Part I Biology and the Environment Chapter 1. Introduction - Organization of Physical and Biological World Chapter 2. Atoms and Bonds Chapter 3. More About Chemical Bonds Chapter 4. Molecules Past and Present Chapter 5. Water: Oceans, Lakes and Rivers Chapter 6. Water Use Chapter 7. Water Use in Nuclear Power Plants Chapter 8. Conventional Power and Water Use Chapter 9. Water Use and Electrical Power Chapter 10. Radiation Chapter 11. Clean Water Act Chapter 12. Biomes Chapter 13. Carbon, Bio-fuels and Biomes Chapter 14. Energy Flow Chapter 15. Nutrient Cycles Chapter 16. Changing America Landscapes Chapter 17. Succession Chapter 18. Winterkill and Summerkill

Part II Biology, Cells, Cellular Processes, Classic and Molecular Genetics Chapter 20. DNA, Protein and Cells Chapter 21. Photosynthesis - No Sun No Sugar, No Water No Oxygen Chapter 22. Metabolism - putting foodstuffs to work Synthesis: Metabolic Processes Underlying Natural Cycling of Carbon On Earth Chapter 23. Cell Division, Mitosis and Meiosis Chapter 24. Oogenesis Chapter 25. Cell Division Post Fertilization Chapter 26. DNA (deoxyribonucleic acid) Chapter 27. Crossing Over - Recombination Chapter 28. Translocation Down Syndrome Chapter 29. Independent Assortment Chapter 30. DNA Shared With Relatives Chapter 31. DNA Fingerprinting Chapter 32. Punnett Squares - Predicting Inheritance Chapter 33. Fur Coat Color Inheritance in Labrador Retrievers Chapter 34. Genetics of Human Hair Color Chapter 35. Sex-linked Genes Chapter 36. Human Blood Types and Genetics: Co-Dominance Chapter 37. The Rh Factor Chapter 38. Sickle Cell, Hemoglobin Heredity and Co-Dominance

Part III. Evolution of Life on Earth Chapter 40.Introduction to Evolution Chapter 41.Darwin and Evolution Chapter 42. Human Evolution and Evolution of Mammals Chapter 43. Timeline of Major Evolutionary Events On Earth

Laboratory Exercises

Part I Chapter 1 Introduction

Chapter 1 Introduction Water is the theme in BIO 102. It is the primary molecular constituent of cells and thus of multicellular organisms. The oxygen we breathe is produced by photosynthesis which would not take place without water. Our metabolic respiration requires oxygen and produces metabolic water. Water defines where large scale ecosystems develop on the planet. The oceans drive our planet's water cycle and weather patterns. Water is where life evolved on our planet. In short, without water earth would be lifeless.

Levels of Organization The natural world can be divided into the living (biotic) and non-living (abiotic). Atoms are the simplest component of the abiotic world. Atoms bond into molecules. Thousands of molecules would be required to form a sub-cellular biological structure such as an organelle (e.g. Chloroplast). Moving to the next level of complexity would be a cell which is the first "living" level of organization. Some organisms are single celled creatures. Some single celled organisms live as colonies but they still are simple single cell creatures. Multi-cellular organisms are typically composed of groups of specialized cells called tissues. The arteries and veins in a human body are tissues. Tissues such as a blood vessel acquire capabilities beyond simply being an aggregate of cells. In the case of blood vessels it is the ability to transport blood. This is an example of "emergent properties." Emergent properties states that the sum of the whole is greater than the sum of its parts because additional functions develop. Tissues form organs and organs are grouped into "organ systems" (e.g., the digestive system). At the highest level of organization is the "organism" (for multi-cellular organisms). Levels of organization above the level of the individual organism are ecological. Populations are groups of a single species living in a defined geographic area and interbreeding. A community (not labeled in figure) is a collection of different species living in a defined area. An ecosystem is the combination of the community of organisms and the non-living components (rocks, minerals, water,etc). Biomes are large scale ecosystems. The largest ecosystem is the biosphere.

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Part I Chapter 1 Introduction

Figure1.1 – Levels of organization from atom to biosphere.

Characteristics Of Living Things How do we define living? (1) First it must be bounded by a membrane and as a consequence of the membrane's differential permeability is able to maintain an internal environment different than its environment, (2) it must be able to acquire matter or energy and harvest (convert) the matter or energy through metabolic processes, and (3) it must have a genetic system that can coordinate these metabolic activities and can replicate.

Prokaryotic vs. Eukaryotic All living things are either prokaryotic or eukaryotic. Prokaryotic organisms do not have their DNA enclosed in a nucleus and their DNA does not occur as paired chromosomes. Prokaryotic organisms do not have organelles within the confines of their cell. Eukaryotic organisms have nuclei which contain DNA in the form of paired chromosomes. Eukaryotic organisms have membrane bound structures or “organelles” within their cells which perform special functions (e.g., chloroplasts, mitochondria, etc). Prokaryotic organisms are considered more primitive and were the first to appear on planet earth. The term "karyote" has its origin in the Greek word

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Part I Chapter 1 Introduction "karyon" which means nut or kernel and is a reference to a nucleus. “Pro” means before and “eu” means true (eukaryote has a kernel and prokaryote came before eukaryotes).

Themes There are five major themes in biology and the two we will cover in BIO 102 are Energy Flow and Evolution. We will also cover the biological processes that facilitate energy flow and provide the genetic basis of evolution. The other three themes are (Cooperation, Structure & Function and Homeostasis). Science does not have an agenda. Science seeks to explain how the natural world functions. Scientists conduct experiments, collect data, and analyze data. Scientist's experiments are not published until the findings are submitted to peer review. A scientist's findings will not become part of common knowledge unless it passes the scrutiny of peer review. Science experiments can be broadly divided into discovery science and hypothesis-based science. In hypothesis-based science a scientist conceives a hypothesis, tests the hypothesis by conducting well-designed experiments which often include some form of control group. A control group is treated exactly like the experimental group except the variable that is the "treatment so-to-speak." Discovery science is more descriptive. Discovery science employs good scientific methods to describe anything from a list of animals and plants that reside somewhere (e.g., Furman's campus, Smokey Mountain National Park) to the genome of a species.

Hypotheses, Theories and Laws A hypothesis is a statement that can be tested. It is a tentative explanation. One might hypothesize that given a cage with light and dark sides crickets will migrate to the dark side because of their nocturnal nature. A theory is a widely accepted general principle or body of principles that has been developed to explain a wide variety of phenomena. As new knowledge is gained, theories are refined to better explain the data. A law is an undisputed mathematical relationship that is consistently found to be true. For example, one of the most famous laws is the Law of Gravity.

Four major theories comprise the field of biology (1) Cell Theory states that all living things are composed of cells or are single cells and new cells come from pre-existing cells. (2) Genes Theory states that genes are the basis of inheritance and that the codes reside in sequences of four nucleotide bases in DNA (the bases are Adenine, Thymine, Guanine and

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Part I Chapter 1 Introduction Cytosine). (3) The Theory of Heredity states that chromosomes are inherited.

(4) The Theory of Evolution states that all living things are descendents of a common organism that existed billions of years ago.

Figure 1.2 – The Three Domains of Life

Domains, Kingdoms... The living world is divided into three domains: the Bacteria, Archea (sometimes referred to as the extremeophylls) and Eukarya. The Domain Eukarya consists of four Kingdoms: Protists which are single celled or colonial and the Kingdoms Fungi, Plants and Animalia. From most inclusive to most specific humans are classified as follows: Domain-Eukarya Kingdom-Animalia Phylum-Chordata (subphylum Vertebrata) Class – Mammalia Order – Primates (all the monkeys and apes) Family – Hominidae (the Great Apes) Genus – Homo Species- sapiens

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Part I Chapter 1 Introduction

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Part I Chapter 2 Atoms and Bonds

Chapter 2 Atoms and Bonds Atoms of elements are the simplest units of organization in the natural world. Atoms consist of protons (positive charge), neutrons (neutral charge) and electrons (negative charge). The simplest element is hydrogen which consists only of a proton and an electron. Protons and neutrons have mass and exist in the nucleus of an atom. Electrons have no mass and orbit the nucleus in defined orbits (valence shells). An element’s atomic number is the number of protons it has. The number of electrons will equal the number of protons. An element’s atomic weight is the sum of the number of protons and neutrons. Carbon has an atomic number of N equal to 6 so it has six protons, six neutrons and six electrons in its most common version. Other “versions” of an element are termed “isotopes.” Isotopes differ in the number of neutrons and thus different isotopes have different weights. At the time the earth was formed from a molten mass elements like uranium were formed in the “starting” ratio of their different isotopes. Isotopes degrade into other forms at predictable rates so the ratios of the different isotopes of an element in a sample can be used to determine the age of the sample. The “half-life” of an isotope is the time that is required for half of an isotope to degrade into the degradation form. Carbon occurs as the common C12 but also as an isotope called C14. C14 differs from say U238 in that it is rejuvenated in the atmosphere. When plants die they stop acquiring C14 so dead plant materials and artifacts derived from plant materials can be dated by examining the ratio of C14 to C12. The isotope C14 has 6 protons but 8 neutrons (6+8=14). It degrades into N14 or Nitrogen which has 7 protons and 7 neutrons. In the process of degrading C14 converts one neutron to a proton and releases some energy. The half life of C14 is about 6000 years so the utility of using C14:C12 ratios in a sample in order to age the sample is useful for relatively modern artifacts (e.g., 10,000 year old pottery, etc). For samples which might be millions of years old isotopes with really long half-lives are used (e.g., U238, 4.5 billion years).

Radioactive isotopes have many uses in the bio-medical fields. Different isotopes of any element behave chemically identically so they can be used as “tracers” to study the fate of chemicals. Isotopes can be used diagnostically to identify tumors. Radioactive isotopes can also be used to treat tumors. Isotopes of uranium and plutonium are used in the nuclear power industry.

Living things are composed of about 25 elements out of 92 naturally occurring elements. Four of these (C,H, O, N) make up 96% of the human body and are called the “major” elements. Minor elements comprise 0.1 to about 1% of the human body and include Calcium, Phosphorus, 6

Part I Chapter 2 Atoms and Bonds Potassium, Sulphur, Sodium, Chloride and Magnesium. Trace elements are present in even smaller percentages but that does not mean they are less important. Many trace elements serve as cofactors in vital chemical reactions.

Bonds Molecules form when two or more atoms bond by sharing or borrowing electrons. Electrons are the basis of chemical bonds between atoms. An “ionic bond” involves the donation of one or more electrons from one atom to another. The space between an atom’s nucleus and its electrons is so large relative to a nucleus’s size that if you could compress or minimize this space the entire human race could fit in a sugar cube (about 1 cm3). Covalent bonds involve sharing of electrons. Electrons orbit the nucleus of an atom in valence or energy shells. Shared electrons spend time orbiting two different atom’s nucleus. The first or inner most shell can only hold two electrons. The second shell can hold eight electrons and the third can hold eighteen. Bonds form because physical laws drive atoms to fill these valence shells by means of donation or sharing of electrons.

Ionic Bonding Sodium has an atomic number of 11 so its electrons are arranged 2, 8 and the 11th or just one electron is in the outer shell. Chlorine has an atomic number of 17 so its electrons are arranged 2, 8 and 7 in the third shell. The third shell does have a capacity for 18 electrons but since the third shell has “sub-shells” of 2, 6 and 10, chlorine’s 7 outer electrons are just 1 electron shy of filling the first two sub-shells (2 and 6). Thus the addition of just one electron would fill the inner two sub-shells of chlorine’s 3rd shell (Fig. 2.1). Sodium “donates” its 11th electron to chlorine. Sodium becomes +1 and chlorine becomes -1 and an “ionic bond” is formed. The product is NaCl or common salt. Sodium is a highly reactive metal and chlorine is a very toxic liquid and gas. But bonded as the crystal we know as salt they are quite harmless. This is an example of emergent properties.

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Part I Chapter 2 Atoms and Bonds Sodium (Na)

Chlorine (Cl)

11th e-

7 electrons arranged 2/2, 5/6 and 0/10 (after bond will be 2/2, 6/6 and 0/10)

Figure 2.1 – An Ionic bond between sodium which gives up an electron and Chorine which accepts it..

Covalent Bonding - Non-polar Covalent Bonding

Covalent bonds involve atoms sharing electrons. Shared electrons orbit both atom's nuclei. Some elements exert greater pull on the electrons so their orbits are not shared equally. This is termed a polar covalent bond and the polar molecule has positive and negative poles. Molecules where the atoms share the electrons equally are non-polar covalent bonds. Methane is a good example of a simple molecule with four non-polar covalent bonds (Fig. 2.2). Carbon has an atomic number of six so two electrons are in the inner orbit (valence shell) and four electrons are in the next shell (which has capacity for eight electrons and thus needs four electrons to fill the shell). Hydrogen has a single electron which of course resides in the first shell leaving space for one additional electron. When four hydrogens bond to a single carbon sharing of electrons results in all four hydrogen's first electron shell filled and carbon's second shell filled. The electrons are shared equally so it is a non-polar bonding.

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Part I Chapter 2 Atoms and Bonds Hydrogen N=1

Carbon N=6 Hydrogen N=1

Hydrogen N=1

Hydrogen N=1

Figure 2.2. Non-polar covalent bonds where carbon shares electrons with four hydrogens.

Covalent Bonding - Polar Covalent Bonds Our watery world begins with the polar covalent bonds that exist between oxygen and hydrogens in the water molecule. All the properties of water that exist are the result of the fact that two hydrogen atoms are polar-covalently bonded to a single oxygen atom. Oxygen has an atomic number of 8. Two electrons orbit in the inner valence shell leaving 6 to orbit in the second shell which always has a capacity of 8. So oxygen needs 2 electrons to fill the outer-most shell. Each hydrogen atom has only a single electron and of course it orbits in the inner-most shell which has a capacity of 2. Hydrogen would like to add a single electron. By bonding and sharing electrons both oxygen and each of two hydrogen atoms fill their outer-most valence shells. But oxygen is very strong electro-negatively speaking. It does not share the electrons equally, but it does share. The unequal sharing results in the water molecule being polar (Fig. 2.3). Since oxygen is not letting the negatively charged electrons find their way to hydrogen as much as orbiting oxygen the oxygen side of the molecule becomes negative and the two sides of molecule with hydrogen atoms become positive. These three poles are responsible for all the properties of water which will be covered.

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Part I Chapter 2 Atoms and Bonds

Oxygen N=8 Hydrogen N=1

+ Hydrogen N=1

+ Figure 2.3. Polar covalent bonds where Oxygen shares electros unequally with two hydrogens

Hydrogen bonds Hydrogen bonds are weak very temporary bonds between adjacent polar covalent molecules (Fig. 2.4). Water is a good example. Electrons are briefly shared between adjacent molecules. This brief sharing occurs between positive side of one molecule and the negative side of the other. This sharing creates partial bonding or cohesion so to speak. It’s what holds the adjacent molecules together. If water were not a polar covalently bonded molecule the hydrogen bonds would never occur. Kinetic energy or heat greatly influences these hydrogen bonds. Coldness results in the hydrogen bonds being a little less temporary or more permanent. In contrast, heat makes the hydrogen bonds more fleeting or more temporary. Heating water to 100 C weakens the bonds greatly and water molecules separate and vaporize into a gas (boils). Cool water to 0 C and the bonds will become permanent and water will solidify into ice. As a solid or ice, the structure is very organized with relatively large spaces between molecules making ice less dense (weight per unit volume) than water. The hydrogen bonds which result because of water's inherent polar covalent bonds are responsible for all of water's unique properties. Hydrogen bonds give water its cohesion properties where water molecules want to stick together. This is what creates the so-called surface tension. Surface tension is why a drop of water on a table top does not just spread out until it is a thin film of water rather than the beaded drop you see. Water adheres to other structures (adhesion) and as it does it will pull other water molecules with it by means of cohesion. Without adhesion and cohesion water could not climb the vascular tissues of trees.

Water has a high specific heat meaning it can absorb a lot of heat or kinetic energy and not change its temperature that much. Water has a high heat of vaporization. When it does change to a gas it takes a lot of heat with it. 10

Part I Chapter 2 Atoms and Bonds

+

+

-

Water is considered the universal solvent because it dissolves more substances than any other liquid. The proportion of free hydrogen ions in a solution of water is termed pH. Since pH is calculated as log10 of the hydrogen ion concentration each change of a single pH unit is a 10 fold change. If pH changes by 2 units a 100 fold change occurs. Most animals maintain internal pH in a narrow range (6.8-7.2) so a change of pH from 7 to say 6 or 8 is a huge change which probably cannot be tolerated.

hydrogen bond

hydrogen bond

+

+

hydrogen bond

-

+

+

+

+

Figure 2.4. Hydrogens bonds are weak, temporary bonds between adjacent water molecules.

CHONPS The elements carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur are very important in the living world. We will touch on the details of their importance later. Hydrogen and oxygen being constituents of water have already demonstrated their importance but much is to follow. Carbon is the earth's fuel for the living world. The fuel is stored in C-H bonds in bio-molecules. Ancient bio-molecules became hydrocarbons or "fossil fuels" over millions or even billions of years. Nitrogen is the element of information. Nitrogen is part of nucleic acids (DNA and RNA) and amino acids which are the building blocks of proteins. Thousands of proteins serve as enzymes or catalysts for thousands of chemical reactions for virtually every biological process needed for life. Proteins are also important structural molecules in cells. All proteins are the result of a sequence of nucleotide bases (adenine, thymine, guanine and cytosine). By the way, the two strands of DNA’s double helix are held together by millions of hydrogen bonds.

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Part I Chapter 2 Atoms and Bonds

Figure 2.5. Weak hydrogen bonds hold the two strands of DNA’s double helix together.

One possible explanation why nitrogenous compounds are so prevalent in the biological world is the versatile bonding ability of nitrogen. Its atomic number is 7 so it has 7 electrons. Two of these are in the inner shell and 5 are in the outer shell. This means it needs three electrons in order to fill the outer shell to that shell’s capacity of 8. It can form three single bonds, a double bond and a single bond or a triple bond.

Figure 2.6. The nitrogen atoms is a versatile bonders because of its valence shells.

Phosphorus is stored energy waiting to be put to work. Stored energy in the form of ATP is the universal energy currency of life. Notice how even ATP contains nitrogen. The energy stored in ATP (adenosine tri-phosphate) lies in the bonding of the third Phosphorus group (left side of diagram below).

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Part I Chapter 2 Atoms and Bonds

Figure 2.6. Adenosine Tri-Phosphate, the Universal Energy Currency.

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Part I Chapter 2 Atoms and Bonds

The Periodic Chart of The Elements

Figure 2.7. The periodic chart of the elements. Columns share common valence characteristics.

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Part I Chapter 3 More About Chemical Bonds

Chapter 3 More About Chemical Bonds Atoms bond with other atoms to form compounds. They do so by exchanging or sharing electrons. The resulting forces from the exchange or sharing of electrons is what holds the atoms together in a bond. Electrons occur in predictable orbits about an atom’s nucleus. The number of electrons orbiting an atom’s nucleus will equal the atom’s number of protons (its atomic number). The “predictable” electron orbits are called valence shells. Think of these orbits or shells as roadways with defined capacities. The first shell only has capacity for just two electrons while the second and third shells have capacities of 8, 18 respectively. Furthermore, the second shell has sub-shells of 2 and 6 (2 electrons in 3 sub-sub-orbits). The third shell has sub-shells of 2, 6 (2 electrons in 3 sub-sub-orbits) and 10 (2 electrons in 5 sub-sub-orbits).

Figure 3.1. The first and second valence shells.

The forces behind the physical laws of chemical bonds is that atoms strive to reach the maximum capacity of the first orbital and then the sub-orbitals beginning with the second major orbital’s inner 2s sub-orbital followed by the 2p sub-orbitals and so on working outward. It turns out that the 4th orbital’s first sub-shell (4s) is actually inside (and hence filled before) the 3rd shell’s outer sub-shell which has a capacity of 10 electrons (Figure 2). Atoms can achieve the state of “filled outer sub-shells” by donating (electron reduction), accepting electrons (electron increase) or sharing electrons.

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Part I Chapter 3 More About Chemical Bonds

Figure 3.2. The first, second, third and lowest energy level of 4th shell.

The shapes of the valence shells or electron orbitals and their distance from the atom’s nucleus are depicted in Figure 3. The order that the shells are filled (by exchange or sharing of electrons in bonds) is from bottom to top (which corresponds to inner to outer).

Figure 3.3. Valence shells 1s, 2s, 2p, 3s, 3p, 4s and 3d.

What holds electrons together? If one atom donates one or more electrons to another atom, the atom which accepts the electron becomes more negative while the atom which donated becomes more positive. Magnetic forces between the positive and negative charged atoms hold the two atoms together. This is an Ionic Bond.

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Part I Chapter 3 More About Chemical Bonds If two atoms share electrons in order to achieve “sub-shell filling” the atoms are held together due to the fact that the electrons which are shared are spending time orbiting both atoms. This is a Covalent Bond. If one of the atoms has a stronger pull on the electrons such that the electrons are not shared equally (but still shared) then it is referred to as a “Polar Covalent Bond” and the molecule has negative and positive sides. Water is the best example of a polar covalently bonded molecule. Since the water molecule has positive and negative sides, adjacent water molecules will share electrons too! This sharing between adjacent molecules is very short lived but it is what gives water its cohesive and adhesive properties. These short-lived shared electrons between adjacent molecules are referred to as “hydrogen bonds.” Two Oxygen molecules bond to form O2 (the form heterotrophs use and autotrophs produce). Since they are equally electronegative or exert equal pull on electrons, the shared cloud of O2 might look like lower illustration.

Figure 3.4. Sharing of electons in a probability cloud in a covalent bond.

Inert Elements and Their Electrons Valence Shells He, Ne, Ar, Kr, Xe, Rn; Atomic Numbers of 2,10,18,36,54,86

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Part I Chapter 3 More About Chemical Bonds

Figure 3.5 The filling order of valence shells.

Left to Right the order valence shells are filled. The lower number (e.g. the “18” on 3p618 ) is the cumulative number of electrons beginning with inner-most shell working outward from nucleus. Inert elements have no vacancies in sub-shells.

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Part I Chapter 4 Molecules Past and Present

Chapter 4 Molecules Past and Present Organic Compounds contain Carbon. Life’s molecular diversity is based on carbon. Covalent bonding enables carbon to form complex structures (multiple single bonds, double bonds, ring structures, isomers). Hydrocarbons contain only Hydrogen and Carbon. Hydrocarbons are used as fuels by modern man. Examples are peat, coal, natural gas and the compounds derived from crude oil. Rubber is a polymer of isoprene shown (below left), which ends up a medium length chain of alternating single (C-C) and double-bonded (C=C) carbons (right, below).

Figure 4.1 The building block for natural rubber and its polymer.

Natural rubber comes from tapping rubber trees such as Hevea braziliensis. Methane, Ethane and Propane (shown below) are the three simplest hydrocarbons and differ only in the number of carbon atoms and the associated hydrogen bonded to the carbon.

Figure 4.2. Three simple hydrocarbons which differ by the number of carbons.

Isomers of Butane (C4H10) have the same formula but differ in their shape and properties.

Figure 4.3. Two isomers of butane which differ not by carbons but by arrangement.

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Part I Chapter 4 Molecules Past and Present Some Hydrocarbons form rings (e.g., Benzene, shown below). Naturally occurring ring shaped hydrocarbon molecules include the terpines which give turpentine is characteristics.

Figure 4.4 A ring structure hydrocarbon.

Fossil Fuels Fossil fuels were created from bio-molecules by geological processes. The Carboniferous Period occurred 360-286 (333) million years ago and created “coal forests.” Giant tree ferns and giant horsetails would die, decompose partially, become buried and eventually become peat, lignite and coal. The longer the organic materials are buried and experience heat and pressure the closer to coal they became.

Figure 4.5. Time heat and pressure turn dead materials into coal.

Coal is not a single compound but a mixture of inorganic and organic compounds derived mostly from plant tissues. The combustion of coal for industrial purposes and production of electricity produces a lot of inorganic toxic waste products (ash) which must be disposed of.

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Part I Chapter 4 Molecules Past and Present

Figure 4.6. Coal is a mixture of organic and inorganic materials.

Natural Gas and Crude Oil were created mostly from dead marine algae beginning as long ago as 3.5 billion years. Crude Oil is a Mixture of Hydrocarbons with traces of Nitrogen, Oxygen and Sulfur (1-2%) and Metals (1o C/m) is the metalimnion and the gradient is termed the thermocline. The lower stratum is called the hypolimnion. It is a reservoir of cool water. It can serve as a summer refuge for coldwater (e.g., trouts and salmons) and coolwater fish species (walleye, perch and temperate basses) providing it has a sufficient reserve of dissolved oxygen. Lakes and reservoirs which support both warmwater species (which generally occur in shallow warm water near shore in the summer) and coldwater species (which must retreat to deep cool waters during the summer) are termed two-story fisheries. 39

Part I Chapter 5 Water, Oceans, Lakes and Rivers

Figure 5.13. Temperature stratification in deep southern reservoirs

As fall wears on the air temperature continues to decline, day length decreases and the angle of the sun is less direct. All these factors produce a gradual decrease in the epilimnion's temperature. At some point the density differences between the epilimnion and hypolimnion will be small enough that wind energy will overcome their resistance to mixing. A lake or reservoir is said to be undergoing a turnover when the epilimnion and hypolimnion mix. In the southeast U.S. the overturn is initiated in October, November or December and continues all winter and early spring until the spring/summer onset of summer stratification. Since most lakes and reservoirs in the southeast U.S. demonstrate only one mixing per year they are termed monomictic. More specifically, they are termed warm monomictic because they are stratified in the summer. Lakes in northern Canada and Alaska are typically cold monomictic. The mix only once per year but do so in the summer. These lakes never get warm enough to summer stratify. They do stratify but do so in winter. They show reverse stratification. A snow-covered layer of ice on the surface keeps the water just below the ice at 0 to 1 C. More dense 4 C water occurs deeper, hence a reverse stratification (reverse indicating that water near the surface is slightly colder than deeper water).

In the north-temperature regions of the mid-west, northern U.S. and southern Canada lakes and reservoirs are normally dimictic because they demonstrate two mixings per year. Like a southeastern U.S. reservoir they mix in the autumn following summer stratification. But they often show reverse winter stratification (e.g., 0 at the surface and 4 C deep). Eventually the winter stratification breaks down in the spring and the spring mixing occurs. Spring mixing is followed by a gradual warming and summer stratification. Generally, summer

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Part I Chapter 5 Water, Oceans, Lakes and Rivers

Figure 5.14. Temperature stratification in deep northern lakes and reservoirs.

Hypolimnions of deep lakes are where species which have evolved over millions of years to be adapted to cold water live. It is their refuge, particularly in the summer months. Hypolimnions of culturally eutrophic lakes are impacted by the thriving phytoplankton in the surface waters. The dead phytoplankton sink into the hypolimnion where decomposers such as fungi and bacteria break them down as a food source. And in doing so utilize oxygen in the hypolimnion. Because the hypolimnion does not mix with the epilimnion all summer it has no sources of oxygen. What oxygen is in the hypolimnion must last all summer. If the demand for oxygen by the decaying phytoplankton is great enough dissolved oxygen will drop below the lower tolerable limit for fishes which is in the 3 to 5 ppm (=mg/l) depending upon species.

Reservoirs and Dams Reservoirs look like lakes but they are not actually lakes. The differences are beyond the scope of BIO 102. Reservoirs are damed rivers. Rivers are damed in order to produce hydroelectric energy, provide cooling water for fossil fuel and nuclear fuel electrical stations, water storage for domestic and agricultural purposes and flood control. Recreational use of reservoirs is viewed as a byproduct of the main purpose for them being built. Reservoirs have many negative effects on ecology. Most reservoirs inundate hundreds of thousands of miles of stream habitat. The animals adapted to the stream habitat disappear and are replaced by those species which typify the lower reaches of rivers. The ecology is changed from one where a detritus-based ecology is replaced by a sun-driven ecology. Dams prevent the migration of fish species which demonstrate annual spawing migrations. The natural habitat of their offspring is lost. Even if the species are stocked above the dam their migration downstream is difficult. Migratory fish moving downstream must either pass over the dam or through the turbines where the high gforces result in mortality.

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Part I Chapter 5 Water, Oceans, Lakes and Rivers

Figure 5.15. Longitudinal profile of a deep man-made reservoir.

Understanding Significance of Thermoclines and Hypolimnion Most natural lakes have fish and invertebrate species that only utilize the bottom of lakes or are adapted to cool waters and will not come to the surface or near-shore in summer. They are restricted to the hypolimnion. Such fishes are referred to as coldwater (e.g., trouts, salmons and others) and coolwater species (pikes and perches). Once a lake is “stratified” in late spring or early summer, the hypolimnion will no longer receive any oxygen input. The hypolimnion has a fixed amount of dissolved oxygen until the thermocline breaks down in Fall and lakes mixes again. If community metabolism and decomposition of detritus by bacteria and fungi in hypolimnion lower dissolved oxygen below about 3 ppm (mg/l) fish and other creatures die.

Fig.5.16. The seasonal progression of temperature vs depth curve from left to right (winter to summer) then back right to left (summer to winter). Once ice melts water mix again and slowly warm. As waters warm a gradient develops but a gradient does not signify a thermocline. At some point the density

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Part I Chapter 5 Water, Oceans, Lakes and Rivers differences between the upper waters and the lower waters resists mixing and “stratification” exists (a thermocline where water changes 1 degree Celsius per meter).

Thermoclines In Deep Tropical Lakes and Reservoirs Deep tropical lakes and reservoirs can display multiple thermoclines. Recall from the water density vs temperature curve that as water warms the differences in density become progressively stronger with each degree of warming. The density differences between 35o C and 30 o C water is much greater than 30 o C and 25 o C. As a result temporary thermoclines can develop in the upper waters. The length of time they persist is a function of the density differences and events which have enough energy to disrupt the thermocline. Strong thunderstorms with cool rain and wind are typical events which might disrupt these short-lived thermoclines. A persistent thermocline exists deeper. It persists for longer periods of time because of its depth which results in it being less likely to be disturbed by rain and wind. Lakes in steep-sided volcanic calderas have less exposure to wind and little or no streams feeding the lake. The persistent thermocline in these lakes can last for years perhaps even decades or longer.

Figure 5.17.. Temperature vs depth plot for a deep tropical lake or reservoir.

Lake Nyos in Cameroon, Africa is a steep-sided deep (e.g., 680 feet) lake which occupies a volcanic caldera. On August 12 1986 it overturned releasing a large amount of CO2 resulting in the death of 1700 people. The CO2 had been trapped in the hypolimnion below the persistent thermocline. The origin of the CO2 was seepage into lake from the volcano. Either a landslide or a localized downburst of cool rainwater delivered enough energy to disrupt the thermocline which had persisted for perhaps hundreds of years. Like a shaken can of carbonated beverage 43

Part I Chapter 5 Water, Oceans, Lakes and Rivers the CO2 was released and being heavier than air followed the outlet stream downhill through the villages. A permanent piece of PVC pipe has been installed to vent CO2 continuously from the hypolimnion and hopefully preventing a future accident

. Figure 5.18. Cameroon in tropical Africa.

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Part I Chapter 5 Water, Oceans, Lakes and Rivers

Streams and Rivers Streams and rivers are very different than lakes and reservoirs. The physical charactertistic are different and the biota is different. First, streams and rivers do not stratify vertically. There are no thermoclines, epilimnions etc. Streams and rivers do show “longitudinal” changes from headwaters to the most downstream reaches where they generally empty into a lake or ocean. The longitudinal changes include slight warming downstream, lesser gradient downstream and changes in the food web. So lets start with the food web of a small stream ecosystem. First and foremost is that the vast majority of energy that ends up in the animals at the top of the stream food web is derived from detritus from the surrounding terestrial ecosystem. So streams are referred to as “detritus-based” ecosytems in contrast to lakes and oceans where sunlight drives the energy flow. The detritus enters the stream as organic matter (OM) in one of three forms: Coarse Particles, Fine Particles or Dissolved (CPOM, FPOM and DOM respectively).

CPOM that falls or blows into the stream is quickly colonized by fungi and bacteria which breakdown the dead matter. They coat it making CPOM slippery. In fact the bacterial and fungi tissues are rich in protein and the most important source of dietary nutrients for a feeding category called “shredders.” Shredders are various taxonmic categories of larval and nymph stages of aquatic insects which eat the CPOM but really benefit from the fungi and bacteria. The rain pounding on the surrounding forest canopy, washing across the forest floor and peroclating through shallow soils on its way to the stream bring with it dissolved organic matter (DOM) in the form of amino acids, sugars etc. Microbes in the water can utilize this DOM and some of the DOM physically aggregates or floculates into very small particles of FPOM. Another feeding category of aquatic insects collects theses fine particles of organic matter by making funnelshaped webs and filtering FPOM from the water. These are called “Collectors” and includes such things as mayfly larvae and caddisfly larvae. The arrow from FPOM to Collectors does not reach the Collectors in the illustration below but FPOM is their main foodstuff.

The photosynthetic pathway of primary production accounts for about only 5% of energy flow. Algae and mosses growing on rocks is scraped off by invertebrates such as snails and relatives of shrimp. This feeding group are referred to as “grazers” or “scrapers.” Finally, shredders, collectors and grazers are all preyed upon by predators which include larger predatory aquatic insects but mostly fishes. And of course bigger fish species eat smaller fish species and sometimes birds, mammals and other animals eat the fishes too. The one process that can not be overlooked is that all reaches of a stream or river are exporting lots of FPOM downstream to the next reach, and so on and so on. So the reaches far downstream in rivers become progressively more dependent upon FPOM. The reaches of a river system far downstream get progessively wider permitting photosynthsis because a canopy of trees is no longer shading the river. So primary production and FPOM becomes important sources of energy for the creatures 45

Part I Chapter 5 Water, Oceans, Lakes and Rivers living in the far downstream reaches. Collectors such as mussels and freshwater clams become more common and the fish community more resembles what you would expect in a reservoir or lake.

Figure 5.19. Food web in a small stream ecosystem.

Notes: m = microbes themselves are FPOM; a = single celled algaes are themselves FPOM; f = fecal material produced by small animals is technically FPOM also. Shredders, Collectors and Scrappers are all preyed upon by larger insect predators and fishes and most of the insect predators are preyed upon by fishes.

Longitudinal Changes In Stream Energy Flow River systems exist as thousands of head-water streams which join into fewer numbers of larger streams and then a fewer number of small rivers and finally large rivers which for the most part find their way to the ocean or a large lake system. Headwater streams are almost completely dependent upon detritus in the form of CPOM, DOM and FPOM (defined previously) for energy to drive the ecosystem. Photosynthesis accounts for as little as 5% of the energy flow. Further downstream the canopy no longer shades the flowing water and photosynthesis becomes progressively more important. But the thousands of headwater streams and hundreds of small rivers export huge quantities of FPOM downstream. FPOM becomes a major food source for 46

Part I Chapter 5 Water, Oceans, Lakes and Rivers freshwater invertebrates in the lower reaches of rivers where photosynthesis by phytoplankton also serves as a source of energy for consumers. Headwater streams and rivers are characterized by cold and cool-water fishes which slowly changes to warm-water fishes downstream.

Figure 5.20. Longitudinal changes in energy pathways in a river system.

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Part I Chapter 6 Water Use

Chapter 6 Water Use Water Treatment This short article attempts to describe the typical processes by which we acquire water for our households and dispose of spent water. Public water supplies come from a few common sources indicated by the circled number one in Figure 1. Some cities have highly controlled watersheds with little or no sources of contamination (e.g., Greenville, S.C., Boulder, Colorado). Many cities draw their water intake from lakes and reservoirs that receive considerable public use, rivers, groundwater and even saltwater by means of desalination. The raw intake water is treated with a coagulant to remove organic matter (e.g., algae, detritus and even zooplankton). The coagulant, algae and detritus is called flocculate which settles to the bottom as sludge. The water above the sludge is then filtered through sand filters and possibly even activated carbon in order to further polish it. Typically this polished water has fluorine added and it is then pumped to storage and distribution systems for delivery through a network of pipes to homes and businesses.

Figure 6.1 A typical drinking water treatment plants.

Wastewater - Septic System 48

Part I Chapter 6 Water Use Waste water in our homes and businesses are typically called gray and brown water. Gray water comes from washing machines and sinks, and brown water from toilets. Most homes and business in the U.S. do not separate gray and brown waters. Gray waters are suitable for irrigation. Waste water either exits the home to a septic tank system (Fig. 6.2) or to the domestic waste water collection network of pipes. Septic tanks are normally only used in rural or suburban areas where sufficient land exists to accept the output from the septic system. This is influenced by soils type and slope but it typically has requirements for about a quarter acre of land or more. Bacteria in the septic tank break down sludge (heavy organics) and the effluent or liquid leaving the tank percolates into the soil by means of a gravel leach field. Grasses and trees absorb the nutrients.

Figure 6. 2. Typical septic tank design.

Wastewater - Sewage Systems Urban areas where the density of homes and businesses is high utilize sewage treatment systems (Fig. 6.2). Wastes are collected from 1000's of homes and businesses and pumped to a centralized sewage treatment facility (Fig. 6.3). The incoming sewage is screened and distributed to a series of alternating tanks where sludge which settles in the tanks is removed and separated from the liquid component of the waste sewage. Eventually the sludge is dried and sent to landfills for disposal. The liquid component is trickled over rock beds where algae, bacteria and fungi remove nutrients. It is then treated with chlorine to kill microorganisms which pose a health hazard to the public. The effluent is then discharged into a stream, river, lake or ocean. The effluent must meet federal EPA guidelines for solids, nutrients, microorganisms and more. Every sewage plant is has a permit which allows so many thousands 49

Part I Chapter 6 Water Use of gallons per day of effluent meeting a certain criteria to be discharged. Larger sewage plants require larger rivers to accept their waste. More often than not, another municipality downstream will utilize the same river for drinking water described above. As the stream or river moves downstream it acquires tributary streams which further dilute the sewage effluent.

Figure. 6.3. Typical sewage treatment plant design.

Storm Water Storm water is the rain water that flows across impervious surfaces such as roofs, parking lots and roads and into storm drains. Sometimes during exceptionally heavy rains where the soil is already saturated rainwater may flow across grassy and wooded landscapes and into storm water drains. Storm water drains normally collect and distribute water back to a creek, river, lake or bay. Rain which falls on impervious surfaces runs off much faster than rain which falls onto forested landscapes. Rain which fall onto soils can penetrate the soil and be taken up by plants or penetrate deeper into soils eventually recharging the aquifers. Rain which runs off impervious surfaces and saturated soils causes unnatural spates or high flows in creeks and rivers. The spates increase erosion of stream banks and reduces the quality of aquatic habitat. Runoff from impervious surfaces carries with it many unnatural pollutants from parking lots and roads. Runoff from urban and suburban areas also carries with it microbes in the waste materials produced by dogs, cats and livestock. Older urban areas constructed their buried utilities such that storm water and waste water often lie side-by-side under city streets (Fig. 6.4 lower). Major rain events overwhelm the capacity of the two side by side systems and waster water will mix with storm water. The result 50

Part I Chapter 6 Water Use is that untreated sewage will make its way into public waters and sewage wastes which are diluted with storm water will be directed to the sewage plants. Untreated sewage which enters public waters represents a health threat.

Figure 6.4. Upper illustrates modern system of buried utilities where storm water is kept separate from waste water. Lower illustrates common buried utilities where storm water and sewage can overflow and mix.

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Part I Chapter 7. Water Use At Nuclear Power Plants

Chapter 7 Water Use In Nuclear Power Plants Uranium U235 is enriched to about 5% which is far less than the 99% enrichment in weaponized uranium. U235 emits neutrons which strike other U235 atoms which continues the controlled chain reaction. In the process a great deal of heat is released. The rate of the controlled chain reaction is regulated by a inserting neutron absorbing materials between the U235 rods. These are the control rods. They contain pellets of neutron absorbing materials like cadmium. Furthermore, water which is used to absorb the heat from the reaction acts likes a moderator preventing neutrons from traveling too fast and failing to continue the chain reaction. These processes take place in a reactor vessel made of stainless steel or other exceptional metals.

Figure 7.1 A typical design of a nuclear power plant.

The heated reactor water is also pressurized so temperatures higher than 100 C can be achieved. This water is circulated through a heat exchanger and transferred to another water system used to generate steam. The water circulating over the rods is confined to the plumbing of the reactor vessel and the heat exchanger because it is radioactive. All the processes described so far take place in a containment building designed to contain and radiation or radioactive gases that might escape the reactor vessel and the associated plumbing. The water in the steam generator is also in a closed loop separate from the environment. The steam produced turns a turbine which in turn spins a generator and electricity is supplied to the "grid." In order to reuse this water and prevent it from escaping to the environment a third source of water is used to cool the steam, produced liquid condensate so it can be converted to steam over and over. Water is withdrawn from a river or lake and passed over the condenser's 52

Part I Chapter 7. Water Use At Nuclear Power Plants heat exchanger. This water carries waste heat and is either returned to the natural water body or sent to a large evaporative cooling tower where it trickles over surfaces cooled by air before return to a river, lake, reservoir or ocean.

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Part I Chapter 8 Water and Coal Power Production

Chapter 8 Conventional Power and Water Use Steam has been used to power paddle boats, steam ships, steam locomotives and even cars. The principle behind steam engines is that some source of fossil fuel is combusted and used to heat water. The boiled water produces steam which is directed through a turbine which is propelled by the movement of the steam (hot gases). Gears are driven from the turbine resulting in paddles, propellers or wheels turning. These examples used water once and were required to refill their water. The same principle is used in electric power generation using fossil fuels. Fossil fuels such as coal, gas or oil are combusted and steam is generated from a closed water loop. Huge amounts of coal are pulverized at coal-fired power plants. It is combusted in what might be described as an inferno and the hot gases of combustion boil water into vapor. The hot water vapors turn turbines which in turn rotate electric coils and generate electricity. The hot vapors are condensed with cooling water and reused. The cooling water typically is withdrawn from a river or lake and returned to the body of water a little bit warmer. Sometimes the cooling water is trickled down giant cooling towers where clouds of steam are produced. Clouds of steam of course are different than the smoke resulting from combustion of fossil fuel. The later can contain acid forming compounds if the exhaust is not "scrubbed" of acidic compounds. The mineral ash left over after combustion of coal is highly toxic because of the heavy metals. Most ash is simply stored on-site.

Fig. 8.1. Simplified design for a coal-fired power plant.

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Part I Chapter 8 Water and Coal Power Production

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Part I Chapter9 Water and Power Production

Chapter 9 Water Use and Electrical Power Almost all electrical power generated in the United States requires water in order to produce power. The average household in the U.S. uses 11.2 Megawatt hours (MWh)1 annually. Sources of electric power produced by utilities include 1) coal-fired plants, 2) natural-gas-fired plants, 3) nuclear-powered plants and 4) hydroelectric (dams). Together these four constitute 93 percent. Minor sources include solar and wind power. The one thing fossil fuels, nuclear and hydropower have in common is that they require large volumes of water (measured in units of volume per unit time) in order to provide power.

Hydropower The largest requirement (net loss) per MWh of electricity produced is for electricity produced using hydropower. Hydropower averages 4500 gallons per MWh. The need for water per unit time is obvious when you consider that water must move downhill and pass through a generator in order to produce electricity. Evaporation off the surface of the reservoir of water is the major source of "net loss" water consumption. Since most reservoirs are constructed in-line within a river, water is going to pass downstream regardless of the dam. Evaporation off a reservoir is orders of magnitude greater than off a river system. Hydropower has virtually no footprint in terms of carbon dioxide emissions and thus does not contribute to climate change.

Negative impacts of dams Dams change the entire ecology of the damned watershed. Hundreds or thousands of miles of creeks, streams and rivers are changed from a flowing ecosystem dominated by biota derived from CPOM and FPOM (Chapter 5) to a standing water ecosystem where autotrophic photosynthesis is the basis of the food web. Species which require fast flowing water are replaced by species which prefer standing warmer waters. Dams prevent migration of fish, discharge cold oxygen-poor waters (see Hypolimnion in Fig. 9.2) downriver below the dam and fragment populations of animals genetically. Depending upon the slope of flooded terrain and the height of a dam, hundreds or thousands of mile of mainstem river and tributaries will be covered by deep water and no longer be flowing stream habitat (Fig. 9.1).

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Figure 9.1. Demonstrates the loss of river and stream with the construction of a medium-sized dam.

Pumped Storage and Peak Needs Energy demand is not uniform over a 24-hour period. There are peak demand times in the early morning and early evening. Energy needed for these peak demand periods can be met using "Pumped-Storage." Water is pumped to an uphill reservoir during low-demand periods when there is unused excess capacity in the electric grid (e.g., while you sleep). Water can be quickly released to flow back downhill through the generators for virtually instant electricity during peak periods. How it Works: Water for Power Plant Cooling

Figure 9.2. Pumped storage generally requires two reservoirs. The lower dam has a conventional oneway generator.

In the United States, 90 percent of electricity comes from thermoelectric power plants—coal, nuclear, natural gas, and oil—that require cooling water. The remaining ten percent is produced 57

Part I Chapter9 Water and Power Production by hydroelectric and other renewable energy facilities. Some renewable energy technologies are thermoelectric as well, including certain types of concentrating solar, geothermal, and biomass power plants. Why is Cooling Necessary? Thermoelectric power plants boil water to create steam, which then spins turbines to generate electricity. The heat used to boil water can come from burning of a fossil fuel such as coal or natural gas, from nuclear reactions, or directly from the sun or geothermal heat sources underground. Boiled water produces steam. Once the steam has passed through a turbine, it must be cooled back into water before it can be reused to produce more electricity. Also, because of inefficiencies much heat is not converted to turbine movement and must be dissapated. Colder water cools the steam more effectively and allows more efficient electricity generation2. It is fairly obvious that burning of coal or natural gas produces heat. Nuclear reactors produce incredible heat when an isotope of Uranium such as U235 is struck by a neutron (from another nearby U235) and releases three neutrons initiating a chain reaction. When U235 is hit by a neutron it splits into two lesser mass atoms, releases about three neutrons (which can strike other U235 atoms) and releases heat (which converts liquid water to steam) and radiation in the form of gamma rays (high energy photons or "wave"). The resulting two smaller atoms also release gamma radiation, in addition to beta particle radiation (very fast electrons). Of course both gamma rays and beta particles are dangerous to biological tissues.

Types of Cooling Even though all thermoelectric plants use water to generate steam for electricity generation, not all plant cooling systems use water (see dry cooling, Table 1). There are three main methods of cooling: Once-through systems take water from nearby sources (e.g., rivers, lakes, aquifers, or the ocean), circulate it through pipes to absorb heat from the steam in systems called condensers, and discharge the now warmer water to the local source. Once-through systems were initially the most popular because of their simplicity, low cost, and the possibility of siting power plants in places with abundant supplies of cooling water. This type of system is currently widespread in the eastern U.S. Very few new power plants use once-through cooling, however, because of the disruptions such systems cause to local ecosystems from the significant water withdrawals involved and because of the increased difficulty in siting power plants near available water sources. Once through cooling systems require large volumes of water per unit time but nearly all of it is returned to the source of water (albiet measurably warmer). Coal and nuclear power plants might pass 25,000 gallons per MWh but "net loss" comsumption is about 300 gallons per MWh (Table 1). Wet-recirculating or closed-loop systems reuse cooling water in a second cycle rather than immediately discharging it back to the original water source. Most commonly, wet-recirculating systems use cooling towers to expose water to ambient air. Some of the water evaporates; the 58

Part I Chapter9 Water and Power Production rest is then sent back to the condenser in the power plant. Because wet-recirculating systems only withdraw water to replace any water that is lost through evaporation in the cooling tower, these systems have much lower water withdrawals than once-through systems, but tend to have appreciably higher net water consumption. In the western U.S., wet-recirculating systems are predominant. Recirculating systems withdraw about 1000 gallons per MWh and net loss is about the same (1000 gallons per MWh) amount since cooling is achieved by means of evaporative cooling (Table 1).

Figure 9.3. The diagram above show how both "Once-through" and Wet-recirculating cooling systems work (the difference is at the asterisk *)

Dry-cooling systems use air instead of water to cool the steam exiting a turbine. Dry-cooled systems use no water and can decrease total power plant water consumption by more than 90 percent3. The tradeoffs to these water savings are higher costs and lower efficiencies. In power plants, lower efficiencies mean more fuel is needed per unit of electricity, which can in turn lead to higher air pollution and environmental impacts from mining, processing, and transporting the fuel. In 2000, most U.S. dry-cooling installations were in smaller power plants, most commonly in natural gas combined-cycle power plants4. About 43 percent of thermoelectric generators in the United States use once-through cooling, 56 percent recirculating, and 1 percent dry-cooling (2008 data). In 2008, some 30 percent of electricity generation involved once-through cooling, 45 percent recirculating cooling, and 2 percent dry-cooling. (In some cases, those same power plants also produced electricity using non-steam systems, such as combustion turbines.)5

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Part I Chapter9 Water and Power Production Other Key Issues The geographic location of power plants has a huge impact on cooling technology options, water availability, type of water used for cooling, and environmental impacts. Solar and geothermal power plants, for example, must be located in areas with high solar radiation and geothermal energy, respectively—locations that may be arid and far from conventional water resources. In these situations, dry cooling may be an option, or alternative water sources may be available, but such choices can affect power plant performance and local environments. Although many power plants use freshwater for cooling, waste water and salt water are other possibilities with advantages and disadvantages. Salt water is an obvious and abundant option for coastal power plants, for example, but such plants face similar challenges as inland plants with regard to damaging the local aquatic ecosystems through excessive withdrawals or thermal pollution (from discharges of hot cooling water. Table 1: Water withdrawn and consumed for power plant cooling, in gallons of water required per megawatt-hour of electricity produced 6.

1

A 1000 watt appliance run for 1 hour uses 1 kilowatt hour which is 1/1000 of a MWh

2

U.S. Department of Energy (DOE), 2008. Estimating Freshwater Needs to Meet Future Thermoelectric Generation Requirements. Washington, DC. 3

Though no water is required for dry-cooling systems, power plants using dry-cooling systems also require water for system maintenance and cleaning. 4

Small power plants are defined as having an electric generating capacity less than 300 MW. Dougherty, B., Page, T., & Bernow, S. 2000. Comments on the EPA’s Proposed Regulations on Cooling Water Intake Structures for New Facilities. Boston, MA: Tellus Institute. 5

Union of Concerned Scientists. 2012. UCS EW3 Energy-Water Database V.1.3. www.ucsusa.org/ew3database.

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J. Macknick, R. Newmark, G. Heath, and K.C. Hallet. 2012. Operational water consumption and withdrawal factors for electricity generating technologies: a review of existing literature. Environmental Research Letters. 7 doi:10.1088/1748-9326/7/4/045802. http://www.ucsusa.org/clean_energy/our-energy-choices/energy-and-water-use/water-energyelectricity-cooling-power-plant.html

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Part I Chapter 10 Radiation

Chapter 10 Radiation Higher frequency radiation has enough energy to break chemical bonds. This is why it is dangerous to biological tissues. It can disrupt physiological processes causing sickness or death and cause genetic damage. Ultraviolet radiation is the form most persons will encounter due to sun exposure. Radiation associated with nuclear energy production includes neutrons and ionizing radiation (alpha particles, beta particles and gamma rays).

Ionizing Radiation is so named because it can cause atoms and molecules to become ions or electrically-charged molecules. Ionizing radiation causes tissues to produce free radicals (molecule with unpaired valence electron) and oxidants (electron thief) that damage or break DNA leading to cell death or mutation. 1) Alpha Particles - In general, alpha particles have a very limited ability to penetrate other materials. In other words, these particles of ionizing radiation can be blocked by a sheet of paper, skin, or even a few inches of air. Nonetheless, materials that emit alpha particles are potentially dangerous if they are inhaled or swallowed, but external exposure generally does not pose a danger. It is believed that Russian dissident Alexander Litvinenko was killed by being poisoned with Polonium-210 (strong alpha emitter) in 2006. A lethal dose is about 50 nanograms (nanogram =10-9 grams). 2) Beta particles, which are similar to electrons, are emitted from naturally occurring materials (such as strontium-90). Such beta emitters are used in medical applications. In general, beta particles are lighter than alpha particles, and they generally have a greater ability to penetrate other materials. As a result, these particles can travel a few feet in the air, and can penetrate skin. Nonetheless, a thin sheet of metal or plastic or a block of wood can stop beta particles. 3) Gamma radiation is very deeply penetrating and is ionizing. The result of this is that it breaks apart many different kinds of molecules. If it breaks DNA molecules, for example, this can cause problems. When this happens, cells try to repair themselves. If this fails, they often die, but sometimes they replicate themselves with bad genetic code, and this can cause tumors or cancer. Exposure to intense gamma radiation can cause death in hours, days, weeks or months depending upon dose. Gamma radiation has highest penetration power (Fig. 10.1). Several feet of concrete are required for protection.

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Figure 10.1. Relative penetrating power of alpha, beta and gamma radiation.

4) Neutrons are given off by unstable isotopes of naturally occurring elements. The half-life of an isotope is the time required for an isotope to decay one half of its neutrons. Here are some half life values. U-238, 4.5 billion years U-235, 704 million years P-239, 24,000 years Strontium-90, 29 years Cesium-137, 30 years Polonium-210, 138 days (only emits hard to detect alpha particles) Isotopes with short half lifes emit more neutrons per unit time and are thus more dangerous. Uranium 235 which is fissile material for atomic power plants and bombs has a relatively long half life and small pieces can be handled with gloves. If a mass of U235 approached critical mass a chain reaction can emit large amounts of heat and radiation. Louis Slotin and another researcher died from exposure to radiation in 1946 at Los Alamos, NM (Manhattan Project) when a screwdriver he was using to keep two masses of U235 apart slipped and the two pieces started to go critical and released a burst of gamma rays. Neutrons are high-speed nuclear particles that have an exceptional ability to penetrate other materials. Neutrons are the only one that can make objects radioactive. This process is called neutron activation. Because of their exceptional ability to penetrate other materials, neutrons can travel great distances in air and require very thick hydrogen-containing materials (such as concrete or water) to block them. Fortunately, however, neutron radiation primarily occurs inside a nuclear reactor, where many feet of water and concrete containment buildings provide effective shielding. Controlled chain reactions of U235 in nuclear reactors gives off many more neutrons per unit time than sub-critical masses. The resulting lesser weight atoms produced by splitting or fission of U235 are also unstable. These products resulting from the splitting of U235 also release ionizing radiation. Spent fuel rods are those rods where sufficient U235 splitting has rendered them inefficient as a nuclear fuel. They still have U235 and also the resultant unstable elements 63

Part I Chapter 10 Radiation which fall into two atomic mass ranges: 80-110 (includes Strontium) and 130-150 (includes Cesium). The remaining Uranium and fission products give off a, b and gamma radiation.

U235 and nuclear power. The nuclear power industry requires U235 enriched to about 5%. By comparison, weapons grade U235 is 90% pure. The remaining uranium in the power plant fuel is U238. In nature uranium occurs as 99.3% U238 and 0.7% U235. Industry grade Uranium cannot become super-critical (explode in nuclear blast). Industry grade Uranium 235 can support a chain reaction that can produce enormous amounts of heat. The heat is removed and put to work for steam generation and electrical power production. If the heat is not removed the nuclear fuel will melt the reactor core's structure vaporizing metal and concrete resulting in a disaster such as Chernobyl in Ukraine or Fukushima in Japan. When U235 is struck by a neutron it splits (fission) into two lesser weight atoms, releases heat, releases gamma radiation and three neutrons. If the U235 is of sufficient mass and density the three neutrons will strike three more Uranium 235 atoms (Fig. 10.2), which in turn will release three neutrons, heat and gamma radiation. Thus a chain reaction is initiated.

Figure 10.2. A U235 struck by a neutron releases three neutrons. Heat and gamma radiation are produced.

A controlled chain reaction must sustain the chain reaction, capture and remove heat and shield the environment from gamma radiation. Long rods of U235 pellets are positioned close to one another in order to facilitate neutrons striking other U235 atoms. Water passing over the Uranium fuel not only transfers heat to the steam generators but also serves to facilitate or "moderate" the chain reaction. Control rods made with a good neutron absorber such as Cadmium act as a set of brakes to slow the chain reaction (by preventing some of the neutrons from striking Uranium). The control rods are slid in between the uranium fuel rods. Eventually the rods containing the U235 pellets become depleted of sufficient U235 that they are no longer efficient enough for suitable heat output. They are said to be "spent" fuel rods. The spent rods still have U235 but they also have highly radioactive by products from the splitting of U235 into lesser weight atoms. Spent fuel rods are dangerous and must be cooled for 10-20 years before 64

Part I Chapter 10 Radiation dry storage. Even in dry storage they will be radioactive for 250,000 to 1,000,000 years. Presently all spent fuel rods are stored at power production sites. There is no national storage facility for spent fuel rods.

Figure 10.3. Nuclear reactor vessel.

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Part I Chapter 11 – The Clean Water Act

Chapter 11 Clean Water Act 1972 America's waters were in a steady state of "water quality" decline prior to the 1970's because of unabated pollution. The same industrial power that won WWII and that made the U.S. a Cold War industrial powerhouse was polluting our streams, rivers, lakes, estuaries and oceans. Fish kills were common in the Great Lakes and many beaches were unsafe to swim in because of sewage contamination. The post WWII population explosion was straining our natural resources. In 1971 David Zwick, a third year law student working for Ralph Nader published "Water Wasteland." Zwick was part of Nader's Raiders. "Water Wasteland" was a series of case histories of polluted rivers and lakes. For example, the story on the Mahoning River describes water in Youngstown Ohio as being 140 degrees F in the 1950's and 100 F in the 1960's. The River was lifeless and still 90 F when it reached the OH-PA border. "Water Wasteland" was more-or-less the basis for the Clean Water Act. Congress only had to rewrite it into statute form. Grass roots support from Mayors of major cities was also key to passage of the CWA. Mayors like Carl Stokes of Cleveland linked environmental decline to urban decline which provided more impetus for passage of pollution legislation. The Clean Water Act was passed in 1972 was amended in 1977. The Federal Water Pollution Control Act's (commonly referred to as the Clean Water Act) purpose was "to restore and maintain the chemical, physical, and biological integrity of the nation's waters." The 1972 statute frequently uses the term "navigable waters," but also defines the term as "waters of the United States, including the territorial seas. Today, navigable waters is interpreted as any body of water ever used in commerce and any lesser stream tributary to a navigable body of water. A historical record of timber (logging) being floated down a stream would constitute "navigable." Point sources of pollution have discrete identifiable points of entry into waters (Fig. 11.1). The 1972 CWA introduced the National Pollutant Discharge Elimination System (NPDES), which is a permit system for regulating point sources of pollution. The CWA also has provisions to regulate dredging, filling in of wetlands and damning flowing water. Point sources include industrial facilities, sewage treatment facilities operated by municipal governments, other government facilities (such as military bases) and private developments.

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Figure 11.1. Point and non-point sources of pollution.

A new federal agency was born, the Environmental Protection Agency (EPA). The EPA sets standards for pollutants. States can issue more strict standards and are responsible for enforcing standards. All states have agencies such as Ohio EPA, SC DHEC, GA EPD, NC DENR, and TN DEC.

Non-point sources are the sum total of countless sources of pollutants that enter our creeks, streams and rivers from millions of sources including roofs, yards, parking lots and paved surfaces and agricultural fields. Non-point sources have been poorly addressed. Recent changes require new developments to capture and hold the fast runoff from impervious surfaces. The runoff is diverted to small retention ponds (Fig. 11.2) where it slowly percolates into ground water rather than rushing to a stream where it scours and erodes the stream as it carries nonpoint pollutants into the stream. These runoff or holding ponds develop flora similar to natural wetlands and act to remove pollutants as the the water percolates into the pond's soils. The non-point pollutants would include animal feces from pets and small farms, fertilizers (Nitrogen and Phosphorus) from yards and commercial landscaping, wastes from leaking septic fields and the drippings from automobiles parked on blacktop and concrete. Runoff from agricultural fields is virtually unregulated.

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Figure 11.2. Cross-section of a retention pond.

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Part I Chapter 12 - Biomes

Chapter 12 Biomes Biomes are large scale terrestrial ecosystems. They are often described by their principal vegetation but of course the entire plant and animal community is influenced by the principal vegetation. Precipitation and temperature are the two major environmental factors which influence biome development. Latitude and altitude in turn affect precipitation and temperature. Increasing altitude can mimic latitudinal changes.

Figure 12.1 Distribution of biomes of the world.

Deserts are defined by their dryness. The benchmark is when annual rain is less than 30 cm. North America has four deserts. The Great Basin and Mohave are considered cool deserts. The Sonoran and Chihuahuan deserts are considered warm deserts. The Great Basin is that vast portion of western U.S. that has no outflow of water. Rivers drain into it but not out to ocean. Even within the Great Basin there are sub-basins (endorheic) with no outflow to the Great Basin.

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Figure 12.2 The four deserts o the United States.

The Great Basin has many salty lakes and ancient mineral-laden dry lake beds. Salinity builds up because the rivers bring in minerals including salt and then evaporation drives off the water leaving minerals behind. Over thousands of years the minerals become more concentrated. Some of these former saline lakes have completely dried (salt flats).

Grasslands

receive sufficient rain to support vast expanses of grasses. Creek and river

riparian edges running through grasslands will support trees. In the United States we called these grasslands the American Prairie. They were once populated by great herds of buffalo but we converted grasslands to America's agricultural bread basket. The grassland's soils are very rich in nutrients. North America and north Central Asia support large grasslands.

Savanna is the biome described as grasslands with scattered trees. South central Africa and southern Brazil have vast Savanna Biomes.

Chaparral

is the “Mediterranean” biome that develops in close proximity to expansive

stretches of cool ocean waters. Southern California, Spain and the south of France have chaparrals. It is characterized by shrubby vegetations many of which are adapted such that their seeds germinate following low-heat fires. Suppression of fires and accumulation of dry fuel (dead plants) contributes to devastating destructive wild fires.

Tropical Forest biomes develop close to the equators. Some are drier than others so they range from tropical forests to lush tropical rain forests where annual rainfall can exceed several hundred inches. Soils in tropical forests are poor in nutrients because the nutrients are quickly released from decaying matter (detritus) and are quickly taken up by forest trees and 70

Part I Chapter 12 - Biomes understory. Tropical forests cleared for agriculture have limited potential due to nutrient-poor soils. The lush forests also support many arboreal species of plants and animals. Tropical forests typically contain more species of trees in a few acres than an entire forest in the US.

Temperate Forests North of the tropics the forests transition into subtropical then the Temperate Forest Biome. Most of the eastern US is within the Temperate Forest Biome. Oak, Hickory and many deciduous hardwoods characterize this biome. This biome is cold in the winter and warm in the summer, but it is moderate or temperate compared to more southerly and more northerly biomes. This biome receives moderate amounts of rainfall in order to support the forests. Their soils are nutrient rich.

Boreal Forests North of the Temperate Forests in the northern hemisphere deciduous forests give way to expansive coniferous forests of spruce, fir and hemlock trees. This is the Boreal or Coniferous Biome (sometimes called Taiga) or the great north woods. Northern Maine and Canada contain the bulk of Boreal Forest in the Western Hemisphere. Elevations between about 7000 and 10,000 feet in the Rocky Mountains are mostly Boreal forest. Some of the mountain tops in the southern Appalachian Mountains have fragmented "islands” of boreal forest which are relicts from the last ice age. Temperate Rain Forests such as the Pacific Northwest's Olympic peninsula are a wetter variant of the Conifer or Boreal Forest Biome. Tundra North of the Boreal Forests and also at elevations in excess of 10,000 feet the conifer forest transition into the Tundra. The tundra has permanently frozen soils (frozen soil water) a foot or so below the surface. This permanently frozen soil is termed "permafrost." Permafrost prevents large trees from taking root so the biome is characterized by dwarf willow trees, grasses and annual flowers. These plants are adapted to life in shallow spongy soil and must complete their annual cycle in about 8 weeks (the short arctic summer) In summary, water is probably the single most important environmental factor which influences the distribution of biomes. Latitude and altitude are also important. Extreme latitudes and altitudes result in frozen water in soil so it is frozen water that causes permafrost in the tundra. Tropical forests range from medium dry to extremely wet (rain forest). Deserts are defined by their dryness (annual rain less than 30 cm). Chaparral biomes develop in close proximity to large cool oceans. A plot of mean annual temperature vs mean annual precipitation (Fig. 12.3) can be used to illustrate the combinations of temperature and precipitation that the biomes occur at.

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Figure 12.3 How water and temperature influence the distribution of biomes.

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Part I Chapter 13 – Carbon, Bio-fuels and Biomes

Chapter 13 Carbon, Bio-fuels and Biomes Worldwide 21 billion metric tons of CO2 are released into atmosphere each year from all sources. Natural processes can process about 11 billion metric tons of CO2 leaving an excess of 10 billion metric tons annually. Photosynthesis by aquatic and terrestrial plants is the principal means of CO2 reduction. CO2 from transportation is a major contributor to global CO2. Combustion of two octane (gasoline, C8H18) molecules produces 16 CO2 molecules . What if all the CO2 released for transportation came from ethanol derived from carbohydrates produced by plants? Plants build their carbohydrates by removing CO2 from the atmosphere. The metric tons of CO2 released while driving would be removed by plants as they sequestered CO2 to make their structural carbohydrates. The plant’s carbohydrates have to be fermented to ethanol which introduces some inefficiency (i.e., energy costs) but nothing like the impact of combusting fossil fuels which were sequestered billions of years ago CO2 and the Greenhouse Effect – CO2 is called a “greenhouse gas” because its presence in the atmosphere causes radiant heat to be reflected back to earth, warming the planet akin to being in a greenhouse (Fig. 13.1).

Figure 13.1. CO2 and methane are “greenhouse gases” which trap heat.

The Keeling Curve (research began under the supervision of Charles David Keeling) Fifty years of CO2 measurements high atop Mauna Kea on the Big Island of Hawaii (the most remote island chain on the planet) clearly shows that CO2 levels have increased steadily since 1960. Research on ice cores at the South Pole has shown the planet has demonstrated a cyclic

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Part I Chapter 13 – Carbon, Bio-fuels and Biomes pattern of highs and lows in CO2 concentrations with a periodicity of about 100-150 thousand years, but the high levels were always around 300 units of CO2.

Figure 13.2 The Keeling Curve (left) and cycles of CO2 measured at the South Pole.

Can alternative energy sources meet the world's 2030 energy needs? Perhaps as many as 6x 106 sq km of wind farms (100,000 of typical current farm) would be needed. Solar energy farms the size of Spain (0.5 106 sq km) would be required. Current dams provide 4% of 2030's estimated energy needs but are environmentally damaging.

BIO-FUELS

are derived from renewable plant products. Ethanol is a bio-fuel with much

potential. Corn can yield about 333 gallons of ethanol per acre. Sugar cane yields about twice as much but requires sub-tropical or tropical temperatures. Sugar beets yield just a bit more per acre than sugar cane. Switchgrass yields about 1200 gallons ethanol per acre per year and grows just about anywhere in the U.S. Fast growing soft wood trees such as poplar can yield 2000 gallons of ethanol per acre per year U.S. Gasoline Use - The U.S. uses about 133 billion gallons of gasoline per year. This translates to about 200 billion gallons of ethanol per year because ethanol has a lower energy density per unit volume. Using corn would probably require 600,000,000 acres of corn production which probably exceeds the arable acres in U.S. (The arable acres in US might be as low as 460,000,000 acres of total 920,000,000 acres in production). Switchgrass would require only 153,000,000 acres and poplar trees only 100,000,000 acres. Both of the latter two use less fertilizer than corn and would leave plenty of arable acres for food production.

BIOMES and CO2 removal

- The rate of CO2 removal by a biome is directly related to a

2

biome's productivity (kcal/m /year). Thus, the most productive biomes would sequester the most CO2 per unit area.

CO2 removal per unit area - Biomes that are very productive only make substantial reduction in 74

Part I Chapter 13 – Carbon, Bio-fuels and Biomes global CO2 if their aggregate total area is substantial. Estuaries, swamps and marshes are very productive per unit area, but their total area on earth is just too small to substantially lower globa CO2.

Figure 13.3. Comparison of ecosystems and their capacity to sequester CO2 per unit area.

Total CO2 removal by biome - The Open Oceans are a major source of CO2 reduction due to the ocean’s total size. Tropical rain forests and temperate forests finish the top three biomes in terms of capacity to sequester CO2.

Figure 13.4. Comparison of ecosystems and their total capacity to sequester CO2

Remember that oxygen production by plants is directly related to CO2 removal. Fifty percent of the ocean oxygen is produced by a blue-green prokaryotic algae (Cyanophyta) in the genus Prochlorococcus which is a prokaryotic single called organism with only 2000 genes. Prochlorococcus has probably been on earth since the dawn of life on earth. It probably produces 20% of the earth's oxygen and conversely removes 20% of the CO2 on our planet.

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Part I Chapter 14 – Energy Flow

Chapter 14 Energy Flow Energy flows and nutrients (re) cycle. A trophic level is a set of species occupying one level of the ecological food chain. The lowest trophic level is that set of organisms that can manufacture their energy and biomass using only sunlight and drawing inorganic nutrients from the soil or water. There are rare food webs where chemosynthetic bacteria derive their energy from inorganic compounds rather than light (as done by cyanobacteria, algae and plants) and serve as the base of the food web. Feeding upon this lowest tier of organisms are animals classified as herbivores. The concept of a food web was clearly articulated as early as 1880, but it was not until 1942 that Lindeman introduced the term "trophic level" to describe the ecological hierarchy of consumption. Higher levels are predatory species, eating animals one level below them.

Primary producers - The lowest trophic level is typically populated by primary producers, those organisms which can synthesize the entirety of their biomass solely from primary energy (such as sunlight) and primary nutrients extracted from the environment (e.g. nitrate, phosphate). Primary producers are typically plants and algae. They are also often termed autotrophs. Primary producers may be either terrestrial or aquatic. Common aquatic species include microscopic phytoplankton and diatoms, and much larger species such as kelp. Terrestrial species include the whole gamut of trees, shrubs, flowers and grasses as well as ferns, mosses, lichens and other non-vascular plants.

Herbivores or First Order Consumers - The second level of the trophic chain consists of organisms that consume primary producers. Such species are often termed herbivores. Herbivores may be very small organisms such as zooplankton that graze on microscopic plants such as phytoplankton; however, herbivores also include many enormous mammals such as rhinoceros and elephants.

If a significant percentage of the herbivore trophic level is removed, plant growth may go unchecked. For example the removal of herbaceous fishes by overfishing has caused an increase in the standing crop of algae on many coral reefs in the Caribbean Sea. Conversely, a sudden and large increase in the population size of herbivores, often caused by an decrease in the population of their predators, can greatly reduce the standing biomass of plants (wolves and elks, will be discussed later). The invasion of introduced (non-native) herbivores can produce adverse effects on the native plant community. 76

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Figure . 14.1. A marine trophic pyramid. All five trophic levels contribute to the pool of detritus (arrows 1-5). Decomposers return nutrients to the primary producers

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Carnivores (second, third and fourth order consumers)

- The third and higher

levels of the trophic chain consist of carnivores, animals that feed on other animals. Carnivores may vary greatly in size and feeding strategy, ranging from large and fierce animals such lions and sharks to small internal parasites. Carnivores may play important roles in the ecosystem by controlling the population sizes of herbivores that ultimately influence the biomass of plants in an ecosystem. For example, the loss of wolves in Yellowstone National Park in the United States allowed the elk population to increase so much that they greatly affected the growth of willows.

Decomposers - Every trophic level produces dead matter that is utilized as a foodstuff by decomposers. Decomposers, also known as detritivores, are a special group of organisms that are capable of breaking down dead or dying tissue of other species. Unlike scavengers, who ingest dead biomass for internal digestion, the decomposers are capable of breaking down cells of other organisms using biochemical reactions that convert the prey tissue into metabolically useful chemical products, without need for internal digestion. The most common decomposers are fungi, bacteria and archaea, the latter two being micro-organisms. The decomposers return nutrients to the soils and water making nutrients available to primary producers.

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Food Webs

- Sometimes the term food web is used rather than food pyramid. The reason is

that in reality the passage of energy from one trophic level to another can take many pathways in resulting in complex “spider-web-like” diagrams.

Figure 14..2. Simplified diagram of a food web. Actual food webs are more complex.

Energy considerations - Ecologists often evaluate the energy flow among various trophic levels, particularly with respect to efficiency of energy conversion from one production or consumption level to the next. Typically there is a substantial loss of energy and biomass as one views successively higher trophic levels. This observation can be best understood by noting all the processes of energy transfer among each connection in the trophic chain (or food chain). For example, the lowest level of primary producers is rather efficient at combining sunlight with carbon dioxide and nutrients to produce plant or algal biomass; a variant of this process, also rather efficient is for some deep sea extremophiles (known as chemolithotrophs), who obtain energy by the chemical oxidation of inorganic compounds and can grow in the absence of light. H.T. Odum spent years making meticulous measurements in a spring system in Florida. He found an average transfer of 13% from one trophic level to the next (Fig. 14.3). So we will use 10% as an approximation of energy transfer. The Laws of Thermodynamics are responsible for the losses of energy with transfer from one trophic level to the next. “Energy is neither created or destroyed but it can change forms” and “whenever energy changes forms some is lost as entropy (heat).”

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Figure 14.3. H.T. Odums study in Silver Springs, Florida.

Much of the plant biomass is wasted, in the sense that it is not consumed by herbivores; instead, considerable portions die and decay, feeding the decomposers. Thus, only a fraction of the biomass store of primary producers ends up being consumed by the next higher trophic level. In the case of herbivores, again much of the built up herbivore population dies and decays without feeding a higher trophic level; however, additional losses of energy are sustained at the herbivore level through (a) Respiration loss (an intrinsic ongoing energy cost of survival for all herbivores; (b) Expended locomotion energy loss (again a major expenditure for all but the most sedentary of aquatic creatures); (c) Non-assimilation losses (e.g. urine, feces, bleeding, sloughing of skin and hair, saliva loss).

The ratio of net energy (or biomass) production at one level to net production at the next higher level is called the conversion efficiency. As a result of all these cumulative losses, the energy conveyed from the herbivore trophic level to the carnivore level is greatly reduced. It is typical for an order of magnitude less energy (or biomass) to result in each successively higher trophic level. The most efficient trophic energy transfer is probably consumption of phytoplankton by zooplankton, which process can be approximately forty percent energy efficient. At the opposite end of the efficiency scale is consumption of plants by herbivores, which have large quantities of indigestible biomass; in such cases up to two orders of magnitude of energy loss may be sustained in such a trophic cascade. In most terrestrial ecosystems the maximum number of trophic levels is four or five; however, there are many aquatic systems which manifest many more trophic levels due to the presence of successive levels of carnivory with a great variety of faunal sizes. 79

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Ecological pyramid

- An ecological pyramid is an idealized construct to illustrate how

energy, biomass, and population size, vary between trophic levels in an ecosystem. Conventionally, this concept is illustrated by placing primary producers at the bottom of a diagram and the highest trophic levels at the top of the diagram. The size of the portion of the diagram associated with each trophic level is intended to depict the amount of energy, biomass, or number of individuals found in each trophic level.

Energy flows through the food web beginning at the base of such a hypothetical pyramid, by photosynthesis, and then moving up to higher trophic levels. The concept of an ecological pyramid can often be useful in visualizing a trophic chain; however, caution must be used, lest oversimplification may presume that all trophic chains have more member species at lower levels. Such a conventional notion is often, but not always, true. So what does all this science me to you? See “Biomagnification.”

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Biomagnification Terrestrial plants and aquatic plants including algae (phytoplankton) convert sunlight into plant biomass. They are producers in terms of ecological roles. Animals that consume plants are primary (herbivores) consumers. In oceans and lakes primary consumers are very small shrimplike invertebrate animals (crustaceans) called zooplankton. Zooplankton consume phytoplankton (algae). Next, secondary consumers consume the zooplankton. Secondary consumers are mostly small non-game fishes such as sardines, anchovies and small herrings. Tertiary consumers (e.g., larger predatory fish which eat smaller minnow-sized forage fish) consume the secondary consumers. Fourth level consumers eat the tertiary consumers. In the oceans this would include really large long-lived fish like swordfish, larger sharks, tuna and marine mammals such as orcas and sea lions. Producers, consumers, secondary consumers, tertiary consumers and fourth level consumers are "trophic levels" in nature's food pyramid. A fundamental principle which has its roots in the laws of physics is that each trophic level is only about 10% of the lower level on which it feeds (energy can neither be created or destroyed but can change forms; whenever energy changes forms some is lost as entropy, heat). The cost of living results in 90% of the energy consumed being spent for the purposes of living and lost as entropy and only 10% retained as biomass. Thus we construct trophic pyramids which depict the flow of energy and declining biomass at higher trophic levels.

Figure 14.4. A trophic pyramid demonstrating bio-magnification. The dots could represent the passage and concentrating of a persistant element or compound.

There are a number of chemicals which while present at low concentrations in the water become "bio-magnified" with each increasing level in a trophic food pyramid. This is because they are consumed, absorbed into the consumer's blood but the consumer has no means to eliminate the toxin. The consumers can not break it down metabolically and can not excrete it. 81

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These toxins present at low levels in the water are absorbed into and adsorbed onto algae. Primary consumers eat the algae, digest the algae and toxin, absorb digested algae and toxins into their bloodstream. The foodstuffs derived from the algae are metabolized but the toxins persist. The toxins pretty much stay for the life of the consumers. The result is that the consumers have a much higher concentration of the toxins in their tissues than the algae did. The toxins have become "bio-magnified."

This process of "bio-magnification" is repeated with each tropic level. At the top of the food or trophic pyramid the concentration of toxins is 1,000's or millions of time more concentrated than in the water or phytoplankton.

These toxins which can be bio-magnified include DDT (an insecticide widely used until the 1970's in U.S. but still used in third world countries), other chlorinated pesticides, PCBs (poly chlorinated biphenyls, a by-product in manufacturing of certain lubricants), and heavy metals like Mercury (Hg), Cadmium (Cd) and others (e.g., copper, chromium, lead, nickel and zinc). DDT was responsible for drastic decline in Eagles, Osprey, Pelican and other waterfowl. It was manifested as eggs without shells which results in no reproduction. In a 1967 study in Long Island Sound biomagnification of DDT was:

water to zooplankton (by means of phytoplankton) -800x, zooplankton to small fish #1 -31x small fish #1 to larger fish #2 - 1.7x Larger fish #2 to gull - 4.8. Overall biomagnifcation was in excess of 200,000 magnification. While DDT is no longer applied in the US it is used in third world countries. A modern case study in Lake Kariba, Zimbabwe (Africa) showed that DDT bioconcentrated from 0.002 ppb (parts per billion) in the water to 2.5 ppm (parts per million) in algae, 5-10 ppm in large fish and 34 ppm in crocodiles. PCBs are carcinogens. PCB mixtures were produced from approximately 1930 to 1979 under more than 100 trade names. Many subtle variants of PCBs have been manufactured. Their toxicity and persistence in environment varies. Some variants have half lives of 40 years meaning that in 40 years half of the toxic material is still present, in 80 years 25% is still present 82

Part I Chapter 14 – Energy Flow and in 120 years 12.5% is still present. There are sites of contamination where contamination was so high that environmentally safe levels of the PCBs will not occur for several hundred years. PCBs also have toxic non-carcinogenic effects in animals including humans (immune system, the reproductive system, the nervous system and the endocrine system). Heavy metals are dangerous on many levels including birth defects. Fish species which are at the top of the aquatic food pyramid are more likely to have elevated levels of these toxins. The FDA has issued an advisory for young women not to consume certain species of fishes (e.g., swordfish and other large predatory fishes). Bio-magnification results in low levels of certain elements or compounds in water becoming highly concentrated in animals at the pinnacle of the trophic food pyramid. The elements or compounds are characterized as being digested and absorbed but incapable of being broken down and eliminated by metabolic pathways in animals.

One of the most unusual forms of bio-accumulation is Ciguatera poisoning. Ciguatera is a foodborne illness caused by eating certain reef fish whose flesh is contaminated with toxins originally produced by dinoflagellates which adhere to coral, algae and seaweed. Herbivorous fishes eat the corals etc and pass the toxin to the next trophic level and so on. It becomes bioconcentrated in large predatory fish and can result in severe illness if these fish are eaten by humans. Ciguatera toxin is extremely stable, unaffected by cooking.

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Part I Chapter 15 – Nutrient Cycles

Chapter 15 Nutrient Cycles Nutrients cycle from inorganic forms (e.g., CO2, NO3) to organic forms (e.g., carbohydrates, proteins) by means of biological processes. Carbon, nitrogen, phosphorus and sulfur will be covered because of their importance to biological molecules and the environment. Often the productivity of primary producers is limited by availability of Nitrogen and/or Phosphorus. If one or more of these nutrients is limiting it is referred to as a "limiting factor."

Carbon - Carbon cycles largely in the buildup and breakdown of organic molecules (Fig. 15.1). The primary producers remove CO2 for the air and water and build bio-molecules. These biomolecules are passed up the food chain and are re-assimilated into the biomass of the higher trophic levels. The majority of the carbon is released as CO2 during the respiratory processes of the consumers (recall that only about 10%) of a trophic level is retained by the next level). CO2 can also be deposited as carbonates (e.g., CaCO3, limestone) in ocean processes and added to sedimentary rocks. The specifics of CO2 removal in photosynthesis and release during respiration will be covered later.

Figure 15.1. Carbon cycling

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Nitrogen - Nitrogen occurs in biological forms as amino acids, nucleic acids and ATP. Every single insect and crustacean on the planet has an exoskeleton made of chitin. Chitin is a cellulose-like polymer but each building block (monomer) has nitrogen in it. Nitrogen occurs in inorganic forms as N2, NH3, NO2 and NO3 in the environment. The Nitrogen Cycle (Fig.15.2) depicts the movement of nitrogen between these forms in both terrestrial and aquatic ecosystems. Equivalent processes occur in both ecosystems. Nitrogen comprises 78% of the air and air dissolved in waters in the form of N2. Nitrogen fixation is the term used to describe the biological conversion of N2 to NH3 (same as NH4OH) by certain varieties of soil and water bacteria and by blue-green algae (Cyanophyta, a prokaryote). These organisms are called "nitrogen fixers" and they are the entry point for N2 into biological forms. Some higher plants have developed symbiotic relationships with nitrogen fixers which live in nodules in the plant’s roots. The Legumes (peas and beans) and alder trees have these symbionts which provide the plant's roots with readily available NH3. Most primary producers do not have the symbionts so they must absorb NH3 and NO3 from the wet soil or water. Decomposers such as fungi and bacteria that utilize dead matter or detritus release NH3 to the soil and water. All the consumers also produce nitrogenous wastes mostly as ammonia and urea. The second step in nitrogen conversion in soils and waters is nitrification. Bacteria in the soil and water convert ammonia (NH3 or NH4OH) to NO2 then NO3. These two steps represent "nitrification." NO3 can be absorbed by the roots of terrestrial and aquatic plants and by algae. When plants absorb NO3 they must reduce it to NH3 before incorporating it into bio-molecules. NO3 is in fact the primary form of nitrogen applied to agricultural crops. It is also implicated as a source of cultural eutrophication (more about it latter). NO3 can be converted back to free gaseous N2 in soil and water by denitrifying bacteria. This completes the cycling of nitrogen from a gas form to living organisms and back.

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Figure 15.2. The Nitrogen Cycle

Phosphorus - ATP is the universal energy currency.

The energy stored in the

bond of the third PO4 group on adenosine tri-phosphate (ATP) (Fig. 15.3) is the energy which drives most biological reactions (muscle contractions, nerve firings). Without ATP life would come to an abrupt halt. Only about 50 g of ATP is in human body and is used over and over. In fact daily turnover of ATP is about 100 kg/day (2000X).

Figure 15.3. ATP/ADP molecules

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Phosphorus is released to the soil or water as H2PO4 (the primary inorganic form of P) (Fig. 15.4) when decomposers breakdown detritus from dead primary producers and dead consumers. It will be absorbed by the roots of plants or taken in by algae and then passed up the food chain. Over geological time periods inorganic phosphorus will be deposited in sedimentary rocks. Slow erosional processes from wind and water will slowly return some of this deposited phosphorus to the water and soil as H2PO4. NASA has demonstrated that a substantial amount of phosphorus deposited in the Amazon originates from dust from the Sahara of North Africa. Before modern industrial man cycling of phosphorus was more-or-less in harmony with depositional and erosional processes in equilibrium. Excessive amounts of phosphorus entering streams, rivers and then lakes and oceans causes eutrophication (succession lecture).

Figure 15..4. Erosional processes and the phosphorus cycle

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Sulphur - Proteins are composed of amino acids, and two essential amino acids contain sulfur: methionine and cysteine. Every protein made starts with the amino acid methionine. Sometimes it is cleaved off before the final protein is completed but it is the initial amino acid in every polypeptide in living organisms. Cysteine is very common in proteins too.

Figure 15.5. Sulfur Cycle

The decomposers release SO4 from detritus into the soil and water (Fig.15.5). Primary producers absorb SO4 and incorporate it into plant proteins. These proteins are then passed up the food chain. There are bacteria in the soil and water which can reduce SO4 to H2S and even elemental sulfur. Other bacteria can do the reverse. Elemental sulfur can become incorporated into coal and sedimentary rocks over long geological time periods. Volcanos and deep sea vents can release this sulfur. Today these natural releases of sulfur are small and localized. In contrast, combustion of coals which are rich in sulfur is adding significant amounts of SO4 to the atmosphere. It forms sulfuric acid with atmospheric water and falls as "acid precipitation." Acid rain and snow does serious damage to forests and streams depending upon where it falls, the amount of SO4 and the capacity of the soil or water to buffer against pH change. Soils and streams poor in limestone and more granitic have little capacity to resist pH change from acid precipitation. (See Coal Use Trends and the Clean Air Act). 88

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Part I Chapter 16 – Changing Landscapes

Chapter 16 Changing American Landscapes - http://harvardforest.fas.harvard.edu/dioramas European settlers to eastern North America found primeval forests largely untouched by man as they moved inland from the coastal settlements.

Figure 16.1. Primeval forests circa 1700

European settlement occurred largely during the 18th century in most of the Eastern U.S.. Through forest clearing, hunting, and trapping, the abundance of many species changed rapidly and the wilderness was gradually transformed into a domesticated rural landscape.

Figure 16.2. Small patches of forest were cleared for farming during mid-1700’s.

The peak of deforestation and agricultural activity occurred from 1830 to 1880. Across much of eastern U.S., 60 to 80 percent of the land was cleared for pasture, tillage, orchards and buildings. In the south the crops were rice, cotton and tobacco. Small remaining areas of woodland were subjected to frequent cuttings. Tracts of land that were cleared for timber were not replanted as they are today and relied on “natural succession” for reforestation.

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Figure 16.3. Mid-1800’s saw deforestation reach it peak in the Eastern U.S.

Beginning in the mid-1800s and continuing for more than a century, farming declined on a broad scale across. Abandoned pastures and fields rapidly developed into forests. These forests were dominated by pines. It was the beginning of the Industrial Period and people returned to cities. Old Field Succession started.

Figure 16.4. The mid to late 1800’s saw the start of farm abandonment. In the south the effects of the civil war on agriculture also results in land use changes.

Figure 16.5. Old field succession resulted in mature stands of pines as succession proceeded.

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Part I Chapter 16 – Changing Landscapes As the "old-field" stands of pines reached middle age in the early 1900’s, it became evident that they contained a valuable and rapidly growing crop of second-growth timber. As pines became marketable portable sawmills appeared across the eastern U.S.

Figure 16.6. Harvest of second growth timber during early 1900’s.

Clear-cutting of the "old-field" pines in the early 1900’s led to the succession of mixed hardwoods across much of the landscape. The inability of pines to sprout after being cut, in contrast to the prolific sprouting of our hardwood species, facilitated this succession.

Figure 16.7. Secondary forests ,early to mid 1900’s.

1930 - One of the characteristic features of the hardwood forest that developed after the clearcutting of the "old-field" pines is the predominance of multi-stemmed sprout clumps. Fastgrowing species that sprout prolifically -- red oak, red maple, white ash, birches.

Key Dates Summary Pre-colonization to 1700 - Settlers begin to colonize old growth primeval forests 92

Part I Chapter 16 – Changing Landscapes . 1750 - Forests transformed into a patchwork of farms

1850 - Forest mostly gone and remaining forests regularly cut, agricultural lands maximized

1900 - Abandoned farms undergoing succession (old fields to pine)

1930 to present - Secondary forests are different than their primeval forests because of regular timber harvests.

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Part I Chapter 17 – Succession

Chapter 17 Succession Succession is the change in the biota over time on a parcel of land large or small. Succession is typically described by the changes in the plant communities that occur but changes in animal communities also take place.

Terrestrial Succession Primary succession is the changes in biota over time that occur on barren land with little or no soil. The time scale for succession is about 300 years or longer on hard surfaces like volcanic rock. The speed with which succession takes place is dependent upon latitude and altitude among other things as these influence growing season length. Pioneer species which are typically annual plants first colonize the ground and the process of soil development begins. Later, more grasses, perennial plants and shrubs take root so-to-speak. Eventually pines and other soft wood trees become established and mature. Hardwood trees eventually replace many of the pines in temperate forest biomes. This is the climax community. The climax community is of course dependent upon which biome the succession takes place in. Laval flows generally present an opportunity to study primary succession. Kilauea Volcano on the Island of Hawaii (the Big Island) has produced massive lava flows in the last 50 years. Pioneer plants manage to take root in crevices where water collects. Eventually soil will develop and more pioneer plants will colonize the lava fields. The island of Maui, Hawaii has not seen massive flows for thousands of years and has many well established plant communities on what was once dark volcanic rock. Secondary succession takes place after an event which disrupts a community. Secondary succession can take 100-300 years. Clearcutting and devastating hot crown forest fires are the most common spark for secondary succession. Clearcutting is the forestry practice of removing all the trees from a tract of land. Extreme forest fires burn all or most the trees. Note that “controlled burns” is the practice of buring understory and dry detritus to prevent to much fuel from collecting on the forest floor. Hurricanes, paths of tornados and even land slides can lead to succession. The largest event in the U.S. was the 1988 forest fires in Yellowstone National Park. Many studies have documented the recovery (succession) that has taken place since that year's fire.

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Figure 17.1. Secondary succession of plant communities after a fire takes 100-200 years depending upon extent of the burn and the climate and biome..

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Eutrophication and Cultural Eutrophication (Aquatic Succession) Eutrophication is a process. It is a natural process that takes place over 1,000's of years. Some scientists believe that a steady state equilibrium might be achieved at some point along the oligotrophic-mesotrophic-eutrophic gradient (Fig. 17.2). If this were true a lake might remain mesotrophic. Oligotrophic means "few foods" while eutrophic means "many foods." These are references to the availability of nutrients and primary productivity of the food web. Lake Superior in the North American Great Lakes and Lake Tahoe are good examples of oligotrophic lakes. They are deep, clear and cold. Winter concentrations of nitrogen and phosphorous are relatively low. Their fish communities are dominated at the top of the fish food pyramid by coldwater fishes in the salmonid family (trouts). Lake Erie in the North American Great Lakes is a eutrophic lake. So are most reservoirs in the Southeast U.S. They are warmer, pea-soup green in color. Winter concentrations of nitrogen and phosphorous are relatively high. The fish community is a warmwater fish fauna dominated by sunfishes, basses and catfishes. Cultural eutrophication is a process resulting from human disturbance of aquatic lake ecosystems. It has profound impacts on the fish communities. Culturally eutrophic lakes become so from excessive nitrogen and phosphorous inputs. These inputs are generally from domestic sewage effluents and agricultural runoff. A culturally eutrophic lake (Fig. 17.3) becomes very productive but is generally still quite deep (which means that the hypolimnion does not mix with surface waters in the summer). The constant rain of detritus (dead organic matter mostly from algal production) from the surface waters to the deeper waters add organic materials to the deep waters. These organic materials are decomposed by fungi and bacteria with a consequent reduction in the concentration of dissolved oxygen. Throughout the summer the deep water receives no additional oxygen inputs because it is isolated from the surface waters. As a result, the deep waters can become devoid of oxygen These deep cool waters are normally refuge for fishes that prefer cool and cold water. Cultural eutrophication normally renders the deep sections of a lake as unsuitable fish habit with a resulting change in the fish fauna of a lake. Cultural eutrophication can be reversed and corrected. Restoring fish communities is another matter. In the lower Great Lakes of the U.S. and Canada coldwater fishes which were relatives of the trouts were lost forever. Stocking programs can restore certain species to lake or reservoir following pollution abatement and a return of acceptable water quality characteristics. However, most stocking programs are limited to the gene pool of readily available hatchery fishes. Criteria for Classifying Lakes (Forsberg and Ryding 1980)

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Figure 17.2. The horizontal line represents the thermocline which separates epilimnion from hypolimnion. If the left or middle lake became as productive as the eutrophic lake while still deep the hypolimnions could suffer oxygen depletion.

Average annual primary production can be predicted from average chlorophyll a concentration. BIO 102 will perform a lab on Eutrophication measuring chlorophyll.

Figure 17.3 Primary production in relation to chloropyll in water.

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Part I Chapter 18 – Winterkill and Summerkill

Chapter 18 Winterkill and Summerkill In Lakes [primary production, nutrient cycles, consumers, decomposers, photosynthesis and respiration all come together] Winterkill and summerkill are events that take place in the winter in the north and during the summer in the south respectively. What they share in common is that the oxygen dissolved in the water drops below levels at which fish can survive (approximately 3 ppm). The circumstances that result in a winterkill or summerkill are quite different. Winter kill develops slowly and is not known until ice thaw. Summerkill happens suddenly and is known at sunrise. The common feature is that micro organisms will lower oxygen content in the water if excessive amounts of organic matter (e.g., from dead algae) are present.

Winterkill Winterkill (Fig. 18.1) occurs in northerly latitudes or high altitudes in the winter but often is not realized until after the ice melts in the late winter or early spring. Typically a lake that is likely to experience winter kill is shallow and receives excess nutrients (N and P) from agricultural and domestic sources and has a rich phytoplankton population (bloom). During early winter before ice cover sets in the body of water continues to receive inputs of oxygen from the air. Ice cover isolates the lake or pond from physical inputs of oxygen but limited photosynthesis occurs under the ice. Once snow covers the ice the light penetration is severely limited. Eventually respiration by the aquatic community particularly decomposition of dead matter by the decomposers results in depletion of oxygen. Of course a very deep lake has a larger pool of oxygen but a shallow productive lake has a small oxygen reservoir. Fish die under the ice and often the "winterkill" is not realized until ice thaw. One species of fish seems to be well adapted to survive winterkill conditions. The mudminnow is often the only species of fish remaining after a winterkill.

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Figure 18.1. Progression over the winter leading to “winterkill.” (Source:http://finfarm.com/wpcontent/uploads/2014/01/winterkill.jpg)

Summerkill Summerkill occurs in southerly latitudes during the summer, especially July through early September. Like winterkill,a lake that is likely to experience summerkill receives excess nutrients (N and P) from agricultural and domestic sources and has a rich phytoplankton population (bloom). During the months of July through early September the water temperatures are at their highest and one of the properties of water is that warm water can not hold as much oxygen as cold water. Consequently water bodies are more vulnerable to oxygen depletion in summer. Couple that with the fact that metabolic rates of fishes as well as microbes are elevated by warm water temperatures translates into the fact that the aquatic community will use more oxygen each day than it would during the winter. A summerkill typically happens 99

Part I Chapter 18 – Winterkill and Summerkill during late summer and occurs sometime between sunset and sunrise but most often in the hours before sunrise. Once the sun sets, the ability of phytoplankton to produce oxygen drops off rapidly. In fact, at some point in the late night or early morning the phytoplankton will actually be consuming oxygen from the water. If the lake has a high content of detritus from decaying algae stimulated by the excess nutrients, decomposers (bacterial, fungi) will use much of the oxygen in the water. Their oxygen consumption along with that of the fish, invertebrates and the algae in the dark can result in the oxygen being lowered below the threshold at which fish survive (e.g., about 3 ppm). Oxygen only has to dip below this level for a short period. Just like persons, fish can not hold their breath waiting for oxygen levels to return. Hence the old saying "fish only die once."

Figure 18.2. Changes in dissolved oxygen (mg/liter) from early evening until sunrise during a summerkill event.

Finally, any body of water including streams and rivers can experience fish kills if the dissolved oxygen is reduced from inputs of materials rich in organic compounds which decomposers can utilize as a foodstuff resulting in consumption and lowering of available oxygen. Fish kills from oxygen depletion can happen in estuaries and rivers receiving discharge from industrial and domestic waste treatment plants, runoff from agricultural feedlots and processing facilities and even downstream of dams if discharge of water from the dam is suddenly reduced. These types of fish kills are of course more likely to occur in summer because of the reduced capacity of water to hold oxygen coupled with higher rates of respiration of the aquatic organisms, but can occur any month of the year. 100

Part I Chapter 20 – DNA

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Chapter 20 DNA, Proteins and Cells DNA - The Common Thread All living organisms and viruses (non-living) share a commonality in DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). Prokaryotic organisms have a single strand of circular DNA rather than pairs of matching or “homologous” chromosomes which characterize eukaryotes. However, all DNA is made of long sequences of four nucleotides (Adenine, Thymine, Cytosine and Guanine). Furthermore, all DNA is arranged in a twisted ladder-like arrangement termed a double helix.

Figure 20.1. The double helix.

Adenine on one side of the double helix is bonded to Thymine on the other side. Similarly, Cytosine is bonded to Guanine. All four bases can appear on either of the strands. A "gene" is typically hundreds or thousands of nucleotides in length. Genes contain the code to build specific proteins. These proteins can be structural or functional. Enzymes which regulate virtually all biological functions are proteins. Many genes serve to regulate other genes, turning them on and off as needed. An organism's genome is a list in order of the nucleotides along it single strand of DNA in the case of a bacteria (prokaryote) or along its pairs of chromosomes (most eukaryotes; 46 chromosomes in humans). All organisms build proteins in more-or-less the same way. The double strand of DNA must partially open (sometimes referred to as the "bubble") and a single strand of "complementary" messenger RNA (mRNA) is formed. The sequence of nucleotides in the mRNA is complement to the code on one of DNA strands meaning the mRNA has a Adenine if there was a Thymine on the DNA, a Cytosine if the DNA had a Guanine, and a Guanine if the DNA had a Cytosine. One difference between mRNA and DNA is that mRNA utilizes Uracil rather than Thymine. So if the DNA had an Adenine the complement mRNA would have Uracil instead of Thymine.

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Figure 20.2. Messenger RNA synthesis.

The mRNA is passed to a ribosome where protein is constructed using the sequence of bases in the mRNA. A third type of nucleic acid, transfer RNA is required to convert the code or sequence of bases on the mRNA into a polypeptide. Transfer RNA (tRNA) are only 75-100 nucleotide bases long. There is one portion of the tRNA where a sequence of three nucleotide bases serves to align with the code of the mRNA. Generally speaking, there is one tRNA for each amino acid. The tRNAs differ in their three bases. So the code on the mRNA is converted into a sequence of amino acids three bases as a time.

Figure 20.3a. Polypeptide synthesis. Transfer RNA brings amino acids according to the code.

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Figure 20.3b. The structure of transfer RNA (tRNA consist of 76-90 nucleotide bases. The “anticodon loop” is the three base sequence which aligns with mRNA.

Cells Cell theory states that 1) all living organisms are made up of one or more cells, 2) nothing smaller than a cell is considered alive, and 3) new cells are formed from existing cells. Cells must meet three criteria in order to be considered living. First, they must be bound by a membrane and because of its selective permeability of the membrane, the cell can be different than its surroundings.(Figure 4). Lipids can traverse the membrane fairly easily but the passage of water, proteins and carbohydrates must be facilitated by specialized pores.

Figure 20.4 . A cell membrane consisting of two layers of phospholipids with fatty acid tails turned inward and pores for passage of water, proteins and carbohydrates.

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Figure 20.5. The bi-lipid membrane consists of phospholipids with two fatty acid tails (non-polar) turned inward and polar heads which consist of choline, a phosphate group (PO4) and glycerol.

Secondly, cells must acquire energy through metabolic processes. Third, living organisms must have a genetic system to regulate the metabolic processes and this genetic system must be capable of replication.

Nucleic acids are the one thing that viruses, bacteria and higher eukaryotic organisms have in common. The shape and complexity of the nucleic acids differs between these three categories. Viruses are about 1/10 to 1/100th the size of a typical bacteria or prokaryotic cell. They contain no cytoplasm. A virus has straight or circular DNA or RNA that is protected by a protein capsule. A virus genome is about 1000 to 1,000,000 nucleotide bases compared to 3 billion base pairs for humans. Prokaryotic cells do not have nuclei or discrete organelles. They do contain DNA but it is not in the form of chromosomes. Prokaryotic DNA is circular and contains only about 1,000,000 nucleotide bases (compared to 3 billion base pairs for humans). Prokaryotic cells are 1/10 to 1/100 of typical eukaryotic cells. Prokaryotic cells do not contain organelles but they do have ribosomes and internal membranes which conduct similar functions as eukaryotic organelles. Bacteria are surrounded by a bi-lipid membrane. Often there is a thick cell wall and capsule coating outside the membrane. Some species have a few to many external filaments (pilli, flagella) which might serve to facilitate attachment or locomotion in the case of longer filaments (Fig. 20.5). Toxins and destructive enzymes (proteins) produced by bacteria are responsible for tissue damage and symptoms of bacterial infection.

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Figure 20.6. A diagramatic bacteria.

Bacteria are broadly divided into categories defined by their shape and ability to be stained. Bacteria occur as cocci (round), bacilli (rods) and spirochetes (spiral-shaped) (Fig. 20.6). They stain either positive or negative (not stained) with Grams stain. So a bacteria might be described as a Gram Positive Bacillus. Shape and stain can be determined quickly from a sample and assist in a prescribed course of treatment for a bacterial infection.

Figure 20.7. Three shapes of bacteria.

Bacteria can exchange DNA and fragments of DNA (plasmids) by means of conjugation (Fig. 7). They can acquire external DNA fragments from the environment. Bacteria divide by a simple process called binary fission or binary division. The circular DNA duplicates, the cytoplasm divides and one of the two circular chromosomes travels with each of the two dividing portions of the bacterial cell.

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Part I Chapter 20 – DNA Figure. 20.8. Bacterial conjugation.

Eukaryotic Cells Eukaryotic cells contain organelles. The organelles include the nucleus which contains the DNA in the form of chromosomes. The nucleolus inside the nucleus manufactures the ribosomes which move to the rough endoplasmic reticulum. Chromosomes are termed chromatin when the cell is not dividing. The rough endoplasmic reticulum (ER) contains circular ribosomes which are where proteins are made. Other molecules are made in the smooth ER. The Golgi Apparatus packages the molecules made by the ER into their final form and initiates their transport in the cell. Vessicles (vacuoles) transport molecules to and from the cell membrane.Cells can engulf external particles and surround the particles with a membrane which separates from the plasma membrane and becomes an internal vesicle. Lysosomes clean up unneeded particles and molecules. Microtubules and filaments provide a weak skeleton of sorts within the fluid cytosol (cytoplasm). Mitochondria are the energy plant. They convert the breakdown products of mostly carbohydrates and lipids to ATP, the “Universal Energy Currency.” Plants including algae have chloroplasts which convert sunlight and CO2 to ATP and sugar. Mitochondria and chloroplasts have circular DNA which is remarkably similar to the circular DNA of prokaryotes.

Figure 20.9. A diagramatic eukaryotic cell.

Endosymbiotic Theory of Origin of Mitochondria and Chloroplasts in Eukaryotic Cells Cells in active tissues like human muscles and liver have about 1000 mitochondria per cell. They divide by binary fission like bacteria. Their DNA is circular like that in bacteria. You got your mitochondria from your mother's ovum. Your father did not contribute to your mitochondria in 107

Part I Chapter 20 – DNA any way. So your mitochrondria were your mother's who got them from her mother, who got them from her mother, ad infinitum. Mitochrondria in eukaryotic cells have been passed forward in time since the dawn of eukaryotic life. Before mitochondria existed in eukaryotic organisms it is widely accepted that they existed as prokaryotic organisms which are believed to have taken up residence in a primitive Eukaryote (the Endosymbiotic Theory). The prokaryote was engulfed by a primitive eukaryote but instead of digesting it, the membrane-surrounded engulfed prokaryote was retained in a symbiotic relationship which assisted metabolism (and photosynthesis in the case of engulfed cyanobacteria) in the primitive eukaryote (Fig. 20.10).

Figure 20.10. The Endosymbiotic Theory for origin of mitochondria and chloroplasts.

Viruses Viruses do not meet one of the three functions all living things share. They do not have capacity to harvest energy through metabolic processes. Viruses do contain a genetic system that can control metabolic processes of its host. Viruses are protected by a membrane. It is not like the bi-lipid membrane of all living cells. Viruses are covered by a protein coating. Viruses have a few different forms. Some are linear and some are multi-sided looking more like a machine.

Inside the virus is either DNA or RNA. Some viruses attach to a host’s cell at specific external sites and inject their nucleic acid into the cell. Other viruses gain entry into the cell by being engulfed and taken into the cell in a vessel. The virus and its nucleic acid are then able to escape the vesicle. Viral Forms. (1) (Fig. 20.11a) Viruses that contain DNA enter the nucleus and then proceed to make RNA which will travel to the rough ER and begin to make more viral particles. (2) (Fig. 20.11b) Viruses that contain RNA utilize the rough ER to synthesize more viral particles. (3) (Fig. 20.11b) Some viruses (retro viruses) have RNA which is reverse transcribed into DNA (the opposite of the step where DNA is transcribed to mRNA) which is then incorporated into the host’s DNA. This new code is incorporated into the host cell’s genome and then proceeds to manufacture RNA which will build more viruses.

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Part I Chapter 20 – DNA Regardless of which of the three categories in terms of mode of action the result is that the genetic machinery of the host cell is used to manufacture more viruses. Eventually the cell is ruptured releasing more viruses.

Figure 20.11a. Pathways for non-retroviruses.

Figure 20.11b. Pathway for retroviruses

Zoonotic Diseases Zoonotic disease is a disease that can be passed between animals and humans (Fig. 20.12). Zoonotic diseases can be caused by viruses, bacteria, parasites, and fungi. Some are caught by close contact and some from bites. These diseases are very common. Scientists estimate that more than 6 out of every 10 infectious diseases in humans are spread from animals. Many people interact with animals in their daily lives. We raise animals for food and keep them in our homes as pets. We might come into close contact with animals at a farm, a county fair or petting zoo or encounter wildlife when we clear wooded land for new construction. In third world countries humans, domestic animals including livestock and poultry, and wildlife live in close contact. Animals can serve as vectors for the transmission of zoonotic disease to humans and/or serve as a reservoir for the infectious organism. Mutations of the organism while in the "reservoir" can change the rate of infection when it jumps to people. A partial list of zoonotic diseases includes: Influenza, Bubonic plague, Malaria, west Nile Virus, Dengue Fever, Ebola, HIV, Lyme Disease, Rocky Mountain Spotted fever, rabies, Giardia, and ringworm to name a few.

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Figure 20.12. The relationship between humans, domestic animals and wildlife with respect to zoonotic diseases.

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Part II Chapter 21 – Photosynthesis

Chapter 21 Photosynthesis - No Sun No Sugar, No Water No Oxygen Pigments Biological pigments, also known simply as pigments or biochromes are substances produced by living organisms that have a color resulting from selective spectral color absorption. Biological pigments include plant pigments and flower pigments and animal pigments (e.g., hair color, etc). Pigments do much more than provide color for plants and animals. Photosynthetic pigments act an “antennae” and capture photons of light. Others transfer the photon’s energy to other pigments. Still, others harvest this energy and use it to facilitate pumping hydrogen ions across a membrane creating a gradient where the hydrogen ions are more concentrated on one side than the other. This gradient is the underlying potential energy for ATP synthesis. While hemoglobin might be thought of as a red biological molecule its color in insignificant compared to its role in transporting oxygen in humans and many other animals. The Pigments of Photosynthesis Chlorophyll a, b, lutein, beta-carotene, zeaxanthin, lycopene, P680, P700 etc. all work together to capture and harvest energy from sunlight. The portions of the spectrum they utilize are the reds and blues (Figure 21.1).

Figure 21.1. The spectral absorption curve for three photosynthetic pigments.

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Part II Chapter 21 – Photosynthesis Notice in Figure 21.2 (below) that the spectral absorption by pigment #4 phycoerythroblin (pigment utilized by blue-green algae, Cyanophyta, Prokaryote) has peak absorption in the 500600 nm range and that photosynthetic bacteria that utilize pigment (#1) called bacteriochlorophyll absorbs below 400 nm and close to 800nm.

Figure 21.2. Comparison of prokaryotic pigments to eukaryotic pigments.

Notice the similarity between chlorophyll and hemoglobin.

Figure 21.3. Chlorophyll utilizes a different metal than hemoglobin.

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Part II Chapter 21 – Photosynthesis Photosynthesis

Recall that one of the Laws of Physics states that "Energy can neither be created or destroyed, but it can change forms." Photosynthesis demonstrates this law of physics. Primary producers are the basis of the ocean, forest and grassland ecosystems that fuel our planet. The "fuel" is the carbohydrates built from glucose. In order for terrestrial and aquatic plants and algae to build glucose a source of energy is needed. This energy is energy stored in the form of ATP and NADPH. These two energy-rich molecules in turn derive their energy from converted solar energy. Photosynthesis consists of two major steps. The “light reaction” is the conversion of sunlight's energy into ATP and NADPH while the "dark reaction" or Calvin Cycle is the synthesis of glucose from CO2, a precursor 5-C molecule (which is recycled), ATP and NADPH. Along the way oxygen is produced and water is used. The General Formula for Photosynthesis:

6CO2 + 6H20 → C6H12O6 + 6O2

The Light Reaction - In the membrane-bound chloroplasts is an internal set of membranes called the thylakoids. They contain the pigments and metabolic pathways which will capture the sunlight's energy and synthesize ATP, NADPH and split water (H2O) into Oxygen gas, a free electron (e-) and a hydrogen proton ( H+) (note: in prokaryotes these functions occur on internal membranes inside the cell but of course not in an organelle).

There are two pigment systems or photosystems which capture photons from the sunlight, Photosystem II then Photosystem I. Chlorophylls are just one of the pigments and biomolecules involved in the conversions. Sunlight striking the thylakoid membranes contains photons which are initially captured by pigments in Photosystem II. The excited pigments pass the electron from pigment to pigment temporarily "exciting" the pigment to higher energy level. [not required BIO 102 - These pigments include lutein, zeaxanthin, B-carotene, lycopene and chlorophyll b.] Eventually the energy of the photon reaches a variant of Chlorophyll, P680.

A variant of chlorophyll a P680 accepts the electron and becomes highly excited and releases an electron to a series of pigments called the Electron Transport Chain (ETC). [not required BIO 102 – The ETC consists of pigments plastoquinone, cytochromes and plastocyanin]. P680 needs to replace the lost electron. It does so by stealing an electron from water! H2O is split into a Hydrogen proton (+), Oxygen gas (O2) and a free electron (-). The OEC or Oxygen Evolving Complex performs the splitting of water. The free electron replaces the electron lost when P680 was excited by the photon's energy. The Oxygen gas is released to the air and water. All the Oxygen on planet earth is made this way. No water, no plants, no oxygen! It is that simple. (WATER ESSAY).

The ETC accepted P680’s released electron. The energy of that excited electron is used to pump hydrogen ions (H+) across the thylakoid membrane creating an area of higher concentration of 113

Part II Chapter 21 – Photosynthesis hydrogen ions inside the thylakoids. Think of this like blowing up a balloon. There is stored potential energy in an inflated balloon waiting to be released. Similarly, there is stored potential energy in the buildup of H+ on the other side of the membrane inside the thylakoids. The electrons which have passed through the ETC will serve as the "make-up" electron for Photosystem I. Like Photosystem II, Photosystem I consists of pigments which gather photons from sunlight, pass it from pigment to pigment and eventually to P700. Like P680, P700 releases a high energy electron and needs to replace the lost electron. It does so by accepting the electron from the ETC (an electron that can be traced back to P680 and then to water). The electron that P700 releases will not be passed to an ETC. It will be used to convert NADPH+ to a more energy rich NADPH. NADPH is one of the two energy rich molecules which will be used in the Calvin Cycle. [not required BIO 102 – Ferrodoxin and FNR (ferredoxin-NADP reductase) facilitate this electron transfer]. What about the so-called balloon of hydrogen ions (i.e. the buildup of hydrogen ions on the inside of thylakoids). The potential energy of this gradient will be converted to chemical energy in the form of ATP. Integrated into the thylakoid membrane is the ATP pump. It is a means by which the hydrogen ions can equilibrate with the lower concentration on the other side of membrane (I.e., akin to releasing pinch on balloon). The ATP pump is an physical portal consisting of enzymatic surfaces. Each time a hydrogen ion enters the portal which is very much like a department store revolving door, the portal rotates. When the portal rotates it exposes the catalytic surface and an ATP is made from ADP + P. The potential energy stored in the H+ gradient is converted to chemical energy in the third P of ATP. One by one, ATP's are synthesized. As long as sunlight is striking the chloroplasts, ATP (and NADPH) will be synthesized. Hence it is called the Light Reaction. The ATP and NADPH will be used to form glucose from its precursors.

Figure 21.4. The light reaction in the thylacoid membrane.

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The Calvin Cycle or Dark Reaction The Calvin Cycle or Dark Reaction are the light-independent reactions of photosynthesis that convert carbon dioxide and other compounds into glucose. These reactions occur in the stroma, the fluid-filled area of a chloroplast outside of the thylakoid membranes.

Figure 21.5. The Calvin Cycle or Dark Reaction

CO2 is combined with an existing 5-Carbon molecule (Fig. 21.5) [not required BIO 102 – the 5Carbon compound is RuBP (Ribulose biphosphate) ; note: Ribulose is 5-C sugar in DNA]. The resulting 6-Carbon molecule is split into two 3-Carbon molecules. Energy present in the third ATP bond of ATPs and in NADPH is used to make the 3-Carbon molecules more energy dense. Some (2 of every 12) of these 3-Carbon molecules are converted into 6-Carbon glucose. Some (10 of every 12) are recycled into six 5-Carbon (RuBP) (note: 10 x 3-Carbons or 30 Carbons converted into 6 x 5-Carbons, also 30-Carbons). Some ATP is also used for this step. It takes six turns of the Calvin cycle to produce one net glucose molecule. This makes sense since six turns brings in 6 carbons in the form of CO2 . All the ADP + P and NADP+ produced in Calvin Cycle are then reused in Light Reaction. 115

Part II Chapter 22 – Metabolism

Chapter 22 Metabolism - putting foodstuffs to work Metabolic processes include those chemical reactions that living organisms use to breakdown foodstuffs into building block molecules. Furthermore, the building block molecules are either used to build more complex molecules (new cells, tissues, storage) or perform work. In order to perform work the energy of the molecules must be converted into ATP, the universal energy currency of life. Work is muscular movement, nerves firing impulses, etc. Work is living and reproducing. Foodstuffs with stored energy come in three primary forms: carbohydrates, lipids and proteins. All three categories must be broken down first into their respective monomers before they can be used as building blocks or as sources of energy. For higher organisms like humans the first step is digestion of consumed foodstuffs. Digestive enzymes in our mouths, stomachs and small intestines breakdown carbohydrates to simple sugars, proteins to amino acids and lipids to glycerol and fatty acids. These building blocks are absorbed into the bloodstream in the small intestine where an enormous surface area of micro villi facilitates the absorption (Fig. 22.1).

Figure 22.1. The human digestive system .

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Part II Chapter 22 – Metabolism Glucose will be used to explain the conversion of a food molecule to energy. Other monosaccharides, glycerol and fatty acids (from lipids) can also enter the metabolic pathway. Even amino acids from proteins can be metabolized for energy but most animals do this as a last resort. [see Appendix A]

Step 1. Glycoloysis: Glucose to pyruvate in cytoplasm. A single 6-carbon, glucose is split into two 3-Carbon molecules of pyruvate. This produces a "net" of 2 ATP (Fig. 22.2). The addition of phosphorous to the ADP molecules to form ATP at this stage is referred to as a "substrate-level" phosphorylation (it does not involve the ATP-synthase pump). Also, two NAPH (energy rich) are made from NAP+. This first step does not require oxygen (it can be done anaerobically). It is a very primitive step in metabolism and is universal to living cells. It does not produce much energy (ATP) per glucose Certain simple “anaerobic” organisms (i.e., living without oxygen) can exist with only this simple metabolic function.

Figure 22.2. Glycolysis occurs in the cytoplasm. A net 2 ATP is made.

Step 2. This step applies to most eukaryotic cells. The pyruvate in the cytoplasm enters the mitochondria. It is groomed for the citric acid cycle (aka Kreb's Cycle). A CO2 is removed leaving a 2-Carbon fragment to which Co-Enzyme A temporarily attaches. Now the 2-Carbon fragment is called Acetyl-CoA. In removing a CO2 some energy is harvested in the form of energy rich NADH (NAD+ =>NADH). [Note: Carbon Cycling Essay. The release of a CO2 per pyruvate is the first of two points in the complete metabolism of glucose where CO2 is produced.] With the help of Coenzyme A the 2-Carbon fragment enters the Citric Acid Cycle and combines with an existing 4-Carbon molecule. The 6-Carbon molecule resulting from the 4-Carbon and 2Carbon joining will have two CO2 removed. [Note: Carbon Cycling Essay. The release of two CO2 per pyruvate is the second of two points in the complete metabolism of glucose where CO2 is produced.] This will recycle a 4-Carbon molecule. In the process, energy will be transferred to NADH and FADH2 from their respective precursors and one substrate-level phosphorylation will occur. Since two 2-Carbon Acetyl-CoA are made per glucose the yield (glycolysis and Citric Cycle) per glucose is six CO2 , 4 net ATP (via substrate-level phosphorylations), two FADH2 and ten NADH. (Note: the FADH2 and NADH are the major energy harvest)

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Figure 22.3. Grooming of Pyruvate and the Citric Acid Cycle. Other monosacharides, fatty acids, glycerol and amino acids have entry points in the steps depticted in this figure.

Step 3. Oxidative Phosphorylation. The bulk of ATP made from a glucose molecule is made by harvesting the energy stored in FADH2 and NADH. The energy in these two molecules is used to pump hydrogen ions across a membrane and establish a gradient. The hydrogen ions pass through the ATP-pump producing about 34 ATP per glucose (Fig. 4). Oxidative phosphorylation (i.e., ATP synthesis in presence of Oxygen) is so-named because it only works in the presence of oxygen. The electrons from FADH2 and NADH whose energy was used to pump hydrogen ions are passed finally to oxygen. Oxygen is the “Final Electron Receptor.” Oxygen combines with the electrons, hydrogen ions and forms metabolic water (ESSAY). Since oxygen was used these steps are called aerobic respiration.

Figure 22.4. The energy (electrons) in the energy rich reduced FADH2 and NADH molecules is used to pump hydrogen ions across the membrane into the inter-membrane space. The electrons are received by oxygen producing metabolic water

ATP: The 38 ATP made from complete metabolism of glucose represents about 40% of the potential energy of glucose molecule. The typical human body has 50 g of ATP. One thousand 118

Part II Chapter 22 – Metabolism ATP are used per second! The 50g of ATP is used over and over (ATP to ADP + P; ADP + P to ATP) such that daily turnover is about 100 kg/day for typical 2500 kcal/day caloric intake. When oxygen is not adequate what do higher animals do? Lactic acid is made. Human muscles will convert pyruvate to lactate (lactic acid) in the absence of sufficient oxygen such as occurs in intense exercise (Fig. 22.5). Conversion to lactic acid will replenish NAP+ and allow glycolysis to continue producing a small amount of energy (the substrate-level phosphorylation of ATP). However, the build-up of lactic acid will result in muscle cramps.

Figure 22.5. In absence of oxygen, pyruvate is converted to lactic acid.

There are organisms adapted to survive in absence of oxygen. Some are obligated others are facultative (they can adapt). Lactic acid fermenting bacteria (e.g., Lactobacillus sp.) convert pyruvate to lactic acid (their source of sugar can be lactose).

The baking, brewing and winemaking industries have made use of yeast’s capability to breakdown pyruvate in absence of oxygen. Yeast converts each 3-Carbon pyruvate to 2-Carbon ethanol and a CO2 molecule. In the process they use NADH and replenish NAD+ which sustains the glucose to pyruvate conversion (Fig. 22.6). They only gain 2 net ATP per sugar molecule.

Figure 22.6. Yeast conversion of glucose to ethanol under anaerobic conditions.

APPENDIX

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Part II Chapter 22 – Metabolism Pathways for non-carbohydrates to be metabolized for energy are: 1) Fatty acids originating as lipids are converted to AcetylCoA and glycerol enters glycolyisis 2) Amino acids which originated from proteins are converted to pyruvate or AcetylCoA.

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Part II Chapter 23 – Cell Division, Mitosis and Meiosis

Chapter 23 Cell Division ,Mitosis and Meiosis Recall that “Cell Theory” stated that cells are derived from pre-existing cells. Cells accomplish this by cell division. Prokaryotic cells and eukaryotic cells do this very differently. Prokaryotes like Archae, Bacteria and Cyanophyta utilize binary division. In binary division the circular DNA duplicates and then each strand attached to some point on the inner cell membrane. The cytoplasm splits and one strand goes to each of the daughter cells. Bacteria can also conjugate and exchange DNA and acquire external DNA from their environments. These acquired pieces of DNA are called plasmids. So it would seem that evolution favors genetic diversity.

Figure 22.1. Bacterial conjugation.

Eukaryotic organisms have chromosomes in their nucleus. Cell division requires that the chromosomes be duplicated and then equally divided among the two daughter cells. Chromosomes occur in homologous pairs. Each daughter cell must receive both of each homologous pair. This is mitosis. Meiosis is the process of halving the chromosome count but doing so such that each daughter cell has one of each homologous pair. Daughter cells which result from meiosis are called gametes (sperm and eggs in animals).

Ploidy Ploidy refers to the chromosome number in a cell. Somatic cells are diploid or 2n because they contain two each of every homologous pair of chromosomes. In sexually reproducing plants and animals an adult form contains two copies of each chromosome. One was donated by the male and one by the female parent. The donated pair 121

Part II Chapter 23 – Cell Division, Mitosis and Meiosis are said to be homologous or a “homologous pair” since they contain the same genes along their lengths (the versions of the genes or alleles will of course vary). Gametes are haploid or “n” because they contain just one each of every pair of homologous chromosome.

Mitosis The purposeof mitosis is to produce two exact replicate diploid (2n) cells from one diploid (2n) “parent cell” soto-speak. Interphase -Chromatin (Chromosomes) and the centrosome replicate (both centrosomes have a pair of centrioles). Prophase – Chromatin condenses into Chromosomes, nucleolus dissipates, centrioles migrate, spindles form, nuclear membrane disappears. Metaphase – spindle fibers attached to chromosomes at centromere’s kinetochore and chromosomes align along middle plate (“single file” which means duplicated pairs of homologous chromosomes DO NOT line up side-by-side). Anaphase – spindle fibers shorten and duplicated chromosomes separate and migrate to opposite sides of cell. Telophase – cytokinesis (dividing of cytoplasm; in plants a plate forms and divides cells), spindle fibers disappear, nuclear membrane reappears and chromosomes turn back to chromatin Meiosis The purpose of meiosis is to produce haploid (n) gametes (eggs or sperm in animals) which have one-half of the diploid (2n) chromosome number. Meioisis I – Technically where chromosome number is “halved” Interphase -Chromatin (Chromosomes) and centrosome replicate. Prophase I – Chromatin condenses into Chromosomes, nucleolus dissipates, centrioles migrate, spindles form, nuclear membrane disappears. Homologous pairs of chromosomes come to reside side-by-side and crossing over can occur (see Meiosis I Metaphase in Figure 2) (increases genetic variety). Metaphase I – spindle fibers attached to chromosomes at centromere’s kinetochore and chromosomes align along middle plate (“double file” which means duplicated pairs of homologous chromosomes line up side-by-side). Anaphase I– spindle fibers shorten and homologous pairs of duplicated chromosomes migrate to opposite sides of cell. Telophase I– cytokinesis (dividing of cytoplasm; in plants a plate forms and divides cells) , spindle fibers disappear, nuclear membrane reappears and chromosomes turn back to chromatin Meiosis II. – The two cells produced in Meiosis I technically contain one-half of the chromosomes. These cells contain one “duplicated” chromosome of each original homologous pair. For any single chromosome, the duplicated chromosome is either maternal or paternal. Separating these two copies of each chromosome is what happens in Meiosis II. Interphase or Interkinesis- Interphase II is short. Chromatin (Chromosomes) is (are) already duplicated. The nuclear membrane briefly reappears and the chromosomes uncoil and lengthen in thin threads (chromatin). Prophase – Chromatin condenses into Chromosomes, nucleolus dissipates, centrioles migrate, spindles form, 122

Part II Chapter 23 – Cell Division, Mitosis and Meiosis nuclear membrane disappears. Metaphase – spindle fibers attached to chromosomes at centromere’s kinetochore and chromosomes align along middle plate Anaphase – spindle fibers shorten and duplicated chromosomes separate and migrate to opposite sides of cell. Telophase – cytokinesis (dividing of cytoplasm; in plants a plate forms and divides cells) , spindle fibers disappear, nuclear membrane reappears and chromosomes turn back to chromatin. Four gametes result. In femaile humans and other female mammals three of the four gametes become polar bodies and are not used as ova.

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Figure 22.2. Mitosis and Meiosis side-by-side for 2n=4 cell. Cell membrane left off Anaphase step. The second cell in each diagram depicts what the four chromosomes might appear as if not elongated into chromatin during interphase. Meiosis II’s steps simplified.

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Part II Chapter 24 – Oogenesis

Chapter 24 Oogenesis Oogenesis is the formation of the egg (ovum) in the female. During fetal development females have oogonia which are diploid sex cells. While still in the womb the oogonia divide by mitosis to form 400,000 or more primary oocytes. These primary oocytes will begin the first meiotic division but stall during prophase I. The female is born with these primary oocytes. By the time the female reaches puberty approximately 40,000 of the primary oocytes stalled in Prophase I will remain. Beginning during puberty, each month hormones from the anterior pituitary stimulate a primary oocyte to complete the first meiotic division generating two secondary oocytes of unequal size. The smaller secondary oocyte is called a polar body, containing one set of chromosomes. The larger secondary oocyte is the ovum (egg) that will be released from the ovary for fertilization by the spermatozoa. . If the ovum is not fertilized within 24 hours after release it will be broken down. Only if the ovum is fertilized will it continue the second meiotic division. The fertilized the ovum divides again to produce a second polar body, with the fertilized ovum forming the diploid zygote (Fig. 21.1)

Figure 24.1.Oogenesis.

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Part II Chapter 25 – Cell Division Post Fertilzation

Chapter 25 Cell Division Post Fertilization Once an ovum is fertilized it is called a zygote. In a matter of days it will become an embryo and then a fetus. If the zygote splits into two cell masses while a morula (solid ball of cells) a normal pair of identical twins results. Stem cells are undifferentiated biological cells that can differentiate into specialized cells and can divide (through mitosis) to produce more stem cells. The cells of the morula (solid mass of cells) are totipotent, meaning they can turn into any tissue including a placenta. There are two common types of stem cells in science and medicine: embryonic stem cells, which are isolated from the inner cell mass of blastocysts, and adult stem cells, which are found in various tissues. Stem cells from the “inner cell mass” can develop into anything except a placenta and are said to be pluripotent. Adult stem cells are unipotent, which means they can only differentiate into the tissue type where they occur (bone marrow). The central nervous system is not capable of repairing itself. The peripheral nervous system can repair itself. If the blastocyst (hollow ball of cells) splits early then the identical twins each have their own amniotic sac but share a placenta. If the blastocyct splits into two masses a little later (e.g., days 8-13) the identical twins share a single amniotic sac and placenta. After about day 13 if the late stage blastocyst with embryonic shield splits into two masses conjoined twins result. The severity of the shared organs is related to how late this split occurred. The embryonic stage starts around two weeks after fertilization. At eight weeks the term fetus is used. The terms embryo, human fetus are of course the subject of intense ethical, scientific and legal debate.

Figure 25.1. Oogenesis

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Part II Chapter 26 – DNA

Chapter 26 DNA (deoxyribonucleic acid) Chromosomes in eukaryotic creatures generally occur in pairs. In humans for example there are 22 pairs of autosomal chromosomes and 1 pair of sex chromosomes (XX or XY) for a total of 46 chromosomes. Forty six is the human diploid (2n) number. For each pair of your chromosomes one was contributed by your father and one by your mother. Chromosomes are exceptionally long and thin during Interphase of the mitotic/meiotic phases. It is called chromatin during Interphase. The chromosomes still consist of a double helix with four nitrogenous bases connecting the two strands that comprise the double helix ladder (Fig. 26.1).

Figure 26. 1. (Left) The double helix of DNA showing the four bases Adenine (A), Thymine(T), Cytosine (C) and Guanine (G); (Right) Human Karyotype showing 22 pairs of autosomes and an X and Y sex chromosome.

A gene is a sequence of nitrogenous bases perhaps as short at 300 bases and even as long as several thousand bases. Alleles are variants of a gene and they differ slightly from one another in terms of their sequence of nitrogenous bases. All alleles of a gene reside in the same location or loci on a specific chromosome. An animal or plant’s genome is a list (in sequential order) of the nitrogenous bases along the sum of the chromosomes (nuclear DNA). The genome is a staggering number. There are about 3 billion base pairs which provide the code for 30,000 genes. These 30,000 genes in turn code for 100,000 proteins. This means that the polypeptides coded for by a single gene (three base pairs at a time) must be used to assemble more than one complex molecule like a protein (30,000 genes and 100,000 proteins known). Genomes are determined by using sophisticated biochemical methods and super computers. The genomes of humans and many common animals have been determined. Of course slight variations exist between populations of animals in the exact sequences. Over thousands and millions of years mutations or changes in the nitrogenous sequence of genes that are retained are useful for categorizing animals including humans as belonging to specific groupings (populations or races). 127

Part II Chapter 26 – DNA There are alleles of genes that only differ by a single nucleotide base. The gene which codes for the β-globin portion of hemoglobin has a variant known as Sickle Cell Disease. This Sickle Cell Allele for the β-globin differs from the normal by a single nitrogenous base. The resultant change in amino acid in the β-globin has profound impacts on the functioning of the resultant hemoglobin. White tigers (not albinos) differ from normally pigmented tigers by a single nucleotide change. These minute differences are referred to as SNP’s (Single Nucleotide Polymorphisms). SNP’s that persist in a species are useful for identifying the population that an individual belongs to. It is estimated that SNP’s occur and persist every 7000 years or so. Imagine 10,000 years ago. Man had dispersed throughout most of planet earth and was even populating North America. But there were no planes, trains and automobiles. Man had to travel by foot. A SNP that occurred by means of a mutation in one population and persisted has little chance of “mingling” with the alleles of a distant population. Distance was a formidable barrier to gene variant (allele) dispersal (aka gene flow). Even if dispersal occurred a migrating population with the SNP would likely encounter resistance (i.e., competition and aggression) by populations encountered during migration. So SNP’s are strong measures of an animal’s origin and evolutionary history. Chromosomes have regions at both ends called telomeres. The exact role of telomeres is not known but there is ample evidence that they protect the integrity of the chromosome. By protecting the exposed ends of the chromosome from damage they protect the code which resides in the sequence of nitrogenous bases. It also appears that the length of telomeres decreases with age suggesting some relationship with aging. Embryonic stem cells have very long telomeres while adult cells are much shorter.

Figure 26. 2. Chromosome anatomy showing telomeres.

Mitochondrial DNA Mitochondrial DNA is also very useful for a variety of population analyses. Every living cell’s mitochondria contain DNA that is circular and similar to the DNA of Prokaryotes such as bacteria (The Endosymbiotic Theory Of Organelle 128

Part II Chapter 26 – DNA Origin was covered). This mitochondrial DNA is useful because it does not experience “crossing-over” which is the substitution of equal fragments of homologous chromosomes during Meiosis. A person of two distinct populations might have very different alleles on their maternal vs paternal chromosome. When this person makes gametes fragments of the maternal and paternal might be exchanged (crossover). The resulting gametes have more variation as a result. Since mitochondrial DNA does not crossover it is in a sense more stable.

Mitochondrial DNA is only passed on from woman to woman because only an ovum passes on its cytoplasm to a zygote (fertilized egg) (Fig. 26.3B, the right side).

Figure 26.3. Inheritance of nuclear DNA vs. mitochondrial DNA

Mitochondrial DNA (mDNA) is useful for population analysis and evolutionary studies. An evolutionary clock has been established based upon known rates of mutation or change in mitochondrial DNA and known variation in mitochondrial DNA between populations of humans where there are known dates associated with their migration. Taking these to factors into account a hypothetical woman named “Mitochondrial Eve” was estimated to live between 150,000 and 250,000 years ago. “Mitochondrial Eve” has the distinction as being the a member of a very small population of Homo sapiens whose mitochondrial DNA has persisted and is present in all women today. Suppose there were 1000 female Homo sapiens 200,000 years ago. Any women who did not have any daughters or 129

Part II Chapter 26 – DNA daughters who had daughters did not pass on any of her mDNA. Some that did have daughters who had daughters eventually also reached “mitochondrial dead ends” because no daughters were born downstream. It is estimated that Homo sapiens pre-dates Mitochondrial Eve but there is good evidence that Homo sapiens encountered several “bottlenecks” in its evolution which reduced numbers into the 1,000’s, perhaps less. Several super-volcano eruptions were known to put the northern hemisphere of the earth into an extended multi-decade winter where food supplies would dwindle and many animal populations would decline in numbers. Let’s not forget the Y-chromosome. The X and Y chromosomes of mammals are thought to have evolved from a common X-like chromosome early in modern-mammalian evolution 166 million years ago. Previously a different sexdetermining system was used. The Y-chromosome only takes its characteristic shape during mitosis and meiosis when it shortens and thickens compared to Interphase when it is longer and linear. During Interphase there is a short region called the PAR region (Pseudo Autosomal Region) where it can crossover with the comparable area on the Xchromosome (Figure 4). Beyond the PAR is the SRY or Sex-determining Region of the Y-chromosome (Fig. 26.4).

Figure 26.4. Anatomy of the Y-chromosome. It assumes its “Y-shape” during mitosis and meiosis.

A Conservative Chromosome - The Y-chromosome has not lost any genes since the line which gave rise to the genus Homo (and eventually Homo sapiens) separated from the Great Apes 8-10 million years ago. Humans share all the genes on the Y-chromosome with the chimpanzee. The alleles are different but they are the same genes. In fact, in the 25 million years since the line which gave rise to the Great Apes (which includes Homo sapiens) split from the monkeys like the Rhesus monkey, only one gene has been lost on the Y-chromosome.

The Y-chromosome is only passed on from father to son and so on. And because of its shape only a very small portion of it might crossover with the X-chromosome. Based upon known mutation rates in the Y-chromosome and natural variations if the genome of the Y-chromosome a Y-chromosome clock of evolution has been calculated and a hypothetical man named Y-Adam was thought to exist 50,000 to 150,000 years ago. So why does Y-Adam and Mitochondrial Eve barely overlap (at 150,000)? It is possible that one of the genetic bottlenecks that occurred in Homo sapiens evolutionary history “squeezed” the male population that existed at the time more than the females. Maybe the surviving men in a small bottle-necked population fought battles for resources which further bottlenecked the Y-chromosome. .

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Part II Chapter 27 – Crossing Over - Recombination

Chapter 27 Crossing Over – Recombination “Variety Is The [very] Spice Of Life” - William Cowper 1785 The Task--'The Timepiece' (Book II, lines 606-7);(he was reflecting on the ever-changing fashion of clothes.) For each of your 23 pairs of chromosomes you are going to have one contributed by your mother and one by your father. Consider just one of the non-sex chromosome (e.g., chromosomes #10). The gamete produced by say your mother could contribute #10 from either your mother’s mother or your mother’s father since that is her genetic makeup with regards to #10. Let’s refer to these as #10-MOM-grammy and #10-MOM-grampy. One of your two #10’s is either #10-MOM-grammy or #10-MOM-grampy (your other #10 came from your father’s side of family). During Prophase of Meiosis I taking place in your mother, #10-MOM-grammy and #10-MOM-grampy come to be positioned extremely close to one-another as the “pair of homologous duplicated chromosomes” preparing to line up during metaphase and migrate to opposite poles of cell. Often a piece of #10-MOM-grammy will be traded for a piece of #10-MOM-grampy in two adjacent chromatids. This is crossing over. The crossover is precise. Each chromatid gets the correct genes in their entirety. Now one of the future gametes being made by this cell will have a chromosome #10 which bears Grammy’s genes along it then changes over to Grampa’s genes. Another will have Grampa’s genes along it then change over to Grammy’s genes. The other two of four gametes will preserve just MOM-grammy’s or MOM-grampy’s genes. So the meiotic process in your mother “recombined” onto a single chromosome Grammy’s and Grampa’s genes . Mom has not changed which genes occur on #10, only the sources. Without crossing over, MOM-grammy and MOMgrampy genes could not occur on the same chromosome. Since it is very common for multiple genes along a chromosome to interact now you have new possibilities or variations not possible without crossing over. I like to think of it as mother nature giving you the best of four families because the process was also taking place in Dad with DAD-grammy and DAD=grampy.

Figure 27.1 Crossing Over.. 131

Part II Chapter 28 –Down Syndrome: Non-Disjunction and Translocation

Chapter 28 Down Syndrome Downs Syndrome results from presence of three copies of chromosome #21 (trisomy-21) and can result from two different chromosomal mistakes: non-disjunction or a translocation. Non-Disjunction is the failure of duplicated homologus chromosomes to separate after metaphase of Meiosis I or failure of a sister chromatids to separate during Meiosis II. If non-disjunction occurs during Meiosis I all the gametes have irregular chromosome numbers. If non-disjunction occurs during Meiosis II then 50% of the gametes have irregular chromosome numbers. Generally speaking, in the human species only trisomy 21 and trisomy of the sex chromosomes is tolerated and results in viable offspring.

Figure 28.1 Nondisjunction in Meiosis I and II.

Both men and women can be the source of the third or “trisomic” chromosome #21. Trisomy 21 is the cause of approximately 95% of observed Down syndromes, with 88% coming from non-disjunction in the maternal gamete and 8% coming from non-disjunction in the paternal gamete. At age 20 the incidence of Down Syndrome is 1 in 2000 births. At age 30 it is 1 in 900 births. At age 40 it is 1 in 100 and increases to 1 in 10 at age 50. 132

Part II Chapter 28 –Down Syndrome: Non-Disjunction and Translocation The 21st chromosome may actually hold 200 to 250 genes (being the smallest chromosome in the body in terms of total number of genes); but it's estimated that only a small percentage of those may eventually be involved in producing the features of Down syndrome. Why is trisomy 21 linked to women’s age? Unlike men, who produce new sperm daily throughout most of their lifetime, women are born with all their precursor-eggs which are awaiting meiosis. To be more precise, a woman is born with about one to two million immature eggs, or follicles, in her ovaries. These follicles are “waiting” to undergo meiosis. Throughout her life, the vast majority of follicles will die through a process known as atresia. Atresia begins at birth and continues throughout the course of the woman's reproductive life. When a woman reaches puberty and starts to menstruate, only about 40,000 of the original 400,000 follicles remain. With each menstrual cycle, a thousand follicles are lost and only one lucky little follicle will actually mature into an ovum (egg), which is released into the fallopian tube, kicking off ovulation. That means that of the one to two million follicles, only about 400 will ever mature. Relatively little or no follicles remain at menopause, which usually begins when a woman is between 48-55 years of age. The remaining follicles are unlikely to mature and become viable eggs because of the hormonal changes that come along with menopause. What this all boils down to is that older women’s ovum are also “older” and have been subjected to decades of environmental variables with the possible loss of some function(s) (e.g., improper disjunction during meiosis. Translocation Downs Syndrome. This explanation of “Translocation Down Syndrome” will cover three generations: Grandparent, Parent (carrier) and Grandchild (Down Syndrome) It starts with grandparents. Let’s just focus on chromosomes 14 and 21. They are acrocentric which means they are not symmetrical in terms of the location of the centromere. The centromere is near the end of the chromosome. Somehow this makes acrocentric chromosomes more likely to experience translocation. The drawing (Fig. 28.2) below would show normal migration during meiosis.

Figure 28.2

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Part II Chapter 28 –Down Syndrome: Non-Disjunction and Translocation The drawing below (Fig. 28.3) demonstrates the “translocation” where 14 and 21 combine at their short ends and now will migrate as a unit.

Figure 28.3

The translocation results in normal or problematic gametes. The left (Figure 28.4) is the problematic gamete.

Figure 28.4

If the left gamete fuses with a normal gamete (produced by the other grandparent), the result is a carrier of translocation Downs Syndrome (Fig 28.5). This would be the “parent” and he or she would have a full complement of chromosomes (two alleles for each gene) so they are normal phenotypically speaking.

Figure 28.5

There are several scenarios that can happen when the carrier parent makes gametes. Since there are not separate 14 and 21 chromosomes on left side of Figure 28.6, there is a null or void and chromosome number 21 might go left or right. If it migrates left as shown below in Figure 28.6 the resulting gamete will effectively have two copies of 134

Part II Chapter 28 –Down Syndrome: Non-Disjunction and Translocation chromosome 21! Actually, the carrier can produce six different types of gametes since there are effectively three chromosomes that can each travel two different ways (3x2 = 6 combinations). The six types of gametes are: (1)14-21,21; (2) 14; (3) 14-21; (4) 14,21;(5) 21; (6) 14-21, 14.

Figure 28.6

Upon fertilization with a normal gamete, the 14-21 produces a healthy carrier. The 14,21 a normal child. The 14-21,21 a Down’s syndrome child (e.g., 14-21. 21 plus a 14,21 has three copies of #21). The other three do not produce a viable zygote. There is a 1/3 chance of a Down’s Syndrome child among the live births.

The 14-21,21 grandchild will have “Translocation Down Syndrome” which accounts for about 3% of all Down

Figure 28.7

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Part II Chapter 28 –Down Syndrome: Non-Disjunction and Translocation It is estimated that 1/12,500 persons is a carrier for the 14-21 translocation. When a young woman (e.g., < 30 years of age) has a Down’s Syndrome child the 14-21 translocation is suspected and it could have come from the father just as likely as the woman.

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Part II Chapter 29 – Independent Assortment

Chapter 29 Independent Assortment (of chromosomes) An individual which is heterozygous for two genes (e.g., AaBb) can produce four different types of gametes (e.g., AB, ab, aB, and Ab; see gametes in below) if the two genes occur on different chromosomes. This is the principle of “Independent Assortment.” It is based on the simple statistical probability that the two different chromosomes can line up two different ways during Metaphase of Meiosis I. Following migration during anaphase, telophase and then Meiosis II, four different combinations of the alleles are possible (Figure 29.1).

Fig 29.1.A diploid (2n cell)

Figure 29.1

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Part II Chapter 29 – Independent Assortment If you are constructing a Punnett square for the possible gametes that can be made by any individual which is heterozygous for two genes which occur on two different chromosomes it would appear as shown in Figure 2.

Figure 29.2. Partial Punnett Square showing gametes which can be made by AaBb male.

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Part II Chapter 30 – DNA Shared With Relatives

Chapter 30 DNA Shared With Relatives DNA is shared with relatives in a predictable manor (50%, 25%, 12.5% etc). Percentages in table 1 are for the DNA of the autosomal chromosomes (i.e., excluding the X and Y chromosomes).

Table 30.1. Approximate percentage of DNA shared with your family.

50% 25% 12.5%

brothers, sisters and parents grandparents, aunts & uncles cousins & great grandparents

The illustration below is for a child with two siblings and two cousins. The child has one uncle, two aunts and four grandparents. The aunt and uncle shaded in blue (or gray if printed in B&W) married into the family and of course share DNA only at general population levels.

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Part II Chapter 30 – DNA Shared With Relatives

Figure 30.1

The fact that a person and their parents share 50% of their DNA seems straight forward since each parent contributes 50% of the chromosomes that makes up a diploid (2n) zygote (fertilized ovum). There is actually a little variation in shared DNA between siblings (brothers and sisters). This variation (e.g., 47% rather than 50% shared DNA) between siblings occurs because of “independent assortment” and “crossing over” during gamete production by both of a person’s parents. Each time a gamete is made, a person’s parents sort their parent’s (sibling’s grandparents) chromosomes during meiosis I. Statistically speaking this “sorting” is “statistically independent” and brothers and sisters end up with an average of about 50% shared DNA. But it can be a little lower or higher.

Each time you move one step further from your immediate family the shared DNA halves. On the average you share 25% DNA with your grandparents, aunts and uncles. This is subject to a little variation also because of all the independent assortment taking place. Moving one step further to cousins yields 12.5% shared DNA. Twelve and one-half is actually pretty high. It is high enough that marriage among cousins is not a good idea because you and your cousins might share 0.125 x 30,000 genes (12.5% of 30,000). If some of these shared alleles are recessive and deleterious, the children resulting from this marriage might receive two doses of unwanted alleles which normally would be masked by a dominant allele when parents were from more diverse lineages.

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Part II Chapter 31 – DNA Fingerprinting

Chapter 31 DNA Fingerprinting As you know already your somatic cells contain 23 pairs of chromosomes. Twenty two of these pairs are the autosomal chromosomes and the 23rd pair is the sex chromosomes (X and Y). And as you know for each of these pair one was contributed from your father and one from your mother. So you have two alleles for any gene, one on each of the maternal-paternal pair of homologous chromosomes. Any previous inheritance questions you might have solved using Punnett squares probably used upper and lower case letters to represent dominant and recessive alleles of any gene. A genotype resulting from a cross in a Punnett square might have been written PP, Pp or pp which indicated homozygous dominant, heterozygous and homozygous recessive respectively. There are no dominant-recessive alleles where humans are DNA-fingerprinted. But there are differences. Rather than writing genotypes with letters (e.g., PP) genotypes are written 9,7 or 10,6 etc. So what do these “numeric” genotypes mean? On the human set of 23 autosomal chromosomes, 13 chromosomes have regions which might just be “genetic baggage” so-to-speak. Sequences of nitrogen bases (Adenine, Cytosine, Guanine and Thymine) which do not contain the “code” for any proteins and are probably just leftovers from an evolutionary point of view. These areas of repeats are called Short Tandem Repeats (STR’s).

Figure 31.1. Thirteen of the human’s 22 pairs of non-sex chromosomes have regions of regularly repeated nitrogenous bases. These regions are called Short Tandem Repeats (yellow in picture).

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Part II Chapter 31 – DNA Fingerprinting On chromosome number 7 there is a region where these sequences of repeated nitrogenous bases GATA for example might appear : GATA GATA GATA GATA GATA GATA GATA GATA GATA where GATA (Guanine, Adenine, Thymine and Adenine) was repeated nine times. This might be a chromosome #7 inherited from your father. Your other (maternal) chromosome #7 might have seven repeats in the same region: GATA GATA GATA GATA GATA GATA GATA before the “GATA” is interupted by another letter. For this particular region of chromosome #7, every human on the planet has between 5 and 16 repeats the GATA. There are no exceptions. Your maternal chromosome has between 5-16 and your paternal has between 5-16 repeats of GATA. The two numbers which represent maternal and paternal repeats is your genotype for chromosome #7’s STR.

Figure 31.2. Close look at the Short Tandem Repeat region of chromosome #7 where one of the pair has 9 repeats of GATA and the other (inherited from other parent has 7 repeats of GATA.

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Every human chromosome on the planet has between 5 and 16 repeats of “GATA” For chromosome #7’s STR. How many different combinations of 5-16 and 5-16 are there since any individual has two sets of the repeat (e.g., 9,7)? Lots! In fact there are 78 possible combinations.

Figure 31.3. Since all humans have between 5 and 16 repeats of GATA in the STR region of chromosome #7 there are 78 different possible “genotypes” (e.g., 9,7).

Even though there are 78 different combinations, certain combinations tend to be more common in certain races and populations. The likelihood of a “combination” such as 9,7 is used in determining the likelihood of an individual matching evidence from a crime scene. 143

Part II Chapter 31 – DNA Fingerprinting

So far we have just covered one pair of homologous chromosomes where there are 78 different possibilities for any human to show repeats of GATA. But there are twelve more chromosomes with STR’s which further refine the odds of any individual matching crime scene evidence. Take a look at Figure 4. The evidence (from tissue) for the GATA STR (known as D7S820) was 10,11. Suspect B was also characterized by a 10,11 genotype for D7S820. But for Suspect B’s ethnic group a 10,11 occurs in 26% of that ethnic population (frequency = 0.26). If there were a million people in that ethnic group then you would expect 260,000 people to match the 10,11 evidence. Certainly you can not convict someone based upon this single genotype (10,11) when there are 259,999 similar people. But there are twelve more STR’s! Suspect B was a match on all 13. Now the final math. The product of the frequencies in Suspect B’s ethnic group for all thirteen STRs is 0.13 x 0.22 x 0.31…..x 0.38 x 0.10 is really really small. In fact it produces odds of 1 in 6 billion. Which means there might not be a single person on the entire planet earth with the same set of STR’s as the suspect’s and evidence! The calculation of probability is similar to coin toss or dice throw odds. What is the chance of throwing a single die and getting a “6” all thirteen times? It is 0.000000000079 or 1 in 12.725 billion. (1/6 = 0.167 so it is 0.167 x 0.167…. thirteen times).

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Figure 31.4. A suspect’s genotype across all 13 STR’s is examined for a match then the odds are computed of any other individual having that exact match based upon likelihood of those genotypes in suspect’s ethnic group.

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Part II Chapter 32 – Punnett Squares – Predicting Inheritance

Chapter 32 Punnett Squares - Predicting Inheritance Classic genetic inheritance has its roots literally in the Pea plants studied by a German monk in the mid-1800's. Gregor Mendel cross-pollinated thousands and thousands of Pea plants and kept records of the results. He surmised that when two plants produced progeny the ratios of traits like color were predictable based upon each providing some “units of inheritance” and that some of the variants of the inheritable units might dominate other variants. Mendel coined the terms “recessive” and “dominant” in reference to certain traits. Mendel did not know what chromosomes were but he came up with “independent assortment.” He published his work in 1866, demonstrating the actions of invisible “factors” (now called genes) in providing for visible traits in predictable ways. Mendel's research would not be widely accepted by science until the early 1900's. In 1915 Thomas Henry Morgan would unify “chromosome theory” with Mendelian Inheritance. Consider the first half of the 1800's. Persons believed that a tiny little human was inside either a sperm or ovum. There were in fact two schools of thought: spermists and ovism. Eukaryotic organisms have two copies of each gene. One is of paternal origin and the other is of maternal origin (in sexually reproducing organisms). The two copies occur on "homologous" chromosomes. Homologous chromosomes carry the same genes, just different alleles or versions of the genes. Alleles are different versions of the genes (e.g., blue vs brown eye color). Some genes have 3,10 and even more variants or alleles. Many alleles are dominant over other alleles and for the dominant alleles we use capital letters. Dominant alleles mask the expression of recessive alleles. If B is dominate and b is recessive and individual with genotype Bb will appear B. Appearance is the phenotype. Many rare genetic diseases are recessive alleles that are uncommon in the gene pool of a population. The gene pool of a population would be equal to twice the number of individuals in the population since each individual has two alleles for each gene. Furthermore, the gene pool would be an accounting of the total number of each allele. Similarity of genomes is closest in close relatives (50%, brothers and sisters and parents; 25%, a person and their aunts, uncles and grandparents; 12.5%, a person and their cousins). This similarity means that close relatives are more likely to both carry a masked recessive allele and have a higher chance of having a child with two copies of the recessive allele than would unrelated persons. The closer the kinship, the higher the probability of two recessive alleles occurring in progeny. An individual which has two copies of the same allele are said to be "Homozygous" (e.g., BB or bb). If an individual has two different alleles (e.g., Bb) the individual is said to be heterozygous for that gene.

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Figure 32.1. A cell which is heterozygous in Metaphase I of Meiosis. Only two type of gametes are possible, P and p.

Consider the cell shown in Fig. 32.1. This individual is heterozygous and can make P or p gametes. If two heterozygous individuals were crossed (e.g., Pp x Pp) it is said to be a "mono hybrid cross" because one gene is being considered (mono) and both individuals are heterozygous (hybrid). A Punnett Square (Fig. 2) is constructed to solve the possible combinations of gametes that can result from this crossing. One axis is for the male (♂) and the other for the female (♀). The four cells in the 2x2 chart are filled with the “intersecting” combination of gamete. By convention, capital letters (dominant alleles) are written first.

Figure 32.2. Punnett square for a monohybrid cross (e.g., Pp x Pp).

In a mono hybrid cross, 1/4 of the offspring will be homozygous for the recessive trait (e.g., pp). Three fourths will have the dominate phenotype (genotypes PP and Pp). Use a Punnett square to figure the phenotype ratio in a cross between a homozygous PP and a heterozygous Pp.

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Dihybrid crossings. Dihybrid means two genes (on two different chromosomes) and both individuals are heterozygous for both genes. Recall the principle of "independent assortment." Independent assortment means that when homologous chromosomes line up (double file) in metaphase and begin to migrate in Anaphase of. Meiosis I, the direction a paternal and maternal chromosome migrate is purely random (Fig. 32.3).

Figure 32.3. The chromosomes carrying the two genes can from four combinations because of independent assortment.

Since four different gametes can be formed a 4 x 4 grid with 16 outcomes is required (Fig. 32.4). A 9:3:3:1 ratio of phenotypes results from a dihybrid cross. Only 1 in 16 will be homozygous for both recessive alleles (e.g., pprr).

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Figure 32.4. The Punnett Square for a Dihybrid Cross where each parent can form four different gametes.

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Part II Chapter 33 – Fur Coat Color Inheritance in Lab Retreivers

Chapter 33 Fur Coat Color Inheritance in Labrador Retrievers Labrador Retrievers are a popular breed of dog due to their good nature. Three principal coat colors are recognized: Black, Chocolate and Yellow. There are two principal genes responsible for coat color in the Labrador Retriever and both demonstrate a dominate and a recessive allele. In terms of the the pigments of this breed’s fur the two alleles are Black (B) and Chocolate (b) and Black (B) is dominate. Then there is a recessive gene which can mask the ability to express coat color. Let's call this expression gene "E" and it occurs in dominate and recessive alleles. In order to mask the ability to express the coat color the "E" gene must be present as homozygous ee. The presence of two recessive "e" alleles always masks the effects of the B alleles(e.g., B or b) no matter what type of B allele (dominate or recessive) is present. The result of the presence of two recessive "e" alleles is a yellow Labrador Retriever. Thus in order to be guaranteed that the result of a mating of two dark Labradors will not produce any Yellow Labradors at least one of the dogs would have to be homozygous for the "E" allele.

Figure 33.1. llele combinations which produce the three common color phases of Labrador Retrievers (Black, Chocolate and Yellow left to right)

Work out the Punnet square for possible gametes, zygotes and phenotypes for the cross depicted in the Figure 2 below. Pairs of B and E alleles (gametes) should be filled in the four cells below the male and to the right of the female. Possible outcomes (gamete pairings in zygotes) should be filled in the light yellow cells of the table.

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Part II Chapter 33 – Fur Coat Color Inheritance in Lab Retreivers

Figure 33.2. Punnet Square problem for a cross between two dark Labradors, one Black one Chocolate.

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Part II Chapter 34 Genetics of Human Hair Color

Chapter 34 Genetics Of Human Hair Color Human hair color inheritance is not yet fully understood. Hair color is determined by at least two genes on at least two different chromosomes. So here is a general model that works pretty well. The primary gene has probably twenty alleles and occurs on chromosome #19. We will call this the Brown gene, BRN and its alleles BRN1 to BRN19 where the subscripts 1-19 represent darker to lighter respectively. The brown gene alleles regulate the amount of melanins which are synthesized (eumelanin and pheomelanin are two common melanins). Generally, if more eumelanin is present, the color of the hair is darker; if less eumelanin is present, the hair is lighter. Pheomelanin colors hair orange and yellow. Everybody has some of both pigments. Hair color is a function of the relative amounts of these two pigments. The amounts of eumelanin pigments determine the varying darkness ranging from Ebony (BRN1, dark black) to very light brown (BRN19, sandy blonde). These BRN alleles demonstrate co-dominance so none masks the other. Hence persons heterozygous for the BRN gene's co-dominate alleles produce pigments of both BRN alleles resulting in many many shades of hair color ranging from black to very light brown. The BRN gene has at least one recessive allele, Swedish blonde (BRNbln or just bln). Any of the co-dominates will mask the effect of a single dose of bln. Individuals heterozygous for bln show only the dominate allele's phenotype. A true Swedish blonde would be BRNbln BRNbln or more simply written, bln bln. There is second gene on another chromosome (#16) which demonstrates modified epistasis. Let's call this gene R and it has two alleles R (non-red) and r (red). The dominate non-red allele (R) suppresses production of pheomelanin. The homozygous recessive genotype rr results in no suppression of phenomelanin synthesis. An individual who is rr will have varying degrees of redness as a result of additional pheomelanins most apparent with mid and lighter shades of brown. This is because they are synthesizing both eumelanins and pheomelanins. An individual who is homozygous for Swedish blonde, or bln bln will have very bright red hair if the "R" gene is homozygous rr (e.g., bln bln, rr which is homozygous Swedish blonde, homozygous red). Other factors such as aging (including youth aging) can switch activity of these alleles. It is quite common for children to be blonde for five or so years. And of course gray hair can start at any time in adulthood but most commonly after age 50. Example. A sandy blonde-haired woman and a brown-haired man have a bright red-haired child. Explanation: Both parents had to be heterozygous for the red gene (they were Rr) so red was not realized or expressed in them. The woman was probably BRN15 bln, Rr and the man was probably BRN10 bln, Rr. If you work out the Punnett Square there is a 1/16 chance of bln bln, rr. In addition, 3/16 of the cells will combine rr with a BRN phenotype (any BRNx paired with another BRNx or single recessive bln resulting in reddish-brown hair. The r allele in human populations. In Scotland 13% of population are red haired and 40% carry at least one red (r) allele. The frequency of red hair is also high in Ireland followed by Wales, western England, Brittany, the Franco-Belgian border, then western Switzerland, Jutland (mainland Denmark) and southwest Norway. The southern and eastern boundaries, beyond which red hair only occurs in less than 1% of the population, are 152

Part II Chapter 34 Genetics of Human Hair Color northern Spain, central Italy, Austria, western Bohemia, western Poland, Baltic countries and Finland. The presence of the red alleles in Nordic countries is believed to have resulted from Vikings taking Celtic slaves! http://en.wikipedia.org/wiki/Red_hair http://www.eupedia.com/genetics/origins_of_red_hair.shtml

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Part II Chapter 35 Sex-Linked Genes

Chapter 35 Sex-linked Genes Sex-linked genes are genes which occur on the X-chromosome in humans. Recessive alleles of sex-linked genes are more likely to be expressed in males since males only have one X-chromosome and without a second Xchromosome there is no opportunity for the recessive (if present) to be dominated by a second “dominant” allele. Two examples of sex-linked genes are hemophilia and red-green color-blindness. Hemophilia Clotting factors (proteins), platelets and red blood cells work together to repair damage to blood vessels and prevent blood loss. Coagulation involves both a cellular (platelet) and a protein (coagulation factor) component. Platelets are small blood cell fragments that form in the bone marrow—a sponge-like tissue in the bones. Platelets play a major role in blood clotting. When blood vessels are injured, clotting factors help platelets stick together to plug cuts and breaks on the vessels and stop bleeding.

Figure 35.1 Blood clotting

There are 13 blood clotting proteins (coagulation factors) found in the blood. They are designated by Roman Numerals I through XIII. When a blood vessel is damaged, these clotting factors are switched on in a certain order (Blood Clotting Cascade) and work to form a clot. If one factor is missing or present at low levels, this causes hemophilia and other blood clotting problems and a proper clot will not form. The two most common factor deficiencies are: factor 8 (or factor VIII) deficiency and factor 9 (or factor IX) deficiency. The most common, affecting 80% of the hemophilia population - those with hemophilia A - is factor (8) VIII. When these blood clotting proteins aren't present is not easily stopped. People born with hemophilia have little or none of one or more clotting factors, the proteins needed for normal blood clotting. The reason is that their DNA does not code for one or more of the clotting factors. The allele responsible for this deficiency is sex-linked (occurs on X-chromosome) and is recessive. Men either have 154

Part II Chapter 35 Sex-Linked Genes hemophilia or they do not. Women can be carriers if they are heterozygous since they will synthesize the blood coagulation factors if they are heterozygous (XH Xh). (Note: XH is normal clotting). Work Problem. Construct a Punnett Square to answer this question. A man who does not have hemophilia and a woman whose does not (but had a hemophiliac father) have children. What percentage of boys might suffer from hemophilia (e.g., 25%, 50% etc)? Remember a woman’s genotype will be written as X? X? and a man’s X? Y where the question mark subscript (?) is replaced by the allele H subscript for dominant normal and h subscript for recessive hemophilic.

Red-Green Color Blindness Red-green color blindness is another sex-linked trait. The genes occur on the X-chromosome (XB is normal, Xb is red-green color-blind). Red-green color-blindness is recessive so it is more likely to occur in men since they only have one dose of the gene on their single X chromosome and if their X-chromosome is carrying the recessive allele Xb then they will be red-green color-blind. Red-green color blindness is most common (8%) in men of northern European ancestry. Work Problem – A man who is red-green colorblind and a woman who has normal color vision have children. The woman’s father was red-green color-blind. What percentage of male children born to this couple will have red-green color blindness? Remember a woman’s genotype will be written as X? X? whereas a man’s X? Y where the question mark subscript (?) is replaced by the allele B subscript for dominant normal and b subscript for recessive red-green color-blind.

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Part II Chapter 36 Human Blood Types – Co-Dominance

Chapter 36 Human Blood Types and Genetics: Co-Dominance Humans carry genes which dictate the synthesis of molecules in the surface of red blood cells. These molecules include short polymer sugars (Fig. 36.1) and characterize our blood as being A, B, AB or o. If this complex molecule includes one additional sugar beyond the common portion of the molecule it is considered an antigen (Fig. 1). Note that each is identical, except that types A and B have an additional sugar: N-acetylgalactosamine for A, and galactose for B. An antigen which is “foreign” is considered an invader and is attacked by our immune system. The alleles of the genes which are responsible for synthesis of these molecules are: A, which results in antigen A, B, which results in antigen B and o, which results in no antigen being synthesized at the end of the molecule (Fig.36.1). Notice that upper case was used for A and B but lower case for o. This is because A and B are "co-dominate" and o is recessive. A person who is heterozygous with a genotype AB produces both antigens A and B because neither is dominate to the other. Blood types are phenotypes. Genotype AB results in blood type AB. Blood type A can be either AA or Ao genotype. Blood type B can be either BB or Bo genotypes. Because allele o is recessive, an individual must have genotype oo in order to be blood type o. Blood type o is termed the universal donor because their blood has no antigens and would not seem foreign to any person during a transfusion. Blood type AB are referred to as universal recipients because their normal blood has both A and B antigens. Thus no blood would seem foreign since they can tolerate antigens A, B and of course o (no antigen).

Figure 36.1

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Part II Chapter 36 Human Blood Types – Co-Dominance Human Blood Type Work Problem A man who is blood type o walks into a hospital and tells staff "I want to take my baby home." The mother is blood type A but she is in jail and baby is type AB. There are many reasons why he can't take the child home. What is the exact genetic reason?

Reference: http://www.answersingenesis.org/articles/aid/v4/n1/abo-blood-human-origins

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Part II Chapter 37 the Rh Factor

Chapter 37 The Rh Factor The Rh factor is another genetic attribute of human blood type. It refers to whether or not an individual's red blood cells have a bio-molecule called Rh factor in blood cell surfaces. If you do then the presence of Rh is perfectly normal to you since it was part of your physiological makeup from the beginning. If your blood cells do not have the Rh factor then that molecule would seem foreign to you and your body’s immune system would respond by attacking it with antibodies. The Rh factor was discovered and first studied in Rhesus monkeys, hence the name Rh. The gene for Rh has two main variants or alleles. Rh+ allele cause the antigen to be incorporated into red blood cells. Rh+ is the dominant allele. The Rh- allele does not result in synthesis of the molecule in red blood cell membranes. A human will be Rh+ (phenotypically speaking) if their genotype is Rh+Rh+ (homozygous) or Rh+ Rh- (heterozygous). A person whose genotype is Rh- Rh- will be phenotypically Rh-. A fetus which is Rh+ (homozygous or heterozygous) in the womb of a woman who is Rh- results in "incompatibility." Small amounts of the fetal Rh+ antigen can cross the placenta into the mother’s blood (Fig. 37.1). The mother responds by production of antibodies to fight the foreign molecules. The mother’s immune response produces antibodies will cross the placenta and attack the fetus's red blood cells causing fetal red blood cells to experience "lysis" (the fetal blood cells leak - hemolysis). This is serious for the fetus. Often it is not the first child that is at risk but the second, third or latter child with an "incompatible" Rh type. This occurs because the mother was sensitized by the first incompatible pregnancy and her immune system responds quickly in subsequent pregnancies. If genetic consultation identifies the risk of "incompatibility" there are treatments to desensitize the mother to reduce or eliminate her immune system from responding to an Rh incompatible fetus.

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Figure 37.1

The table below shows the frequency of Rh+ in various human populations. The Rh- allele probably was a mutation of the normal Rh+ allele. This mutation occurred among the Basque peoples of Europe perhaps 2000 to 10000 years ago (estimated based upon population genetic studies). At that time the vast majority of the Basque peoples were probably Rh-. Rh negativity confers no known advantage. It is only a problem when Rh- women bear Rh+ children. Five thousand years ago alleles did not mix as freely as they do today since populations were far less mobile. Since its origin, the Rh- allele has declined to about 35% in the Basque region.

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Figure 37.2

Here is a work problem requiring a Punnett Square. Suppose a man who is heterozygous (Rh+Rh-) for the Rh factor and a woman who is Rh- (she has to be Rh- Rh-) have a child. What is the probability (e.g., 25%, 50%, etc) of an “incompatibility” between mother and child?

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Part II Chapter 38 Sickle Cell, Hemoglobin and Co-Dominance

Chapter 38 Sickle Cell, Hemoglobin Heredity and Co-Dominance Sickle-cell anemia illustrates that the terms dominance, incomplete dominance, and co-dominance are somewhat arbitrary. The type of dominance inferred depends on the phenotypic level at which the observations are being made: organismal-level, cellular-level, or molecular-level.

The gene for hemoglobin influences anemia, hemoglobin function and blood cell shape. The advantage of the sickle cell allele HS in terms of malaria resistance is not the primary purpose of the gene(s) which is to code for the synthesis of a globins (for hemoglobin) molecules and bind oxygen. Sometimes this advantage is incorrectly cited as an example of “over-dominance.”

Human red blood cells have hemoglobin consisting of four globins grouped into a molecular complex for carrying oxygen.

Figure 38.1

Four genes on chromosome 11 are responsible for -globin while two genes on chromosome 16 code for -beta globin. The alpha and beta chains are made in precisely equal amounts despite the differing number of genes. Normal red blood cells have a complex consisting of two -globins and two -globins. A single nucleotide mutation in the gene coding for the -globins is the cause of sickle cell. A change of the codon from CTC to CAC causes glutamic acid (an amino acid) to be substituted for valine (an amino acid) in the s-variant of -globin. Persons heterozygous for sickle cell (HBHS) produce both variations of the -globin. In fact, the normal allele produces 50% or more of the globins. There are additional variants of the genes responsible for the -globin. 161

Part II Chapter 38 Sickle Cell, Hemoglobin and Co-Dominance Several hundred variants have been identified but sickle cell is most familiar. The table below lists three genotypes and the effects on anemia (organismal), Sickling of Cell (cellular) and hemoglobin structure (molecular) and the type of dominant-recessive relationship.

Table 38.1 Anemia

Sickling of Cells

Globins in Hemoglobin

(dominance)

(incomplete dominance)

(co-dominance)

H BH B

Normal

Never

2 + 2 

H BH S

Normal

Only under low oxygen

2 + 1  + 1 S

HSHS

Anemia

Sickle Cells

2 + 2 S

-globin Genotype

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Part III Chapter 40 Introduction to Evolution

Chapter 40 Introduction to Evolution – Genes, Alleles, Mutation and Species C. William Beebe said in 1906, "...when the last individual of a race of living things breathes no more, another heaven and another earth must pass before such a one can be again." Living organisms are bounded by a membrane and by virtue of the membrane’s differential permeability are able to maintain a difference from their surroundings. Living organisms are able to harvest energy by means of metabolic reactions. They have genetic machinery which oversees these activities and can replicate. And of course you know the importance of water to these processes. We have covered three of the four theories that unify biology: cell theory, gene theory and the theory of heredity. The fourth, “Evolutionary Theory” states that all living things are descended from a common primitive ancestor. We will cover the theoretical origins of life on a primordial "watery" earth, major steps in the timeline of evolution of complex animals, evolution of vertebrates, mammals, primates, hominids and man. The underlying mechanism for evolution is mutation or changes to the genome (complex sequence of nucleotide bases in DNA). Mutations that are beneficial and persist are infrequent and almost unimaginable amounts of time are required to produce successful genomes. We measure our lives in hours, days, months and years so it is hard to imagine a million years or a billion years. Finally an environmental pressure which acts on or "selects" mutated phenotypes provides the mechanism for natural selection. Natural selection is the means by which small incremental changes are favored or not favored. This is micro-evolution. Given countless generations of small subtle changes eventually a new species will emerge because its genome and resulting phenotype render it incompatible with its ancestors. Macro-evolution is the sum of countless micro-evolutionary changes that result in new species.

DNA-Proteins and Evolution We live in a world of proteins. Muscles, enzymes that catalyze tens of thousands of biological reactions, structural pigments, etc. are all either proteins or derived from proteins directly or indirectly. What the proteins all share in common is they are coded for by sequences of nucleotide bases in DNA. The DNA is the code. Messenger RNA (mRNA) takes the code to the Rough Endoplasmic Reticulum's Ribosomes where transfer RNA (tRNA) (each of which has only three “working or complementary” nucleotides) brings amino acids into place one after another to build a polypeptide. All proteins start with the same start codon, and there are several stop codons (no tRNA corresponds to the three base sequences on the mRNA). One or more polypeptides are assembled into proteins and other bio-molecules. 163

Part III Chapter 40 Introduction to Evolution Mutations or changes to the DNA code will change the mRNA, change the order of tRNA’s nucleotide bases and will change proteins and products of protein-catalyzed biological processes. If the mutation is deleterious it will result in lower fitness and decreased reproductive success (differential reproduction). On the other hand, if the mutation imparts some benefit it will be promoted as a result of increased growth, survival and reproductive success (differential reproduction). Sometimes a single nucleotide base mutation can be dramatic. The difference between normal hemoglobin and the hemoglobin associated with sickle-cell anemia is a single nucleotide base change (SNP, Single Nucleotide Polymorphism). This is natural selection. It acts upon phenotypes which have underlying genotypes which in turn can be traced to sequences of nucleotide bases. Mutations do not happen often. Most are probably deleterious. The key to changing genomes is time, lots of time. Species which only reproduce a few offspring in their life span or have one brood per year would require perhaps thousands of years for natural selection to produce substantial changes. We know that 10,000 years of isolation produced several species of pupfish in the CA/NV desert where there was a large inland lake 10,000 years ago that contained a single species. The species are unique but still similar. It took millions of years to produce their common ancestor. Organisms that are small (e.g., bacteria, insects) have short life cycles and produce thousands of offspring might be expected to show faster change.

Evolution of Human Skin Pigmentation - The evolution of human skin pigmentation is a very good example of mutation of alleles and selective pressures. For a long time human skin pigmentation was thought to have evolved as a means to prevent skin cancer. Skin cancer however would not interfere with reproductive output since it manifests later in life. Researchers sought explanations which would interfere with reproductive output and prereproductive success. UV-A light penetrates deeper than UV-B. It can destroy synthesis of folic acid (foliate) which is required for so many functions including reproduction and development (Fig. 1). UV-A and UV-B are highest at tropical latitudes and even more so in arid regions at low latitudes. Skin pigmentation is controlled by perhaps 20 genes. Darker skin pigmentation reduces UV-A penetration protecting folic acid. In tropics the light is so intense that even with skin pigmentation, sufficient UV-B penetrates skin to promote synthesis of vitamin D which is needed for bone development, especially during early childhood. As man migrated northward out of Africa tens of thousands of years ago, man inhabited areas with reduced solar radiation and lower UV-A and UV-B. At higher latitudes, dangers from destruction of folic acid were lowered but the reduced light meant vitamin D synthesis would be diminished if skin pigmentation was remained high. Consequently evolutionary pressure favored a mutation that reduced skin pigmentation. This mutation has also been identified in Neanderthal man DNA. With reduced skin pigmentation, humans in northerly European areas could produce sufficient vitamin D while exposed to lowered UV levels. The industrial revolution saw many Europeans developing symptoms of vitamin D deficiency including rickets in children. Inuit Native

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Part III Chapter 40 Introduction to Evolution Americans ate diets rich in vitamin D and did not experience the evolutionary pressure for lighter skin pigmentation.

Figure 40.1. UV-A, UV-B and human pigmentation.

Species-Swedish naturalist Carl Linnaeus developed the system of binomial nomenclature which is still in use today. Living creatures are categorized into a genus and species. A genus can of course contain more than one species, most do. There are however some rare plants and animals which are the only species within their genus. The sperm whale (Physeter macrocephalus) is a large toothed whale. It is the only living member of genus Physeter. Subspecies represent distinct populations which are isolated from one-another and demonstrate unique physical and behavioral traits. Sub-species can reproduce with one another. Their differences have not yet isolated them from one another. Species are often conceptualized by their niche. Niche was defined as a multi-dimensional hyperspace but can be visualized as the sum of how a species goes about living (what food and habitat resources it uses in time and space or "its place in nature."

Figure. 40.2. Niche as defined by just three variables.

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Figure 40.3. A multi-dimensional hypervolume (niche).

The ability to describe an animal or plants genome has expanded our ability to discriminate unique populations. Genomes allow scientists to describe quantitatively the relative uniqueness of different populations of a single species or even describe quantitatively the differences between closely related species. Furthermore, based upon assumed rates of mutation, estimates of the amount of time two genomes have been separate can be made. These estimates are measured in 1,000's of years. How do we discriminate close genomes? Areas on the chromosomes near the centromere exist where there are repeated nucleotide sequences much like the regions of DNA (Short Tandem Repeats) used for DNA fingerprinting. Like the fingerprinting technology these areas are not involved in protein synthesis. These areas are called microsatellites and are subject to frequent mutation imparting differences between populations and closely related species. Since they do not code for proteins their mutations are not eliminated by natural selection. They persist and are thus useful for discriminating differences between populations. Time and distance and the consequent lack of gene flow are the two factors which result in divergence of populations. Time and distance result in divergence of alleles. Mutations that produce favorable traits result in further divergence of populations separated by time and space. Given enough time, new species will eventually emerge. So what kind of traits separate one species from another. The most common definition of a species is that it will not produce viable and fertile offspring with another species. In order to two animals or to produce viable offspring there must be (1) chromosome compatibility (karotype), (2) genome compatibility (the chromosomes must contain the same genes at the same location on gene (loci), (3) the two animals must be physically compatible in order to breed, and (4) the two animals must be behaviorally compatible. The latter is also influenced by physiology since the two animals in question must be in a breeding phase simultaneously. What bad things can happen to a species? A species experiences a genetic bottleneck if its numbers are highly reduced for any number of reasons, natural and man-made. Genetic bottlenecks have occurred as a result of natural events. Mt.Toba was a super volcano that 166

Part III Chapter 40 Introduction to Evolution erupted 70,000 years ago. It plunged the earth into a multi-decade volcanic winter. Many species were reduced in numbers. It is believed that humans (Homo sapiens) were probably reduced to 1,000 to 10,000 at this time. Seventy thousand years ago Homo sapiens had not even colonized Europe, South Asia, Indonesia and the Americas. If a very small number of a species colonizes a new area and is isolated from its original populations it is a founder population. It represents a small subset of the original gene pool of alleles. It experiences drift away from the source populations. This type of genetic bottleneck could be deleterious but also can lead to new species given enough time (measured in 1,000 of years). Darwin of course did not know about genes, genomes, etc. But he had witnessed breeding of domestic animals and surmised that the unique finches in the Galapagos Islands might have descended from a founder group and diverged over time because of their isolation. Genetic bottlenecks result from number reductions due to purposeful mass-elimination, overharvesting and overfishing, and habitat destruction. Examples were given of species reduced to less than three dozen individuals from millions. The loss of alleles is permanent. Those sequences of nucleotide bases representing the loss alleles is forever. The alleles are extinct. Examples of genetic bottlenecks given in lecture included a variety of animals including fish, birds and mammals. The elephant seal was hunted to near extinction in the North Pacific. Today, all elephant seals are derived from 30 that survived on Isla de Guadalupe, MX. North Central Eurasia had a bison too. It was the Wisent. They were reduced to 12 individuals and all are derived from private herds. The American Bison was equally reduced. It is estimated that bison once numbered 10,000,000 or more in North America. The Spanish explorer Coranado compared the abundance of buffalo to “fishes in the sea.” They ranged from Florida to Maine and west to the Pacific. The slightly smaller eastern woodland bison subspecies are gone. Those alleles are lost to time. Bison were hunted until there were only about 300 left. The California Condor was reduced to 22 individuals which were brought into captive breeding in order to save the species. Captive breeding is the last resort taken by federal wildlife officials to save a species from extinction. The Whooping Crane numbered only 21 when it was taken into a captive breeding program. The black-footed ferret is a small predatory mammal that eats only prairie dogs. Cattle ranchers went to war against prairie dogs and won. But in the process they just about made the black-footed ferret an extinct species. It was down to 7 breeding individuals when it was taken into captive breeding. Mother nature sometime bottlenecks a species. Once upon a time more than 10,000 years ago the area around Death Valley (CA/NV) was warm and moist. There were several large inland lakes. Fossils show us there was a small fish in those lakes that is the ancestor of about four unique species that presently occur in isolated creeks and pools in Death Valley. They are all evolutionary descendants of the ancestral pupfish. This isolation took several 1000 years. The most extreme isolation is the Devils Hole Pupfish. This species entire range is one pool about the size of a backyard swimming pool, albeit deeper. But 167

Part III Chapter 40 Introduction to Evolution the little fish needed a shallow shelf of rocks for algae it consumed. This small shelf was limiting the population to 200-1000 fish. Private developers were lowering the water table to irrigate future golf courses. In the end and all the way to the Supreme Court of the U.S. the little fish won. Its numbers are around 300. That is 300 for the entire species on the planet. The most extreme bottleneck is the extinction of a species. In the case of extinction, the bottleneck is bottlenecked to zero! When a species no longer occurs on earth, its alleles are lost forever. As C. William Beebe said in 1906, "...when the last individual of a race of living things breathes no more, another heaven and another earth must pass before such a one can be again."

What's in a name? Genus and species. The binomial system of naming plants and animals gives each creature a unique name consisting of a genus and species name. The naming conventions were developed long before the advent of molecular genetics and genome technology. Animals and plants that were similar were organized into similar groupings. Those thought to be most closely related were assigned to the same genus but of course different species names. Morphology was the principal factor used to assign species to genera, genera to families and families to orders. Some species like humans are the only members of their genus (it is believed that Homo sapiens and Homo neanderthalensis coexisted). There are plenty of other examples of “monotypic” genera with only one species. In fact, there are more monotypic genera of animals than genera with two species, with three species, with four species, etc. etc. Humans are characterized as members of the Hominidae family of “Great Apes.” Yes we are apes in the mind of taxonomists! This family includes the gorilla (genus Gorilla), chimps (genus Pan) and orangutans (genus Pongo). Hominids and other families of moneys are in the order of “Primates.” Primates in turn are in Class Mammalia. Let’s use the great cats as an example of a single genus which occur over a wide geographic range. Panthera is the genus of big cats that roar. They actually are the only cats that have the anatomy to roar. Time and distance have produced four unique species found over several continents. Panthera diverged from the other cats 11 million years ago. Evolution of the roaring cats more-or-less took place during evolution of Homo sapiens. The genus Panthera includes Panther leo (lion), P. tigris (tiger), P. onca (jaguar) and P. pardus (leopard).

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Part III Chapter 40 Introduction to Evolution Common names do not follow the same rigid rules as latin names. For example, the Florida Panther is actually a subspecies (listed as Endangered) of the Mountain Lion (aka Puma, Cougar, Catamount) (Puma concolor) which historically ranged across the United States and Canada and as far south as the Andes Mountains in South America. Puma concolor is genetically more similar to domestic cats than it is to Panthera. Its closest genetically speaking relative is the Cheetah. A similar evolutionary situation exists with the bears (Ursus) except that there are fewer species of bears in the family Ursidae compared to cats in Felidae. The living Ursus are the black bear (Ursus americanus), brown bear (which includes Kodiak bear, Grizzly and others) (Ursus arctos), polar bear (Ursus maritmus) and Asiatic Black Bear (Ursus thibetanus).

Species terms used in science and society 01. Umbrella species Umbrella species are so named because if efforts are made to conserve them many other species will benefit as well. The spotted owl in the Pacific Northwest is one such species. Setting aside large tracts of forest for the spotted owl will provide habitats for many species. 02. Endangered (and threatened) Endangered and threatened species is a legal status. The Secretary of the Dept of Interior has the authority to place plants and animals on the Federal Endangered Species list. Endangered species are at risk of becoming extinct. Threatened species are threatened with becoming endangered. Endangered species are protected against all forms of “harm.” An Act of Congress, the ESA of 1973 is the legal authority. States may also have lists of Endangered species and long as their list is not lesser than the federal. 03. Extirpated species Extirpated species still exist but elsewhere. Extirpated species have been extirpated from a geographic range. For example, the Elk was extirpated from South Carolina and many other states. Elk have been reintroduced to Tennessee and a few other Eastern U.S. states. 04. Nuisance species Nuisance species are species that are a health and or commercial risk to humans. Some nuisance species damage crops, prey upon livestock or spread disease. Nuisance species can be dealt with in accordance with state laws. 05. Extinct species Extinct species no longer occur on the earth. They are gone forever. Efforts are underway to restore some extinct species using DNA recovered from frozen carcasses. 169

Part III Chapter 40 Introduction to Evolution 06. Endemic species An endemic species lives or lived in an area naturally. It historically occurred in a defined area. 07. Exotic species An exotic species was introduced to an area accidentally or on purpose. It was not part of the ecology prior to its introduction. Introduced species typically do not have natural predators or check and controls and upset the natural order. 08. Game species Game species are sought after by hunting or fishing. Most game species are regulated by state laws and a license is required. Seasons and limits may apply. There are some migratory game species where federal regulations might also exist. Many popular game fishes are “stocked” in order to bolster their numbers and increase sport fishing opportunities. Stocked fish are raised at state and federal fish hatcheries. Trouts and salmons are two types of sport fishes that are stocked extensively (note: salmons are also commercial species). Sometimes there is ample habitat for adults but spawning habitat limits population so stocking is employed. 09. Naturalized species Naturalized species were originally introduced or were exotic but are so widely established that they are now referred to as naturalized. They will probably be part of the ecology forever. The red fox is an introduced species (gray fox is native or endemic). 10. Captive bred species Captive bred species were bred in captivity and then released to supplement dwindling numbers. Several endangered species are captive bred in order to prevent extinction. Captive breeding is the last resort for an endangered species. 11. Feral species Feral species are domestic animals that have become wild and are breeding in the wild on their own. Examples include feral swine and feral cats. 12. Invasive species Invasive species are exotic species that are a serious ecological or commercial problem. Kudzu is an invasive plant and the zebra mussel is an invasive freshwater mussel. 13. Keystone species Keystone species are vital to the entire ecosystem where they live. Loss of a keystone species causes a domino or cascading effect of ecological problems.

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Part III Chapter 40 Introduction to Evolution Keystone Species – Wolves. When Yellowstone National Park was created in 1872, gray wolf (Canis lupus) populations were already in decline in Montana, Wyoming and Idaho. The last wolves were killed in Yellowstone in 1926. In the 1990’s researchers noticed that all the aspen were 70 years old or older. Aspen saplings were generally missing. The herds of elk had become lazy. Since there were not top predators and no hunting in the park the Elk populations were at all time highs. The elk browsed down saplings and ate all streamside vegetation. Stream ecology suffered. From 1995 to 1997, 41 wild wolves from Canada and northwest Montana were released in Yellowstone National Park. The wolf packs increased in numbers. Elk retreated to high country. Aspen saplings appeared again. Stream-side vegetation returned. Water quality was restored. Wolfs are keystone species. Their absence caused a cascade or domino effect of decline. Generally when top carnivores are removed from an ecosystem suffers. A keystone species might be highly connected with other species in its community. Connectance is actually computed mathematically. See the handout on Connectance. 14. Non-game species Non-game species are the 100’s and 1000’s of small poorly understood species of fish, amphibians, reptiles, birds and mammals. They are not sought after for food or fiber. They have no commercial value. Their values are ecological. 15. Indicator species Indicator species are a select group of species whose presence typically means the ecosystem is healthy. They typically have rigid environmental requirements (i.e., well-defined niche) and do not tolerate habitat quality reduction. Streams which support a small non-game group of fishes called darters are normally healthy streams so darters are often referred to as an “indicator species.” 16. Commercial species Commercial species are sought after for food or fiber, mostly food in modern times. Most commercial species are saltwater fishes. Not too long ago many countries practiced whaling so whales were once a commercial species. Now most whales are endangered or threatened because their numbers were greatly reduced.

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Part III Chapter 41 Darwin and Evolution

Chapter 41 Darwin and Evolution Darwin set sail aboard the HMS Beagle in December of 1831 for five year trip around the world. Darwin was a naturalist-theologian. He had studied theology in a sect that was also "naturalists." He had hoped to be a parson. His role for the trip was "ship naturalist" to document flora and fauna, collect specimens and provide company for the captain at dinner. Darwin would collect thousand of specimens and document thousands of observations. His travels would include three oceans, Tahiti, New Zealand, Australia, Africa, South America, and of course the Galapagos Islands.

Figure 41.1 The HMS Beagle, Darwin and his travels. Darwin was preceded my many early scientists who fell out of the graces of the clergy. Darwin was influenced by early geologists like Charles Lyell who surmised the earth was perhaps 250,000 years old. Geologists in the 1800's had no methods to date rock formations other that conclude that deeper rocks were older. They observed weathering of rocks formations and made crude estimates of the age of the earth. Lyell and Darwin and others realized that natural forces were changing the surface of the earth. The diversity of fauna and flora that Darwin observed and many unique species lead him to formulate hypotheses about where species came from. The official position of the church at the time was that the earth was less than 5000 years old and that all species had been created in the beginning. Darwin hypothesized that present day species evolved from ancestral forms. Following his travels he wrote his hypotheses as "On The Origin of the Species by Means of Natural Selection" in 1859, more than two decades after his return. Most refer to the book as "The Origin of Species." The book had two main points buried in hundreds and hundreds of pages. These points were: 1) Species were not created in their present form, but evolved from ancestral species; 2) he proposed a mechanism for evolution, natural selection. His work would eventually be shelved until the period from 1930-1960 when modern evolutionary synthesis would take place. The thirty years from 1960-1990 saw advances in molecular biology and after 1990 the human genome was determined.

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Part III Chapter 41 Darwin and Evolution Darwin did not make any friends with the clergy. Also, at the time of his writings the prevailing theory about evolution was "Lamarckian Evolution" which was the "Inheritance of Acquired Characteristics." Lamarckian evolution (named after Jean Baptiste Lamarck) went like this. A giraffe stretches to reach leaves higher in a tree than others can reach. Its neck gets longer and it passes this on to its offspring. We now know this is nonsense. Someone who trains to be a weight lifter is not going to have children born to lift weights. Darwin did not know about chromosomes, DNA, genes or polypeptides. But Darwin did recognize that there was natural variation in any species and he proposed that natural forces would act to select favorable traits and act to select against unfavorable traits. This was Darwin's "Natural Selection." Darwin recognized that animal breeders had been selecting for traits they desired in dogs, cattle, poultry and even pigeons. Darwin understood that given enough time natural forces could similarly act on the natural variability inherent in a species. Of course Darwin had no idea that this "natural variation" was due to mutation of genes into new alleles which in turn were expressed as proteins and eventually phenotypes. This was the "modern synthesis" that would take place after 1930. And with the advent of modern molecular genetics and genome determination and we now understand mutation down to single nucleotide bases in DNA. Darwin was demonized by many since he suggested that species are derived from ancestral forms which contradicted biblical creation. Darwin said very little about human evolution. In fact all he wrote in the “Origin” was "light will be shed on the origins of man." Darwin understood the implications but probably wanted to avoid additional scrutiny.

Darwinism was a name applied to survival of the fittest and natural selection. Later "Social Darwinists" would apply the concept of survival of the fittest to human population and class struggles. Today we define evolution as the processes that transformed life on earth from its earliest forms to the vast diversity that characterizes living things today. We now know the basis is mutation of genes, environmental forces or selective pressures on the phenotypes resulting from mutation and time, lots of time.

Micro-Evolution are the slight changes seen in species over measurable time frames. If evolution is the survival of certain alleles because they afford a certain advantage then where can we find an example. The industrial revolution in England provided an case study. The unabated pollution resulted in the countryside surrounding urban centers covered in soot. The trees which were covered in lightly colored lichens were darkened. The peppered moth which was light with dark speckles was well adapted to be cryptically pigmented on light lichens. But the dark soot made them "stand out" and predators easily preyed upon them. This resulted in a shift of alleles from light to dark. In the mid 1900's after passage of Clean Air Standards the

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Part III Chapter 41 Darwin and Evolution opposite happened. Trees were no longer soot covered, lichens once again provided a place for peppered moths to hide and the moths shifted back to light alleles. Macro-Evolution is the appearance of new species. Critics of evolution say "show me macroevolution" as if we could record it on video. Macro-evolution takes a long time. Macro-evolution is inferred from examination of geologic record and study of fossils. We do know that 10,000 to 30,000 years was all that was required for several species of pupfish to evolve from a common ancestor in Death Valley (which was once covered by several large inland seas) subsequent to its becoming dry with isolated fish populations. Artificial Selection is a form of micro-evolution where man is responsible for selection. In the case of bacterial resistance to antibiotics the selection is not desired. Bacteria exist by the millions in any infection and when treated with antibiotics there is the chance that a few will mutate and be resistant. Selective breeding of fish, birds, cats, dogs, cattle and horses has produced variants of these species where man determines which alleles will propagate.

The Scientific Evidence for evolution is overwhelming to a biologist. Here are several of the major areas where there are mountains of biological and geological evidence. 1.Geologic fossil record, transitional fossils, and radio-isotope dating 2.Comparative morphology and vestige structures 3. Comparative Embryology - all vertebrates have 1) Dorsal hollow nerve chord, 2) pharyngeal gill slits and 3) post-anal tail in their embryological development) 4. Taxonomy - Carolus Linnaeus was a sixteenth-century Swedish physician and Botanist. He founded the science of taxonomy, the branch of biology concerned with naming and classifying living things. (he did not believe in evolution but his work provided framework for organizing living creatures) 5. Molecular and genetic evidence -closely related species have similar genomes suggesting common ancestry. With each step further away in a taxonomic tree genomes progressively get more different. 6. Observable Micro-evolution (allele shifts) (antibiotic resistance, peppered moth) 7. Biogeography and Continental Drift explains unique flora and fauna (e.g., Marsupials of Australia) 8. HOX Genes - genes that control development are universal to animals and understood pretty well in vertebrates. In most organisms the various Hox genes are situated very close to one another on the chromosome in groups or clusters. Interestingly, the order of the genes on the chromosome is the same as the expression of the genes in the developing embryo. 174

Part III Chapter 41 Darwin and Evolution Human Evolution is probably the most controversial part of evolution. Many people can accept that ancient life forms existed and the life forms are changing or evolving. But many find it difficult to accept that humans share a common ancestor with the great apes. Even more disturbing is the notion that we have an ancestral form that was a prokaryotic microbe. It is believed that the lineage that would give rise to man diverged from the lineage that gave rise to the chimp, pygmy chimp, orangutan and gorilla 10 to 20 million years ago. There is one small but very important difference. The line that gave rise to humans and our immediate ancestors had only 46 chromosomes compared to 48 for all the apes. One very likely scenario is that a Robertsonian Translocation took place. Evidence for this is very clear when you compare human chromosome number 2 to the chimp’s numbers 12 and 13. About 2 million years ago the genus Homo appeared. The last species of genus Homo to become extinct was H. neanderthalis (the Neanderthal Man). Neandethal man is now considered a distinct species from man based upon DNA samples from a cave in Spain. Recall that estimates for Mitochondrial Eve (ME) ranged from 150,000 to 250,000 years ago. There is a 195,000 year old fossil found in Ethiopia which has a skull like that of modern man. Most evolutionary scientists believe Homo sapiens evolved from a primitive Homo sapiens sometime between 500,000 and 200,000 years ago. If we use 200,000 years before present as the “dawn of man” it took about 1.8 million years to get from Homo erectus to Homo sapiens. Neanderthal Man existed from 400,000 YBP to 30,000 years ago so the Neanderthal Man and modern man coexisted for about 200,000 years. There is DNA evidence that many persons of north central Europe have about 24% Neanderthal genome which indicates the two species interbred.

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Part III Chapter 42 Homididae etc.

Chapter 42 A Comparison of the families Hominidae, Canidae, Felidae, Equidae and Elaphantidae There are five species of apes including humans, 30 species of canids including dogs and wolves, 41 species of felids including the domestic cat, seven species of Equids including the horse and two species of elephants. The five apes have either 46 (humans) or 48 chromosomes (non Homo). Felids all have either 36 or 38 pairs of chromosomes. Felids are the strictest carnivore. Canids which include foxes, coyote-like canids and wolves show a wide range in chromosome number ranging from 34 to 78. Only five of the canids have chromosome counts the same as the dog: the wolf, coyote, African wild dog, dhole, and jackals. Horses, zebras, and asses range from 32-66 pairs of chromosomes. The two species of Elephantidae are the African Elephant and the Asian Elephant (subspecies exist). Elephants have 56 chromosomes. Mammoths and mastodons became extinct only 10,000 years ago or less. Woolly mammoths have been found frozen in ice. Their genome has been ascertained. The wooly mammoth is most closely related to the Asian Elephant but has 58 chromosomes. Efforts are underway to clone the Wooly Mammoth using a de-nucleated Asian Elephant ovum and surrogate female Asian Elephant mother. Studies of the chromosomes of Equus and Canidae have shown that chromosome deletion(s) (Robertsonian Translocation) and chromosome divisions (where a pair of chromosomes becomes two pairs) is the mechanism for the differences in chromosome number seen in these variable families. Where are they found? Humans originated in east central Africa 1-2 million years ago and we're probably genetically bottle necked more recently (e.g., based upon mitochondrial eve and Y-Adam) and of course found their way to all continents. They took an early domestic dog with them to Australia. The remainder of Hominids are restricted to central Africa (gorilla, chimpanzees) and Malaysia/Indonesia where orangutans are now restricted to regions of Borneo and Sumatra. Native canids are found in all continents except of course Antarctica and probably originated in Eurasia. Wolves have been around for a million years and their ancestor (which gave rise to the wolf, coyote and jackal, the 78 chromosome canids) for 10 million years. So their evolution pretty much paralleled human evolution. Cats first appeared 25 MYBP probably in central Asia and spread all continents except Australia and Antarctica. Ancestors of horses first appeared in North America 40 MYBP then utilized a land bridge during a high glacial period (low ocean level) 2.6 MYBP to colonize the Far East, Asia, Europe and Africa. During the last (most recent) glacial period, man utilized the same land bridge to migrate to North America from Asia. Man and wolf were the first to enter into a relationship as social, diurnal hunters. This relationship probably started 100,000 years ago, perhaps 1,000,000 years and domestication at least 10,000 years ago. The success of this relationship paved the way for herding of livestock and agrarian activities. Cats were beneficial to have around human settlements in the agrarian period because they consumed rodents which were pests and disease vectors. Cats were domesticated 10,000 years ago in Egypt. Horses would be domesticated and eventually serve as farm animals and for hunting, 176

Part III Chapter 42 Homididae etc. transportation and warfare. They were probably domesticated 4000 years ago in the Ukraine or Siberia. Przewalski’s horse is considered the wild type horse. The karyotype of the domestic horse differs from that of Przewalski’s horse (66) by a chromosome pair either because of a fusion of Przewalski’s horse chromosomes 23 and 24 in the domestic horse (64). Wild horses in the United States are technically feral domestic horses which are descendants of horses brought here by the Spanish.

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Part III Chapter 43 History of Life On Earth

Chapter 43 History Of Life On Earth The Big Bang Theory says that about 14 billion years before present (BYBP) an explosion produced all matter which started expanding outward. Galaxies formed and solar systems formed in the galaxies which formed. Our galaxy (the Milky Way) formed about 12 billion years ago, and our solar system and earth about 4.6 billion years ago. The planet was not hospitable in terms of what we now have. There was no oxygen in an atmosphere that was the result of volcanic outgassing. The atmosphere was rich in CO2, methane, ammonia and H2S (recent studies challenge this list). The atmosphere was suitable for what we now describe as simple prokaryotic extremeophylls. There are prokaryotic organisms today living in some of the most extreme habitats on earth (deep sea thermal vents, hot acidic springs like those in Yellowstone National Park and elsewhere). Abiogenesis is the theory that a very simple living organism spontaneously developed in the harsh conditions about 3.5 billion years ago, maybe even earlier and that it was able to replicate. The theory of abiogenesis also stipulates that in small incremental steps additional features were acquired by this entity which was capable of duplicating. Eventually a simple prokaryotic organism resulted. There are fossilized "stromatolites" (prokaryotes, Cyanophyta) that are radioisotope dated to about 3.5 BYBP. Photosynthesis must have evolved soon afterwards (perhaps a mere 100 or million years). We know for certain that there was a transition from oxygen free earth to an atmosphere rich in oxygen due to change (oxidation) of older iron deposits from reduced iron Fe+2 to Fe+3 in deposits which are not as old. This transition took place from 3 BYBP to 2 BYBP. The theory of abiogenesis requires the following ingredients: heat, lightning, methane, ammonia, carbon dioxide and water. The theory suggests that given enough time a very simple self replicating organism would evolve from the non-living primordial soup. There are only two other ways to explain life on earth: 1) life arrived from an extraterrestrial source like a comet which traveled from a source that had life, or 2) creation. Science by definition can only attempt to explain abiogenesis or the theory that life was "seeded" so-to-speak. Science can only test the theory of abiogenesis in the lab and that was what Stanley Miller did in 1953 (see illustration below). Miller created amino acids among other things and amino acids are the building blocks 178

Part III Chapter 43 History of Life On Earth of proteins. Subsequent experiments have produced simple polypeptides, simple membranes but no experiments have produced anything meeting the definition of life. We define living as: 1. Life must be a membrane bounded system with differential permeability (can be different than its environment) 2. Life must acquire matter or energy and harvest energy by means of metabolic processes 3. Life must have a genetic system that can coordinate metabolic activity and replicate

Figure 43.1 Stanley Miller’s Apparatus

Sometime after 3 BYBP Eukaryotes evolved (probably @ 2 BYBP) and the most widely accepted theory is that of "Endosymbiosis." Multi-cellular organisms like sponges first appeared about 1 BYBP. So nearly 2 billion years passed while oxygen was added to the water and atmosphere while evolution slowly produced aggregate simple multi-cellular animals. The most primitive animals are invertebrates, they lack an internal skeleton. After about another half billion years invertebrate animal diversity exploded with new life forms. This period is called the "Cambrian Explosion" which was centered in time about 543 MYBP. The seas teamed with invertebrate life forms but the terrestrial ecosystems would seem quite strange by today’s standards. The terrestrial ecosystems were dominated by Bryophytes (small moss-like plants). Animals on land were limited to insects, worms, etc. Forests of giant ferns and horsetails would not be common until the carboniferous period. This evolution of plant ecosystems on land is referred to as the “terrestrialisation” or colonization of land surfaces by life on planet earth. Animals in the oceans were more diverse than on land but still lacking key evolutionary steps. 179

Part III Chapter 43 History of Life On Earth First was the evolution of a stiffening rod running the length of the body and a respiratory system which could facilitate higher activity levels. These two features were seen in "mitrates." Mitrates were small fish-like creatures with a notochord (stiffening rod which facilitates faster swimming) and anterior pharyngeal gill slits which increased breathing efficiency. Mitrates appeared about 450 MYBP and are believed to be the ancestors of the first fish, the Ostracoderms. Ostracoderms were small detritus feeders shoveling food into their unhinged jawless mouths. The Cambrian seas were dangerous places with all kinds of invertebrate creatures that could eat a fish. The evolution of a jaws from the forward pharyngeal gill supports meant they could swallow larger food items. The embryological development of all vertebrates shows us how the jaws develops. There now was "evolutionary pressure" for these jawed fishes to grow larger because being larger meant eating more food sources and at the same time avoiding large invertebrate predators. These first jawed fishes were the Placoderms and the diversity of fishes that developed 400 MYBP was the Devonian Period or "Age of Fishes." Some of the Placoderms got quite large even by today's standards of predators such as the Great White Shark. The jawless Ostracoderms are survived today by a few dozen highly specialized jawless fish called Lampreys and Hagfishes.

The Placoderms are survived today by three major lines of evolution: 1) the sharks, skates and rays which are the cartilaginous fishes numbering just about 350 species, and 2) the boney fishes line of evolution (which includes about 30,000 species of fishes) and 3) the lobefin line of fish evolution (which developed muscular lobed fins and a lung from their ancestor's air bladder). There are only a handful of fish species alive today that are descendants of the early lobefins. These are the lungfishes and Coelacanth. The Coelacanth was thought extinct 70 MYBP but rediscovered in the period before and after WWII. Imagine the excitement of finding a species that was a contemporary of T. rex! Only the oceans are capable of hiding such an animal from science for so long. The remainder of this line left the water! Invasion of the land by vertebrate animals began where the water met the land. The first descendants of lobefins that ventured out of the water found an abundance of invertebrate animals for food and no predators what-so-ever. This line of evolution produced the amphibians. The amphibians that survive today are still tied to water for reproduction. Most amphibians have fish-like larval stages (e.g., tadpole) with gills. As some of the amphibians adapted to terrestrial life they developed scaly skin to prevent water loss and became shelledegg layers so they would not need to lay eggs in water. These were the reptiles and the "Age of 180

Part III Chapter 43 History of Life On Earth Reptiles" was from 235-65 MYBP. About two-thirds of way through the "Age Reptiles" the first mammals appeared (100 MYBP).

Figure 43.2 Early mammals that coexisted with dinosaurs.

An asteroid that struck near the Yucatan 65 MYBP put the earth into an extended winter and spelled an end to large reptiles. Aquatic reptiles, small reptiles and small feathered reptiles survived. So did the mammals which were also small animals. The survivors would provide the genetic stock for all future reptiles, birds and mammals. Humans are the pinnacle of mammalian evolution. Humans are in the Mammalian Order of Primates. The fossil record shows that primates first appeared about 55 million years ago. They were small arboreal species more like today’s lemurs than monkeys. Monkeys appeared 33 MYBP. DNA evidence suggested that apes diverged from monkeys sometime between 25 and 30 million years ago and recently Oligocene (23-34 million years old) fossils produced both monkeys and apes, confirming DNA studies. It was not until about 10-20 MYBP that the ape line of primate evolution produced the human-ape split (46 vs. 48 chromosomes). The genus Homo appeared 2 million years ago and Homo sapiens about 200,000 years ago. Another man (Homo neanderthalensis or possibly a sub-species of Homo sapiens) migrated into Europe 350,000 years ago. Between about 80,000 and 40,000 YBP modern man migrated north and east out of Africa and the result was the extinction of Neanderthal man about 35,000 YBP. It is believed Homo sapiens was in Australia as early as 50,000 YBP. Man arrived in North America 13,000 YPB, Central America 3000 YBP and South America 1000 YBP. The invasion of North America required a land bridge which resulted from the last Ice Age lowering ocean levels.

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Time Line For Major Evolutionary Events and Noteworthy Findings Years Before Present Event 14,000,000,000 Big Bang @14+ million years ago; galaxies formed about 2 million years later 4,600,000,000 Earth Formed 4.6 Billion Years Ago; (all the isotopes of elements in original ratios) 3,500,000,000 Prokaryotes evolved over 3 billion years ago (BYBP) 3,500,000,000 fossil Stromatolites, Cyanophyta, dated 3.5 BYBP) 3,000,000,000 Prokaryotes widely established 3 Billion Years Ago 2,000,000,000 Eukaryotic organisms evolved (Endosymbiotic Theory) 1,000,000,000 Note: 1 billion years ago is 1000 million years! Multicellular Invertebrates 543,000,000

543 MYBP (=0.543 Billion) was the Cambrian Explosion (of invertebrate life forms in oceans)

450,000,000 450 MYBP first pre-fish appeared 400,000,000 400 MYBP was the Age of Fishes (Devonian) 333,000,000

333 MYBP was the Carboniferous Period (fern or "coal" forests; terrestrial animals with mostly invertebrates)

250,000,000 Bacteria trapped in salt deposits Permian Salado Formation in New Mexico 1 200,000,000 235-65 MYBP the Age of Reptiles 100,000,000 100 MYBP small mammals during Late Triassic 70,000,000 70 MYBP Lobefin fish Coelacanth thought to be extinct! 65,000,000

65 MYBP Dinosaurs extinct ; survived by birds, crocdilians and small reptiles and "Proto-Primates"

55,000,000 Primitive arboreal primates 33,000,000 Monkeys appear 28,000,000 28 MYBP Megalodon appears; Monkeys and Apes diverge 15,000,000 20-10 million YBP the line of primate evolution - Homo sapiens diverged from apes 2,000,000 2.0 MYBP Genus Homo appears 1,500,000 1.5 MYBP Megalogon extinct? 350,000 early Neanderthal man in Eurasia 200,000 250,000 - 150,000 years ago homo sapiens (Mitochondrial eve) 72,000 77,000 to 66,000 years ago human genetic bottleneck (Mt Toba) 50,000 80,000 to 40,000 YBP Home sapiens migrates north and east, even to Australia 35,000 Neanderthal man extinct 13,000 Man arrives in North America via land bridge 3,000 Man arrives in Central America (Maya) 1,000 Man arrives throughout South America; 10 million Incas 70 Coelacanth rediscovered! 0 Present; 1 dormant bacteria cultured; origin debated 182

Part III Chapter 40 ??

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