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Biology- Organisms Exam 2 Course Notes

by: Lauren Maddox

Biology- Organisms Exam 2 Course Notes bio 114

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Lauren Maddox

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These course objectives are for Exam 2, covering Photosynthesis.
Biology of Organisms (Bio 114)
Dr. Oliver Hyman
Study Guide
Biology; Science; Organisms; Bio 114
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This 9 page Study Guide was uploaded by Lauren Maddox on Saturday March 12, 2016. The Study Guide belongs to bio 114 at James Madison University taught by Dr. Oliver Hyman in Spring 2016. Since its upload, it has received 64 views. For similar materials see Biology of Organisms (Bio 114) in Biology at James Madison University.


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Date Created: 03/12/16
Photosynthesis Students should be able to: 1. Describe the evolutionary significance of photosynthesis and list several ways in which photosynthesis benefits organisms on Earth. Photosynthesis first evolved in prokaryotes. In 2.7 bya. Cyanobacteria were the first to introduce oxygen into the atmosphere. They were just doing it on the membranes throughout cytosol. Diatoms-single celled protists. Produce half of organic C and O2 in oceans. Green algae do it. Terrestrial Eukaryotes-land plants. It happens in the chloroplast, primary producers for terrestrial food chains. You can outcompete organisms that cant do photosynthesis. Oxygen accumulates in the atmosphere. Allows for evolution and diversification of organisms using O2 for cell respiration. Has formed the ozone layer-protects us from UV radiation. It has a key role in carbon cycling- takes carbon out of atmosphere and uses it to make photosynthesis. It removes anthropogenic CO2. It influences our temperature. Bacterial cells that evolved the ability to use it as an electron acceptor via cellular respiration. These organisms can use much more ATP. Enables cell respiration. Research showed that photosynthesis consists of 2 linked sets of reactions. One set is triggered by light, the other set- Calvin cycle- requires the products of the light capturing reactions. The light- capturing reactions produce oxygen from water; the Calvin cycle produces sugar from carbon dioxide. 2. Identify how matter and energy are transformed during photosynthesis. Matter is conserved: matter on the left side balances the matter on the right side. It is a transfer of energy from light energy to chemical energy in reduced carbon molecule; sugar . Light-energy+ H2O + CO2- --à O2 + chemical energy in the many C -H bonds of sugar . The light energy is captured in a way that is transferred to chemical bonds - light energy from sun to chlorophyll to the primary reaction center to ATP. Called the antenna complex. Photons (light energy) strike a pigment molecule in the antenna complex, the energy is absorbed and an electron is excited in response. This is known as resonance energy transfer. Only happens between pi gments that absorb higher energy photons to those absorbing lower energy photons. Once the energy is transferred, the original excited electron falls back to its ground state. Energy is transferred inside the antenna complex. Then it goes to the reaction center- its excited electron is transferred to an electron acceptor. Electromagnetic energy is transformed to chemical energy. 3. Write the equation for photosynthesis. Identify the stages of photosynthesis in which each reactant is used, each product is produced, where these reactions occur, and the major reduction and oxidation reactions within photosynthesis. 6CO2 + 6H20 à 6O2 + C6H12O6 The carbon in the CO2 and the sugar is reduced. The Oxygen in water and oxygen is oxidized. Light capturing reactions-occur in thylakoids in chloroplast, h20 to o2. Atp and NADPH are produced for the Calvin cycle. The Calvin cycle occurs in stroma- space outside of thylakoids. Atp and NADPH used to reduce co2 to sugar. Resulting sugar used in cellular respiration. It converts CE from light-capturing reactions into chemical energy in sugars. 4. Explain how the light reactions and Calvin Cycle are linked together and how this impacts the time of day that the light reactions and Calvin cycle take place in most plants. They both happen in the chloroplast. Calvin cycle can only use ATP available in the chloroplast from light reactions. Takes place in the day because that is when light reactions occur. 5. Identify all the “forms” (ex. Carbon in sugar or protein or another CO 2molecule) that a carbon atom from a CO 2 molecule in the atmosphere can assume when moving through the carbon cycle (ex. Sugar/starch/cellulose within a plant, CO2 in atmosphere, or sugar/protein/glycogen in a chemoheterotroph. Identify the processes that drive these transformations (cellular respiration, photosynthesis, biosynthesis, storage, etc.). See cycle you did in class and try to draw your own and see how many carbon transfer steps you can come up with). Process Plants Animals Cell respiration C from sugar made by C from consumed plant to C in CO2 sugar converted to C in CO2 Photosynthesis C from CO2 converted NA to C in sugar Biosynthesis C from CO2 converted C from consumed to C in amino acids, sugar converted to C nucleotides and fats, in amino acids, etc. nucleotides, fats, etc. Storage C from CO2 converted C from consumed to C in starch, sugar to C in eventually to C in glycogen, eventually CO2 to C in CO2 Decomposition C from sugar, amino Same acids, nucleotides, fats, starch, glycogen in dead animals and plants converted to C in CO2 by respiration of decomposers 6. Predict the impact that changes in photosynthesis and cell respiration have on the mass of a plant and the CO2 levels in the plant’s environment and why (see problem you did in class) Photosynthesis makes them gain mass, respiration makes them lose. Plants take in more CO2 than they release. They have a net uptake of carbon. In light- co2 is less In dark- co2 is greater, mass is lost 7. Retain knowledge from Exam I to identify similarities and differences between photosynthesis and respiration. Both produce ATP. Different reactants—opposite. Photosynthesis can only occur in sunlight, in respiration sunlight isn’t required. In CR- oxygen is absorbed and co2 is released. In Photo- co2 is absorbed and oxygen is produced. In CR- releases energy, photo requires it. Both use electron transport chain. Photosynthesis is an endergonic suite of redox reactions that produce sugars from carbon dioxide and light energy. Cellular respiration is an exergonic suite of redox reactions that produces carbon dioxide and ATP from sugars. Evolution by Natural Selection 1. Explain the relationship between the terms “evolution” and “natural selection”. Individuals are naturally selected. Populations evolve. All organisms distant from a common ancestor, all organisms evolve through natural selection. 2. List Darwin’s criteria for natural selection and identify these criteria in an example/story of natural selection Individual organisms that make a population vary in traits, some of the trait differences are heritable (coded for in DNA), more offspring are produced than can reproduce so some will reproduce more than others, those that survive best and reproduce most are not a random sample from the population. Natural selection occurs when individuals with certain heritable traits produce more offspring than individuals without those traits. Dot organisms—1. All circles, but different colors living in same area. 2. Purple give birth to purple, blue give birth to blue. 3/4. 2nd generation before reproducing run into predator, the 2 nd generation is all blue, and they reproduce blue. 3. Recognize common misconceptions that people have about evolution and natural selection and explain why they are wrong. 1. Evolution is like a climb up a ladder-organisms are always getting better and more complex- they are branched out. Evolution doesn’t always proceed in a direction of higher complexity (many times complex traits are lost due to natural selection. 2. selective pressures cause organisms to adapt- mutations in dna that lead to new characteristics that give an organism a survival advantage are random and happening all of the time. Selective pressures sort existing variants in the population. 3. Organisms evolve. Organisms can acclimate. Acclimation is not adaptation because the acclimated trait is not heritable. Populations evolve over generations. Organisms can’t evolve in a single generation. 4. In evolution, only the strong survive-some organisms will have different strategies to do things that stronger organisms cant- slides 5. Evolution perfects organisms- some traits are nonadaptive, some traits cannot be optimized due to fitness trade-offs, some traits are limited by genetic or historical constraints (ex. Finch beaks cannot be both deep and narrow, due to genetic constraints. Table in book: Misconception Correction Example Evolutionary change Natural selection Selection doesn’t occurs in organisms just sorts existing cause neck length to variants in increase in organisms; it individual giraffes, doesn’t change only in populations them. Evolutionary change occurs only in populations. Acclimatization doesn’t equal adaptation Adaptations occur Mutation, the Tapeworms are not because organisms source of new lower than their need or want them alleles, occurs by human hosts, just chance. Evolution is adapted to a not goal directed or different progressive. There environment is no such thing as a higher or lower organisms Organisms sacrifice Individual with Lemmings do not themselves for the alleles that cause jump off cliffs into good of the species self-sacrificing the sea to save the behavior die and do species not produce offspring, so these alleles are eliminated from the population Evolution perfects Some traits are Finch beaks cannot organisms nonadaptive. Some be both deep and traits cannot be narrow, due to optimized due to genetic constraints. fitness trade-offs. Some traits are limited by genetic or historical constraints. 4. List the different types of evidence used to support Darwin’s theory of evolution and provide examples of each. Vastness of geologic time- fossil record, rocks Extinction changes the species present over time- if species have gone extinct, then the array of species living on earth has changed over time. Transitional features link older and younger species-extinct forms and present forms have similar traits Vestigial Traits- traits that is useless. Prediction 1: Species are not static, but change through time • Life on Earth is ancient. Most species have gone extinct • Fossil (extinct) species frequently resemble living species found in the same area. • Transitional features document change in traits through time • Vestigial traits are common • The characteristics of populations vary within species and can be observed changing today Prediction 2: Species are related, not independent • Closely related species often live in the same geographic area • Homologous traits are common and are recognized at three levels 1. Genetic (gene structure and the genetic code) 2. Developmental (embryonic structures and processes) 3. Structural (morphological traits in adults) • The formation of new species, from preexisting species, can be observed today 5. Provide evidence to support the theory that all land animals evolved from fish. All have backbones 6. Define and list examples of analogous characteristics that arise through convergent evolution and homologous characteristics. Homologous characteristics- trait shared by 2+ taxa that was inherited by common ancestor (backbones). Analogous characteristics are shared but not from common ancestor. Convergent evolution- similar adaptations that evolve independently. Wings in birds and bats. 7. Recognize clues that suggest that the similarities in two species are due to convergent evolution and not inheritance from a common ancestor. 8. List examples of atavisms, vestigial traits and developmental homologies and explain how these examples support the theory that all organisms are related. Vestigial traits- a reduced or incompletely developed structure that has no function or reduced function, but is clearly similar to functioning organs or structures in closely related species. Phylogeny 1. Identify the parts of a phylogenetic tree. Node= common ancestor. 2. Correctly read and interpret a phylogenetic tree 3. Identify homologies, analogies, synapomorphies (and which monophyletic group they belong to), common ancestors (with identification of which lived most recently), parsimony, and different monophyletic groups on a phylogenetic tree. Monophyletic group- evolutionary unit that includes an ancestral population and all of its descendants but no others. Synapomorphy- trait found in 2+ taxa that is present in their most recent common ancestor but is missing in more distant ancestors. Paraphyletic group- a group that includes an ancestral population and some of its descendants, but not all. 4. Draw a tree of life for the 3 domains eukarya, archaea, and bacteria. 5. Explain why homologous characteristics should only be placed on a tree once (parsimony). We want the simplest tree. 6. Describe the experiments done by Carl Woese that resulted in our current tree of life with 3 domains. He compared nucleotide sequences in ribosomal RNA to study relationships. 1. Fundamental division NOT between prokaryotes and eukaryotes. 2. archaea and eukarya share a more recent common ancestor than archaea and bacteria. This common ancestor was likely a prokaryote with a complex RNA polymerase and histones. 3. Fungi more closely related to animals than plants 4. Microorganisms are way more diverse than we thought 5. Trees are always a work in progress. 7. Correctly place molecular and morphological characteristics of bacteria, archaea, and eukaryotes on the tree of life. slides Prokaryotes: Archaea and Bacteria 1. Give examples of the abundance and diversity (habitat, metabolic, etc.) of prokaryotes 700 species of prokaryotes, 90% of the cells in my body are bacterial or archaeal. They run the world. They are in mud, springs, lakes, oceans, radioactive waste, and the human gut. They are an energy source to make ATP- typically from oxidation of reduced C molecules like sugars or sunlight. They are a carbon source for synthesis of C-C bonds in organic molecules from organic C molecules from other organisms or simple molecules. They can do fermentation, aerobic, cell respiration, and anaerobic cell respiration. Most metabolic diverse, they can get energy from chemical or light, and can get molecules from themselves or already produced molecules. 2. Explain how prokaryotes have been able to introduce so much diversity into their population fast rate of reproduction, ability to exchange DNA 3. Explain the connection between metabolic and habitat diversity and be able to predict the kinds of electron donors and acceptors bacteria or archaea may use in a given environment. Sugar- e-donor. O2- e acceptor. It allows them to live in an environment where other organisms cannot, which lowers competition for resources. Co-exist with other prokaryotic species by cleaning up each other’s mess and again not competing for resources. 4. Sketch the nitrogen cycle and describe the role that different species of bacteria have in this cycle. 5. Provide examples of adaptations of psychrophiles and thermophiles and explain how these adaptations enable survival in extreme temperatures. Psychrophiles <15 C, death over 25 C. found mostly in cold ocean bottoms. Specialized membranes and proteins. Thermophiles- 50 C – 130 C. Found in compost piles, hot springs, ocean hydrothermal vents, artificial hot water areas. They have internal temps. 6. Predict the properties of bacteria isolated from various extreme environments (i.e. what will their membranes be like? What kinds of molecules might they use as electron donors or acceptors?) They have specialized cell membranes, and specialized proteins and DNA. Membranes are more permeable at high temps and less permeable at low temps. Thermophiles would have long, saturated phospholipids while psychrophilic would have short, unsaturated ones. At high temps, proteins and DNA denature- unfold. To prevent this- thermophiles have higher % of GC than AT in Non-Coding region of DNA. Their proteins have more charged amino acids. Resulting in more ionic bonds, which are stronger than H-bonds. 8. Describe binary fission and its consequences with regards to genetic variation. The specific type of asexual reproduction carried out by prokaryotes. Means divide in half. Chromosome attaches to cell membrane, chromosome (DNA) is replicated, cell membrane pinches in “invaginates). Results in two daughter cells, which are identical to each other and the original parent cell. Low error rate, no genetic variation. 9. Distinguish between the 4 general methods for obtaining E and C-C bonds (auto/hetero and photo/chemo) Phototrophs- light feeders. Chemotrophs-chemical feeders. Autotrophs- self-synthesized (using simple molecules like CO2, CH4). Heterotrophs- other feeders, from molecules produced by other organisms (sugar, fat, protein, etc.). 10. Provide examples of how bacteria and archaea have been harnessed for human use bioremediation-process where microorganisms remove contaminants from the environment. Ex. Bacteria use a toxic compound as an electron acceptor or donor and convert it to co2 and water. Biofuels-fuels produced from living organisms—learning to convert high E (reduced) bacterial metabolites into sustainable energy sources. Using methane gas from landfills for power.


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