("Experiments on Plant Hybridization"), presented in 1865 to the NaturforschenderVerein (Society for Research in Nature) in Brünn, Mendel traced the inheritance patterns of certain traits in pea plants and described them mathematically. Although this pattern of inheritance could only be observed for a few traits, Mendel's work suggested that heredity was particulate, not acquired, and that the inheritance patterns of many traits could be explained through simple rules and ratios.

The importance of Mendel's work did not gain wide understanding until the 1890s, after his death, when other scientists working on similar problems re-discovered his research. William Bateson, a proponent of Mendel's work, coined the word genetics in 1905. (The adjective genetic, derived from the Greek word genesis—γένεσις, "origin", predates the noun and was first used in a biological sense in 1860.) Bateson popularized the usage of the word genetics to describe the study of inheritance in his inaugural address to the Third International Conference on Plant Hybridization in London, England, in 1906.

After the rediscovery of Mendel's work, scientists tried to determine which molecules in the cell were responsible for inheritance. In 1911, Thomas Hunt Morgan argued that genes are on chromosomes, based on observations of a sex-linked white eye mutation in fruit flies. In 1913, his student Alfred Sturtevant used the phenomenon ofgenetic linkage to show that genes are arranged linearly on the chromosome.

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Morgan's observation of sex-linked inheritance of a mutation causing white eyes in Drosophila led him to the hypothesis that genes are located upon chromosomes.

Molecular genetics Although genes were known to exist on chromosomes, chromosomes are composed of both protein and DNA, and scientists did not know which of these is responsible for inheritance. In 1928, Frederick Griffith discovered the phenomenon of transformation : dead bacteria could transfer genetic material to "transform" other still-living bacteria. Sixteen years later, in 1944, Oswald Theodore Avery, Colin McLeod and MaclynMcCarty identified DNA as the molecule responsible for transformation. The role of the nucleus as the repository of genetic information in eukaryotes had been established by Hämmerling in 1943 in his work on the single celled alga Acetabularia. The Hershey-Chase experiment in 1952 confirmed that DNA (rather than protein) is the genetic material of the viruses that infect bacteria, providing further evidence that DNA is the molecule responsible for inheritance.

James D. Watson and Francis Crick determined the structure of DNA in 1953, using the X-ray crystallography work of Rosalind Franklin and Maurice Wilkins that indicated DNA had a helical structure (i.e., shaped like a corkscrew). Their doublehelix model had two strands of DNA with the nucleotides pointing inward, each matching a complementary nucleotide on the other strand to form what looks like rungs on a twisted ladder. This structure showed that genetic information exists in the sequence of nucleotides on each strand of DNA. The structure also suggested a simple method for replication: if the strands are separated, new partner strands can be reconstructed for each based on the sequence of the old strand. This property is what gives DNA its' semi-conservative nature where one strand of new DNA is from an original parent strand.

Although the structure of DNA showed how inheritance works, it was still not known how DNA influences the behavior of cells. In the following years, scientists tried to understand how DNA controls the process of protein production. It was discovered that the cell uses DNA as a template to create matching messenger RNA, molecules with nucleotides very similar to DNA. The nucleotide sequence of a messenger RNA is used to create an amino acid sequence in protein; this translation between nucleotide sequenced and amino acid sequences is known as the genetic code.

With the newfound molecular understanding of inheritance came an explosion of research. One important development was chain-termination DNA sequencing in 1977 by Frederick Sanger. This technology allows scientists to read the nucleotide sequence of a DNA molecule. In 1983, Kary Banks Mullis developed the polymerase chain reaction, providing a quick way to isolate and amplify a specific section of DNA from a mixture. The efforts of the Human Genome Project, Department of Energy, Young Ji International School / College

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NIH, and parallel private effort by Celera Genomics led to the sequencing of thehuman genome in 2003.

Discrete inheritance and Mendel's laws

A Punnett square depicting a cross between two pea plants heterozygous for purple (B) and white (b) blossoms.

At its most fundamental level, inheritance in organisms occurs by passing discrete heritable units, called genes, from parents to progeny. This property was first observed by Gregor Mendel, who studied the segregation of heritable traits in pea plants. In his experiments studying the trait for flower color, Mendel observed that the flowers of each pea plant were either purple or white—but never an intermediate between the two colors. These different, discrete versions of the same gene are called alleles.

In the case of pea, which is a diploid species, each individual plant has two copies of each gene, one copy inherited from each parent. Many species, including humans, have this pattern of inheritance. Diploid organisms with two copies of the same allele of a given gene are called homozygous at thatgene locus, while organisms with two different alleles of a given gene are called heterozygous.

The set of alleles for a given organism is called its genotype, while the observable traits of the organism are called its phenotype. When organisms are heterozygous at a gene, often one allele is called dominant as its qualities dominate the phenotype of the organism, while the other allele is called recessiveas its qualities recede and are not observed. Some alleles do not have complete dominance and instead have incomplete dominance by expressing an intermediate phenotype, or codominance by expressing both alleles at once.

When a pair of organisms reproduce sexually, their offspring randomly inherit one of the two alleles from each parent. These observations of discrete inheritance and the segregation of alleles are collectively known as Mendel's first law or the Law of Segregation.

Notation and diagrams

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Genetic pedigree charts help track the inheritance patterns of traits.

Geneticists use diagrams and symbols to describe inheritance. A gene is represented by one or a few letters. Often a "+" symbol is used to mark the usual, non-mutant allele for a gene.

In fertilization and breeding experiments (and especially when discussing Mendel's laws) the parents are referred to as the "P" generation and the offspring as the "F1" (first filial) generation. When the F1 offspring mate with each other, the offspring are called the "F2" (second filial) generation. One of the common diagrams used to predict the result of cross-breeding is the Punnett square.

When studying human genetic diseases, geneticists often use pedigree charts to represent the inheritance of traits. These charts map the inheritance of a trait in a family tree.

Multiple gene interactions

Human height is a trait with complex genetic causes. Francis Galton's data from 1889 shows the relationship between offspring height as a function of mean parent height. While correlated, remaining variation in offspring heights indicates environment is also an important factor in this trait.

Organisms have thousands of genes, and in sexually reproducing organisms these genes generally assort independently of each other. This means that the inheritance of an allele for yellow or green pea color is unrelated to the inheritance of alleles for white or purple flowers. This phenomenon, known as "Mendel's second law" or the "Law of independent assortment", means that the alleles of different genes get shuffled between parents to form offspring with many different combinations. (Some genes do not assort independently, demonstrating genetic linkage, a topic discussed later in this article.)

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Often different genes can interact in a way that influences the same trait. In the Blueeyed Mary (Omphalodesverna), for example, there exists a gene with alleles that determine the color of flowers: blue or magenta. Another gene, however, controls whether the flowers have color at all or are white. When a plant has two copies of this white allele, its flowers are white—regardless of whether the first gene has blue or magenta alleles. This interaction between genes is called epistasis, with the second gene epistatic to the first.

Many traits are not discrete features (e.g. purple or white flowers) but are instead continuous features (e.g. human height and skin color). These complex traits are products of many genes. The influence of these genes is mediated, to varying degrees, by the environment an organism has experienced. The degree to which an organism's genes contribute to a complex trait is called heritability. Measurement of the heritability of a trait is relative—in a more variable environment, the environment has a bigger influence on the total variation of the trait. For example, human height is a trait with complex causes. It has a heritability of 89% in the United States. In Nigeria, however, where people experience a more variable access to good nutrition and health care, height has a heritability of only 62%.

DNA and chromosomes

The molecular structure of DNA. Bases pair through the arrangement of hydrogen bonding between the strands.

The molecular basis for genes is deoxyribonucleic acid (DNA). DNA is composed of a chain of nucleotides, of which there are four types: adenine (A),cytosine (C), guanine (G), and thymine (T). Genetic information exists in the sequence of these nucleotides, and genes exist as stretches of sequence along the DNA chain. Viruses are the only exception to this rule— sometimes viruses use the very similar molecule RNA instead of DNA as their genetic material. Viruses cannot reproduce without a host and are unaffected by many genetic processes, so tend not to be considered living organisms.

DNA normally exists as a double-stranded molecule, coiled into the shape of a double helix. Each nucleotide in DNA preferentially pairs with its partner nucleotide on the opposite strand: A pairs with T, and C pairs with G. Thus, in its two-stranded form, each strand effectively contains all necessary information, redundant with its partner strand. This structure of DNA is the physical basis for inheritance: DNA replication duplicates the genetic information by splitting the strands and using each strand as a template for synthesis of a new partner strand.

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Genes are arranged linearly along long chains of DNA base-pair sequences.

In bacteria, each cell usually contains a single circular genophore, while eukaryotic organisms (such as plants and animals) have their DNA arranged in multiple linear chromosomes. These DNA strands are often extremely long; the largest human chromosome, for example, is about 247 million base pairs in length.

The DNA of a chromosome is associated with structural proteins that organize, compact and control access to the DNA, forming a material called chromatin; in eukaryotes, chromatin is usually composed of nucleosomes, segments of DNA wound around cores of histone proteins. The full set of hereditary material in an organism (usually the combined DNA sequences of all chromosomes) is called the genome.

While haploid organisms have only one copy of each chromosome, most animals and many plants are diploid, containing two of each chromosome and thus two copies of every gene. The two alleles for a gene are located on identical loci of the two homologous chromosomes, each allele inherited from a different parent.

Walther Flemming's 1882 diagram of eukaryotic cell division. Chromosomes are copied, condensed, and organized. Then, as the cell divides, chromosome copies separate into the daughter cells.

Many species have so-called sex chromosomes that determine the gender of each organism. In humans and many other animals, the Y chromosomecontains the gene that triggers the development of the specifically male characteristics. In evolution, this chromosome has lost most of its content and also most of its genes, while the X chromosome is similar to the other chromosomes and contains many genes. The X and Y chromosomes form a strongly heterogeneous pair.

Reproduction When cells divide, their full genome is copied and each daughter cell inherits one copy. This process, called mitosis, is the simplest form of reproduction and is the basis for asexual reproduction. Asexual reproduction can also occur in multicellular organisms, producing offspring that inherit their genome from a single parent.

Offspring that are genetically identical to their parents are called clones.

Eukaryotic organisms often use sexual reproduction to generate offspring that contain a mixture of genetic material inherited from two different parents. The Young Ji International School / College

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process of sexual reproduction alternates between forms that contain single copies of the genome (haploid) and double copies (diploid). Haploid cells fuse and combine genetic material to create a diploid cell with paired chromosomes. Diploid organisms form haploids by dividing, without replicating their DNA, to create daughter cells that randomly inherit one of each pair of chromosomes. Most animals and many plants are diploid for most of their lifespan, with the haploid form reduced to single cell gametes such as sperm or eggs.

Although they do not use the haploid/diploid method of sexual reproduction, bacteria have many methods of acquiring new genetic information.

Some bacteria can undergo conjugation, transferring a small circular piece of DNA to another bacterium. Bacteria can also take up raw DNA fragments found in the environment and integrate them into their genomes, a phenomenon known as transformation. These processes result in horizontal gene transfer, transmitting fragments of genetic information between organisms that would be otherwise unrelated.

Recombination and genetic linkage

Thomas Hunt Morgan's 1916 illustration of a double crossover between chromosomes.

The diploid nature of chromosomes allows for genes on different chromosomes to assort independently or be separated from their homologous pair during sexual reproduction wherein haploid gametes are formed. In this way new combinations of genes can occur in the offspring of a mating pair. Genes on the same chromosome would theoretically never recombine. However, they do via the cellular process of chromosomal crossover. During crossover, chromosomes exchange stretches of DNA, effectively shuffling the gene alleles between the chromosomes. This process of chromosomal crossover generally occurs during meiosis, a series of cell divisions that creates haploid cells.

The probability of chromosomal crossover occurring between two given points on the chromosome is related to the distance between the points. For an arbitrarily long distance, the probability of crossover is high enough that the inheritance of the genes is effectively uncorrelated. For genes that are closer together, however, the lower probability of crossover means that the genes demonstrate genetic linkage; alleles Young Ji International School / College

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for the two genes tend to be inherited together. The amounts of linkage between a series of genes can be combined to form a linear linkage map that roughly describes the arrangement of the genes along the chromosome.

Genetic code

The genetic code: Using a triplet code, DNA, through a messenger RNAintermediary, specifies a protein.

Genes generally express their functional effect through the production of proteins, which are complex molecules responsible for most functions in the cell. Proteins are made up of one or more polypeptide chains, each of which is composed of a sequence of amino acids, and the DNA sequence of a gene (through an RNA intermediate) is used to produce a specific amino acid sequence. This process begins with the production of an RNA molecule with a sequence matching the gene's DNA sequence, a process called transcription.

This messenger RNA molecule is then used to produce a corresponding amino acid sequence through a process called translation. Each group of three nucleotides in the sequence, called a codon, corresponds either to one of the twenty possible amino acids in a protein or an instruction to end the amino acid sequence; this correspondence is called the genetic code. The flow of information is unidirectional: information is transferred from nucleotide sequences into the amino acid sequence of proteins, but it never transfers from protein back into the sequence of DNA—a phenomenon Francis Crick called the central dogma of molecular biology.

The specific sequence of amino acids results in a unique three-dimensional structure for that protein, and the three-dimensional structures of proteins are related to their functions. Some are simple structural molecules, like the fibers formed by the protein collagen. Proteins can bind to other proteins and simple molecules, sometimes acting as enzymes by facilitating chemical reactionswithin the bound molecules (without changing the structure of the protein itself). Protein structure is dynamic; the protein hemoglobin bends into slightly different forms as it facilitates the capture, transport, and release of oxygen molecules within mammalian blood.

A single nucleotide difference within DNA can cause a change in the amino acid sequence of a protein. Because protein structures are the result of their amino acid sequences, some changes can dramatically change the properties of a protein by destabilizing the structure or changing the surface of the protein in a way that changes its interaction with other proteins and molecules. For example, sickle-cell anemia is a human genetic disease that results from a single base difference within the coding region for the β-globin section of hemoglobin, causing a single amino acid change that changes hemoglobin's physical properties. Sickle-cell versions of hemoglobin stick to themselves, stacking to form fibers that distort the shape of red blood cells carrying the protein. These sickle-shaped cells no longer flow smoothly Young Ji International School / College

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through blood vessels, having a tendency to clog or degrade, causing the medical problems associated with this disease.

Some genes are transcribed into RNA but are not translated into protein products— such RNA molecules are called non-coding RNA. In some cases, these products fold into structures which are involved in critical cell functions (e.g. ribosomal RNA and transfer RNA). RNA can also have regulatory effect through hybridization interactions with other RNA molecules (e.g.microRNA).

Nature and nurture

Siamese cats have temperature-sensitive pigment-production mutation.

Although genes contain all the information an organism uses to function, the environment plays an important role in determining the ultimate phenotypes an organism displays. This is the complementary relationship often referred to as "nature and nurture". The phenotype of an organism depends on the interaction of genes and the environment. An interesting example is the coat coloration of the Siamese cat. In this case, the body temperature of the cat plays the role of the environment. The cat's genes code for dark hair, thus the hair producing cells in the cat make cellular proteins resulting in dark hair. But these dark hair-producing proteins are sensitive to temperature (i.e. have a mutation causing temperaturesensitivity) and denature in higher-temperature environments, failing to produce dark-hair pigment in areas where the cat has a higher body temperature. In a lowtemperature environment, however, the protein's structure is stable and produces dark-hair pigment normally. The protein remains functional in areas of skin that are colder – such as its legs, ears, tail and face – so the cat has dark-hair at its extremities.

Environment plays a major role in effects of the human genetic disease phenylketonuria. The mutation that causes phenylketonuria disrupts the ability of the body to break down the amino acid phenylalanine, causing a toxic buildup of an intermediate molecule that, in turn, causes severe symptoms of progressive mental retardation and seizures. However, if someone with the phenylketonuria mutation follows a strict diet that avoids this amino acid, they remain normal and healthy.

A popular method in determining how genes and environment ("nature and nurture") contribute to a phenotype is by studying identical and fraternal twins or siblings of multiple births. Because identical siblings come from the same zygote, they are genetically the same. Fraternal siblings are as genetically different from one another as normal siblings. By analyzing statistics on how often a twin of a set has a certain disorder compared other sets of twins, scientists can determine whether that Young Ji International School / College

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disorder is caused by genetic or environmental factors (i.e. whether it has 'nature' or 'nurture' causes). One famous example is the multiple birth study of the Genain quadruplets, who were identical quadruplets all diagnosed with schizophrenia.

Gene regulation The genome of a given organism contains thousands of genes, but not all these genes need to be active at any given moment. A gene is expressed when it is being transcribed into mRNA and there exist many cellular methods of controlling the expression of genes such that proteins are produced only when needed by the cell. Transcription factors are regulatory proteins that bind to DNA, either promoting or inhibiting the transcription of a gene. Within the genome of Escherichia coli bacteria, for example, there exists a series of genes necessary for the synthesis of the amino acid tryptophan. However, when tryptophan is already available to the cell, these genes for tryptophan synthesis are no longer needed. The presence of tryptophan directly affects the activity of the genes—tryptophan molecules bind to the tryptophan repressor (a transcription factor), changing the repressor's structure such that the repressor binds to the genes. The tryptophan repressor blocks the transcription and expression of the genes, thereby creating negative feedback regulation of the tryptophan synthesis process.

Transcription factors bind to DNA, influencing the transcription of associated genes.

Differences in gene expression are especially clear within multicellular organisms, where cells all contain the same genome but have very different structures and behaviors due to the expression of different sets of genes. All the cells in a multicellular organism derive from a single cell, differentiating into variant cell types in response to external and intercellular signals and gradually establishing different patterns of gene expression to create different behaviors. As no single gene is responsible for the development of structures within multicellular organisms, these patterns arise from the complex interactions between many cells.

Within eukaryotes, there exist structural features of chromatin that influence the transcription of genes, often in the form of modifications to DNA and chromatin that are stably inherited by daughter cells. These features are called "epigenetic" because they exist "on top" of the DNA sequence and retain inheritance from one cell generation to the next. Because of epigenetic features, different cell types grown within the same medium can retain very different properties. Although epigenetic features are generally dynamic over the course of development, some, like the phenomenon of paramutation, have multigenerational inheritance and exist as rare exceptions to the general rule of DNA as the basis for inheritance.

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Mutations

Gene duplication allows diversification by providing redundancy: one gene can mutate and lose its original function without harming the organism.

During the process of DNA replication, errors occasionally occur in the polymerization of the second strand. These errors, called mutations, can have an impact on the phenotype of an organism, especially if they occur within the protein coding sequence of a gene. Error rates are usually very low—1 error in every 10– 100 million bases—due to the "proofreading" ability of DNA polymerases. Processes that increase the rate of changes in DNA are called mutagenic: mutagenic chemicals promote errors in DNA replication, often by interfering with the structure of basepairing, while UV radiation induces mutations by causing damage to the DNA structure. Chemical damage to DNA occurs naturally as well and cells use DNA repair mechanisms to repair mismatches and breaks. The repair does not, however, always restore the original sequence.

In organisms that use chromosomal crossover to exchange DNA and recombine genes, errors in alignment during meiosis can also cause mutations. Errors in crossover are especially likely when similar sequences cause partner chromosomes to adopt a mistaken alignment; this makes some regions in genomes more prone to mutating in this way. These errors create large structural changes in DNA sequence – duplications, inversions, deletions of entire regions – or the accidental exchange of whole parts of sequences between different chromosomes (chromosomal translocation).

Natural selection and evolution Mutations alter an organism's genotype and occasionally this causes different phenotypes to appear. Most mutations have little effect on an organism's phenotype, health, or reproductive fitness. Mutations that do have an effect are usually deleterious, but occasionally some can be beneficial. Studies in the fly Drosophila melanogaster suggest that if a mutation changes a protein produced by a gene, about 70 percent of these mutations will be harmful with the remainder being either neutral or weakly beneficial.

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An evolutionary tree of eukaryoticorganisms, constructed by the comparison of several orthologous gene sequences.

Population genetics studies the distribution of genetic differences within populations and how these distributions change over time. Changes in in a population are mainly influenced by natural selection, where a given allele provides a selective or reproductive advantage to the organism, as well as other factors such as mutation, genetic drift, genetic draft, artificial selection and migration.

Over many generations, the genomes of organisms can change significantly, resulting in evolution. In the process called adaptation, selection for beneficial mutations can cause a species to evolve into forms better able to survive in their environment. New species are formed through the process of speciation, often caused by geographical separations that prevent populations from exchanging genes with each other. The application of genetic principles to the study of population biology and evolution is known as the "modern synthesis".

By comparing the homology between different species' genomes, it is possible to calculate the evolutionary distance between them and when they may have diverged. Genetic comparisons are generally considered a more accurate method of characterizing the relatedness between species than the comparison of phenotypic characteristics. The evolutionary distances between species can be used to form evolutionary trees; these trees represent the common descent and divergence of species over time, although they do not show the transfer of genetic material between unrelated species (known ashorizontal gene transfer and most common in bacteria).

Model organisms

The common fruit fly (Drosophila melanogaster) is a popular model organismin genetics research.

Although geneticists originally studied inheritance in a wide range of organisms, researchers began to specialize in studying the genetics of a particular subset of organisms. The fact that significant research already existed for a given organism would encourage new researchers to choose it for further study, and so eventually a Young Ji International School / College

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few model organisms became the basis for most genetics research. Common research topics in model organism genetics include the study of gene regulation and the involvement of genes in development and cancer.

Organisms were chosen, in part, for convenience—short generation times and easy genetic manipulation made some organisms popular genetics research tools.

Widely used model organisms include the gut bacterium Escherichia coli, the plant Arabidopsis thaliana, baker's yeast (Saccharomyces cerevisiae), the nematode Caenorhabditiselegans, the common fruit fly (Drosophila melanogaster), and the common house mouse (Musmusculus).

Medicine

Schematic relationship between biochemistry, genetics and molecular biology.

Medical genetics seeks to understand how genetic variation relates to human health and disease. When searching for an unknown gene that may be involved in a disease, researchers commonly use genetic linkage and genetic pedigree charts to find the location on the genome associated with the disease. At the population level, researchers take advantage of Mendelian randomization to look for locations in the genome that are associated with diseases, a method especially useful for multigenic traits not clearly defined by a single gene. Once a candidate gene is found, further research is often done on the corresponding gene – the orthologous gene – in model organisms. In addition to studying genetic diseases, the increased availability of genotyping methods has led to the field of pharmacogenetics: the study of how genotype can affect drug responses.

Individuals differ in their inherited tendency to develop cancer, and cancer is a genetic disease.The process of cancer development in the body is a combination of events. Mutations occasionally occur within cells in the body as they divide. Although these mutations will not be inherited by any offspring, they can affect the behavior of cells, sometimes causing them to grow and divide more frequently. There are biological mechanisms that attempt to stop this process; signals are given to inappropriately dividing cells that should trigger cell death, but sometimes additional mutations occur that cause cells to ignore these messages. An internal process of natural selection occurs within the body and eventually mutations accumulate within cells to promote their own growth, creating a cancerous tumor that grows and invades various tissues of the body.

Normally, a cell divides only in response to signals called growth factors and stops growing once in contact with surrounding cells and in response to growth-inhibitory signals. It usually then divides a limited number of times and dies, staying within the epithelium where it is unable to migrate to other organs. To become a cancer cell, a cell has to accumulate mutations in a number of genes (3–7) that allow it to Young Ji International School / College

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bypass this regulation: it no longer needs growth factors to divide, it continues growing when making contact to neighbor cells, and ignores inhibitory signals, it will keep growing indefinitely and is immortal, it will escape from the epithelium and ultimately may be able to escape from the primary tumor, cross the endothelium of a blood vessel, be transported by the bloodstream and will colonize a new organ, forming deadly metastasis. Although there are some genetic predispositions in a small fraction of cancers, the major fraction is due to a set of new genetic mutations that originally appear and accumulate in one or a small number of cells that will divide to form the tumor and are not transmitted to the progeny (somatic mutations).

The most frequent mutations are a loss of function of p53 protein, a tumor suppressor, or in the p53 pathway, and gain of function mutations in the ras proteins, or in other oncogenes.

Research methods

Colonies of E. coli produced by cellular cloning. A similar methodology is often used inmolecular cloning.

DNA can be manipulated in the laboratory. Restriction enzymes are commonly used enzymes that cut DNA at specific sequences, producing predictable fragments of DNA.DNA fragments can be visualized through use of gel electrophoresis, which separates fragments according to their length.

The use of ligation enzymes allows DNA fragments to be connected. By binding ("ligating") fragments of DNA together from different sources, researchers can create recombinant DNA, the DNA often associated with genetically modified organisms. Recombinant DNA is commonly used in the context of plasmids: short circular DNA fragments with a few genes on them. In the process known as molecular cloning, researchers can amplify the DNA fragments by inserting plasmids into bacteria and then culturing them on plates of agar (to isolate clones of bacteria cells). ("Cloning" can also refer to the various means of creating cloned ("clonal") organisms.)

DNA can also be amplified using a procedure called the polymerase chain reaction (PCR).[87] By using specific short sequences of DNA, PCR can isolate and exponentially amplify a targeted region of DNA. Because it can amplify from extremely small amounts of DNA, PCR is also often used to detect the presence of specific DNA sequences.

DNA sequencing and genomics DNA sequencing, one of the most fundamental technologies developed to study genetics, allows researchers to determine the sequence of nucleotides in DNA fragments. The technique of chain-termination sequencing, developed in 1977 by a team led by Frederick Sanger, is still routinely used to sequence DNA

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fragments. Using this technology, researchers have been able to study the molecular sequences associated with many human diseases.

As sequencing has become less expensive, researchers have sequenced the genomes of many organisms, using, a process called genome assembly, computational tools to stitch together sequences from many different fragments.

These technologies were used to sequence the human genome in the Human Genome Project completed in 2003.New high-throughput sequencing technologies are dramatically lowering the cost of DNA sequencing, with many researchers hoping to bring the cost of resequencing a human genome down to a thousand dollars.

Next generation sequencing (or high-throughput sequencing) came about due to the ever-increasing demand for low-cost sequencing. These sequencing technologies allow the production of potentially millions of sequences concurrently. The large amount of sequence data available has created the field of genomics, research that uses computational tools to search for and analyze patterns in the full genomes of organisms. Genomics can also be considered a subfield of bioinformatics, which uses computational approaches to analyze large sets of biological data. A common problem to these fields of research is how to manage and share data that deals with human subject and personal identifiable information.

Mendel's Genetics For thousands of years farmers and herders have been selectively breeding their plants and animals to produce more useful hybrids . It was somewhat of a hit or miss process since the actual mechanisms governing inheritance were unknown.

Knowledge of these genetic mechanisms finally came as a result of careful laboratory breeding experiments carried out Hybridized domesticated horses over the last century and a half.

By the 1890's, the invention of better microscopes allowed biologists to discover the basic facts of cell division and sexual reproduction. The focus of genetics research then shifted to understanding what really happens in the transmission of hereditary traits from parents to children. A number of hypotheses were suggested to explain heredity, but GregorMendel , a little known Central European monk, was the only one who got it more or less right. His ideas had been published in 1866 but largely went unrecognized until 1900, which was long after his death. His early adult life was Gregor Mendel spent in relative obscurity doing basic genetics research and 1822-1884 teaching high school mathematics, physics, and Greek in Brno (now in the Czech Republic). In his later years, he became the abbot of his monastery and put aside his scientific work.

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While Mendel's research was with plants, the basic underlying principles of heredity that he discovered also apply to people and other animals because the mechanisms of heredity are essentially the same for all complex life forms.

Through the selective cross-breeding of common pea Common edible peas plants (Pisumsativum) over many generations, Mendel discovered that certain traits show up in offspring without any blending of parent characteristics. For instance, the pea flowers are either purple or white--intermediate colors do not appear in the offspring of crosspollinated pea plants. Mendel observed seven traits that are easily recognized and apparently only occur in one of two forms: 1. flower color is purple or white 5. seed color is yellow or green 2. flower position is axil or terminal 6. pod shape is inflated or constricted 3. stem length is long or short 7. pod color is yellow or green 4. seed shape is round or wrinkled This observation that these traits do not show up in offspring plants with intermediate forms was critically important because the leading theory in biology at the time was that inherited traits blend from generation to generation. Most of the leading scientists in the 19th century accepted this "blending theory." Charles Darwin proposed another equally wrong theory known as "pangenesis" . This held that hereditary "particles" in our bodies are affected by the things we do during our lifetime. These modified particles were thought to migrate via blood to the reproductive cells and subsequently could be inherited by the next generation. This was essentially a variation of Lamarck's incorrect idea of the "inheritance of acquired characteristics."

Mendel picked common garden pea plants for the focus of his research because they can be grown easily in large numbers and their reproduction can be manipulated. Pea plants have both male and female reproductive organs. As a result, they can either self-pollinate themselves or cross-pollinate with another plant.

In his experiments, Mendel was able to selectively cross-pollinate purebred plants with particular traits and observe the outcome over many generations. This was the basis for his conclusions about the nature of genetic inheritance.

Reproductive structures flowers

of

In cross-pollinating plants that either produce yellow or green pea seeds exclusively, Mendel found that the first offspring generation (f1) always has yellow seeds.

However, the following generation (f2) consistently has a 3:1 ratio of yellow to green.

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This 3:1 ratio occurs in later generations as well.

Mendel realized that this underlying regularity was the key to understanding the basic mechanisms of inheritance.

He came to three important conclusions from these experimental results: 1. that the inheritance of each trait is determined by "units" or "factors" that are passed on to descendents unchanged (these units are now called genes ) 2. that an individual inherits one such unit from each parent for each trait 3. that a trait may not show up in an individual but can still be passed on to the next generation.

It is important to realize that, in this experiment, the starting parent plants were homozygous for pea seed color. That is to say, they each had two identical forms (or alleles) of the gene for this trait--2 yellows or 2 greens. The plants in the f1 generation were all heterozygous. In other words, they each had inherited two different alleles--one from each parent plant. It becomes clearer when we look at the actual genetic makeup, or genotype, of the pea plants instead of only the phenotype, or observable physical characteristics.

Note that each of the f1 generation plants (shown above) inherited a Y allele from one parent and a G allele from the other. When the f1 plants breed, each has an equal chance of passing on either Y or G alleles to each offspring.

With all of the seven pea plant traits that Mendel examined, one form appeared dominant over the other, which is to say it masked the presence of the Young Ji International School / College

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other allele. For example, when the genotype for pea seed color is YG (heterozygous), the phenotype is yellow. However, the dominant yellow allele does not alter the recessive green one in any way. Both alleles can be passed on to the next generation unchanged.

Mendel's observations from these experiments can be summarized in two principles: 1. the principle of segregation 2. the principle of independent assortment According to the principle of segregation, for any particular trait, the pair of alleles of each parent separate and only one allele passes from each parent on to an offspring. Which allele in a parent's pair of alleles is inherited is a matter of chance.

We now know that this segregation of alleles occurs during the process of sex cell formation (i.e., meiosis ).

Segregation of alleles in the production of sex cells According to the principle of independent assortment, different pairs of alleles are passed to offspring independently of each other. The result is that new combinations of genes present in neither parent are possible. For example, a pea plant's inheritance of the ability to produce purple flowers instead of white ones does not make it more likely that it will also inherit the ability to produce yellow pea seeds in contrast to green ones. Likewise, the principle of independent assortment explains why the human inheritance of a particular eye color does not increase or decrease the likelihood of having 6 fingers on each hand. Today, we know this is due to the fact that the genes for independently assorted traits are located on different chromosomes .

These two principles of inheritance, along with the understanding of unit inheritance and dominance, were the beginnings of our modern science of genetics. However, Mendel did not realize that there are exceptions to these rules.

By focusing on Mendel as the father of genetics, modern biology often forgets that his experimental results also disproved Lamarck's theory of the inheritance of acquired characteristics described in the Early Theories of Evolution tutorial. Mendel rarely gets credit for this because his work remained essentially unknown until long after Lamarck's ideas were widely rejected as being improbable.

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GENETICS WORKSHEET Human Inheritance I. OBJECTIVE: To conduct a survey of some Filipino traits and analyze the frequency of the occurrence of these traits.

II. MATERIALS: data sheet III.PROCEDURES: 1. The leader of the group will divide the members into three groups or teams.

Each group will decide which trait to tackle. The number of groups in the class depends on the number of students.

2. Choose 50 students for your sample (i. e. 50 per group) 3. Study your sample and record your findings in the table given in Part IV of this activity.

Listed below are the traits to be studied and their corresponding contrasting characteristics. a. Number of hair…………………….curly or straight b. Characteristics of earlobe…………free or attached c. Ability to curl one’s tongue………..curler and non-curler d. Shape of hairline……………………widow‘s peak or smooth Data Table Table 1: Team Data

Number of Cases (out of 50)

Human Traits

Male

Total

Female

A. Hair 1. Curly 2. Straight B. Earlobe 1. Attached 2. Free C. Tongue 1. Tongue curler 2. Non- curler D. Shape hairline

of

1. Widow's peak 2. Smooth hairline Young Ji International School / College

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Table 2: Class Data

Team

Size of Sample Number of cases exhibiting contrasting traits A 1

1

50

2

50

3

50

4

50

5

50

Total Percentag e

250

B 2

1

C 2

1

D 2

1

2

Legend: A, B, C, D, - represent the different traits 1- Represent the total individuals showing the dominant character 2- Represents the total individuals showing the recessive character

IV. Analysis of Data Collected On the basis of data gathered, determine which of the characteristics you studied is dominant and which is recessive. Write your answers on the blanks below.

A. Hair 1. Trait__________________________________________ 2. Dominant character____________________________________ 3. Recessive character ___________________________ B. Earlobe 1. Trait__________________________________________ 2. Dominant character____________________________________ 3. Recessive character ____________________________ C. Tongue 1. Trait__________________________________________ 2. Dominant character____________________________________ 3. Recessive character ____________________________ Young Ji International School / College

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D. Hairline 1. Trait__________________________________________ 2. Dominant character______________________________ 3. Recessive character _____________________ CONCLUSION:

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