Bio exam 2 study guide questions ch 5 6 7 PDF

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Summary of material covered for test 2 for Dr. Whitehead's BIOL 1030; study guide for test 2; Fall 2015...

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Biology 1030 Exam 2 Study Guide Questions Chapter 5: The Working Cell 1) Describe the steps in the model of active transport that was presented in class.  2) What is the purpose of active transport?  To move molecules against the concentration gradient. This allows cells to maintain internal concentrations that are different from external concentrations. 3) How are large molecules moved across plasma membranes?  Exocytosis  Endocytosis 4) Describe two kinds of endocytosis.  Phagocytosis = “cell eating,” the cell engulfs large molecules and brings them into the cell  Receptor-mediated endocytosis = large molecules are taken in through receptors, use coated vesicles, very specific 5) Explain the difference between kinetic energy and potential energy. Why is chemical energy important?  Kinetic energy – motion  heat, light  Potential energy – due to location/structure  Chemical energy is important because it is found in chemical bonds and determined the energy in reactions 6) What is the first law of thermodynamics?  The energy in the universe is constant 7) Why does energy “flow” rather than “cycle”?  Transformation of energy from one form to another  In any transformation, heat is lost  Energy does not cycle because all energy comes from the sun and will not return to the sun like in a cycle. The ultimate fate of all energy in ecosystems is to be lost in heat. 8) Be able to describe the levels and movement of energy in endergonic and exergonic reactions (what levels are in the reaction products? The reactants? Is energy absorbed from or released to the environment?) Is cellular respiration exergonic or endergonic? Photosynthesis?  Endergonic: energy released  surroundings o The bonds being formed are stronger than the bonds being broken  Endergonic: energy is absorbed from the surroundings o The bonds being formed are weaker than the bonds being broken  Cellular respiration is exergonic o Creates chemical energy from organic molecules  Photosynthesis is endergonic o Uses light energy to form organic molecules to store as energy 9) What is energy coupling? Explain the ATP cycle.  Energy coupling = the use of energy released from exergonic reactions to drive essential endergonic reactions (crucial ability of all cells)  ATP Cycle

o Energy from cellular respiration (exergonic) is used in ATP synthesis (endergonic), ATP hydrolysis is exergonic, energy released by ATP to ADP is used for cellular work (endergonic)

10) Why is phosphorylation important?  Phosphorylation puts the third phosphate on ADP to make it ATP, ATP is a functional currency of energy. ADP cannot be used for energy. 11) Explain energy barriers/activation energy. How do enzymes help overcome energy barriers?  In order for energy to be released, the energy barrier must be overcome. An energy barrier is called the activation energy of a reaction. Enzymes help overcome energy barriers so that the reaction can take place by lowering the activation energy.  An enzyme has an active site, which holds the reactants in a particular way to facilitate the bonding or bond breaking. 12) Explain the steps in the catalytic cycle of enzymes (sucrase?)

13) Why are optimal conditions important for enzymes? What are cofactors?  Optimal conditions are important because environmental factors like temperature and pH can alter the shape of enzymes. Form fits function for

enzymes, therefore a change in form can disable an enzyme. Optimal conditions are the conditions in which enzymes are the most effective in facilitating reactions.  Cofactors are required non-protein “helpers” for enzymes. 14) Describe competitive inhibitors, noncompetitive inhibitors, and feedback inhibition in relation to enzymes. Why is inhibition of enzymes important?  Competitive inhibitors = competes for same active site, but no reaction takes place; “stuck” to active site to prevent the enzyme from bonding to active site  Noncompetitive inhibitors = interacts with enzyme, not at active site, changes shape of enzyme so it can no longer work  Feedback inhibition occurs when the end product of a reaction interferes with the enzyme that helped to produce it. It deactivates an enzyme by binding to a second active binding site that’s different from the one attached to the initial reactant. This changes the shape of the enzyme and thus deactivates it.  Enzyme inhibition is important in metabolic control. Blocking an enzyme’s activity can kill a pathogen or correct a metabolic imbalance. Many drugs are enzyme inhibitors. Too many reactions can be as dangerous as too little. Chapter 6: How Cells Harvest Chemical Energy 1) What are the two processes that provide the energy for life? How are they connected? In other words, compare the products and reactants for photosynthesis and cellular respiration and use them to explain why the two pathways are said to be interdependent.  Two processes that provide the energy for life o Cellular respiration  Glucose and oxygen are used to create CO2 and H2O  Glycolysispyruvate oxidationcitric acid cycleoxidative phosphorylation (ETC)  Glucose is oxidized, oxygen is reduced  Cell captures energy (ATP)  exergonic o Photosynthesis  CO2 enters stoma, H2O enters veins, light captured by pigments  glucose and O2  Water is oxidized, CO2 is reduced  Energy from the sun is consumed  endergonic  Produces organic molecules and O2 in chloroplasts to be used in cellular respiration in the mitochondria, ATP powers most cellular work, CO2 and H20 (products of cellular respiration) return back to the environment to facilitate photosynthesis 2) What is the difference between breathing and cellular respiration? In your body, how are they connected?  Breathing is the inhalation of oxygen, exchange of gases in the alveoli of the lungs to oxygenate the blood, and the exhalation of carbon dioxide  Cellular respiration (aerobic respiration) is the chemical processing of converting food to energy 3) What are the reactants, products and overall objective of cellular respiration?  Reactants: C6H12O6 + 6O2  Products: 6 CO2 + 6 H2O + energy (ATP and heat)  Overall objective: create ATP to be used for cellular work 4) How do cells extract the energy in glucose to use for their cellular processes?

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Glucose molecules are broken apart and rearranged to make products of CO2 and H2O  Energy is stored in the chemical bonds of ATP 5) Define oxidation-reduction reactions. What happens during oxidation? What happens during reduction? Are these types of reactions paired together?  Type of chemical reaction that involves a transfer of electrons  Oxidation is the loss of electrons  Reduction is the gain of electrons  They are paired together because the electrons are transferred 6) What coenzymes (2 main ones) are used in cellular respiration, and what are their reduced and oxidized forms?  NADH and FADH2  NAD+ and FAD+ 7) Describe the general location, structure, and function of an electron transport chain (include in your description the analogy of a staircase).  Inner mitochondrial membrane  Several electron carrier protein complexes embedded in membrane  Create a proton gradient and pump H+ in inner membrane space 8) Explain the basic concept of chemiosmosis.  H+ flows back through ATP synthase, causing ATP synthase to spin, phosphorylates ADP to ATP 9) What is the net energy yield of each stage of aerobic respiration?  Glycolysis  2 ATP  Citric acid cycle  2 ATP  ETC  32 ATP 10) Briefly describe what happens to one glucose molecule as it passes through the steps of glycolysis.  Glucose is energized using ATP o Glucose  glucose 6-phosphate  fructose 6-phosphate  fructose 1, 6-biphosphate  A six carbon intermediate splits into two three carbon intermediates o (glyceraldehyde 3-phosphate)  A redox reaction generated NADH  2 ATP and 2 pyruvate are produced 11)What are the two stages of glycolysis? How do they differ in terms of use or manufacture of ATP? What are the final products of glycolysis?  Preparatory phase: ATP is consumed  Pay off phase: ATP is produced  Final products of glycolysis are 2 NADH and 2 pyruvate 12)Describe the three step process of pyruvate oxidation. What comes out of pyruvate oxidation (What is the end result that enters into the citric acid cycle?).  Carboxyl group removed and oxidized  Reduction of NAD+ to NADH  Coenzyme A combines with oxidized pyruvate to become Acetyl CoA  Acetyl CoA, 2 ATP, and 4NADH enter the citric acid cycle 13) From one glucose molecule, how many NADH, FADH2, and ATPs are produced in the citric acid cycle? What type of phosphorylation is used to make the ATP during citric acid cycle?  One glucose molecule  3NADH, 1 FADH2, and 1 ATP  Substrate-level phosphorylation

14) By the end of the citric acid cycle, from one glucose molecule what is the total NADH and FADH2 production? (Include the yield from the previous portions of cellular respiration)  6 NADH  2FADH2 15) Explain how electron transport chains in the mitochondria receive electrons. (Which molecules donate them?)  The NADH and FADH2 produced in the previous steps donate the electrons for the electron transport chain 16) What happens to hydrogen ions (protons) as electrons pass down an electron transport chain? Where inside the mitochondria does this gradient form? Where is the concentration of protons highest?  The hydrogen ions are pumped through the ETC proteins using the energy lost by the electron.  The protons move from the mitochondrial matric to the intermembrane space.  The concentration of protons is highest in the intermembrane space. 17) What is produced as hydrogen ion (protons) flow down their gradient and through what enzyme in the membrane? What type of phosphorylation is this?  ATP is produced as the protons flow back through ATP Synthase  Oxidative phosphorylation 18) What happens to the electrons once they get to the end of an electron transport chain? What role does oxygen play? And what compound is formed as a byproduct at this point?  The electrons are released by the ETC at a low energy level and attach to oxygen  Oxygen is the terminal electron receptor  Water is formed as a byproduct of this 19) Compare and contrast aerobic respiration and fermentation.  Both start in cytoplasm with glycolysis and produce 2 ATP  Aerobic respiration moves to the mitochondria and continues with Acetyl CoA formation, the citric acid cycle, ETC, and oxidative phosphorylation. This produces 34 more ATP, with oxygen as the terminal electron acceptor  Fermentation starts and ends in the cytoplasm, oxygen is not the terminal electron acceptor, NAD+ is regenerated, only produces 2 ATP 20) How do organisms recycle NADH (to regenerate NAD+) through cellular (aerobic) respiration? What about through fermentation?  Cellular respiration o The NADH produced in step 1 and step 2 are used in step 3 to donate electrons to the electron transport chain. NADH is oxidized back to NAD+  Fermentation o Pyruvate is reduced, NADH is oxidized to NAD+ 21) What evidence do we have that glycolysis was one of the first energy-harvesting metabolic processes?  All 3 domains use glycolysis o LUCA – last universal common ancestor was capable of glycolysis  Glycolysis does not require oxygen o No oxygen in the atmosphere 3.5 billion years ago  Occurs in cytoplasm, no need for membrane

o Prokaryotes didn’t have membranes, only prokaryotes 3.5 billion years ago 22) Is glucose the only molecule that can enter the metabolic pathways of cellular respiration? List three other energy sources for cellular respiration (macromolecules/general categories), and have a basic understanding of how each can enter the pathways of cellular respiration.  Carbohydrates o Enter in glycolysis  Fats o Glycerol enters in glycolysis o Fatty acids enter in pyruvate oxidation  Proteins o Amino acids enter in anywhere Chapter 7: Photosynthesis 1) Distinguish between autotrophs (be able to differentiate between chemoautotrophs and photoautotrophs) and heterotrophs, and give examples of each. Are plants the only photoautotrophs?  Autotrophs are producers, they get their carbon from CO2 o Photoautotrophs = photosynthesis, light energy o Chemoautotrophs = energy from inorganic chemicals  Heterotrophs are consumers, they get their carbon from organic molecules 2) What are the raw materials that plants need for photosynthesis, and how are they obtained? Relate it to leaf anatomy.  Water comes in through the veins  CO2 comes in through the stomata  Energy to excite electrons comes from photons of light from the sun 3) Describe the structure of chloroplasts by using the following terms: stroma, thylakoid, thylakoid space, thylakoid membrane, grana, chlorophyll, inner and outer membrane.  Stroma = fluid inside the chloroplast  Thylakoid = double membrane structure within chloroplast  Thylakoid space = space between the outer and inner membranes of the thylakoid  Grana = stack of thylakoids  Chlorophyll = substance the absorbs light, green color, important for conversion of solar energy to chemical energy  Inner membrane = membrane within a thylakoid, location of ETC  Outer membrane = membrane that surrounds the thylakoid as a whole 4) What are the basic reactants and products of photosynthesis? Which reactant is reduced and which is oxidized in photosynthesis? Where does the oxygen of each reactant go in the product molecules? How do we know this?  6CO2 + 6H2O  C6H12O6 + 6O2  CO2 is reduced, H2O is oxidized  CO2 oxygen  glucose and water  H2O oxygen  O2 release  We know this because scientists traced the process of photosynthesis using isotopes 5) What are the two stages of photosynthesis and where do they occur? What are the reactants and products of each stage, and how are the two stages linked?

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Light reactions o Occur in thylakoid membrane o Reactants: light, H2O o Products: CO2, ATP, NADPH  power dark reactions  Dark reactions o Occur in stroma of thylakoid membrane o Reactants: CO2, ATP, NADPH (From light reactions) o Products: G3P 6) What is nicotinamide adenine dinucleotide phosphate (NADP+) and what are its reduced and its oxidized form?  NADP+ is an electron carrier  Reduced = NADPH  Oxidized = NADP+ 7) How is wavelength of light related to its energy?  As wavelength decreases, energy increases 8) What are the things than can happen during the interaction between electromagnetic radiation and molecules/matter? How does this relate to an object’s color. Which is the only interaction in which energy is captured to be used in biological systems? What happens to electrons in pigment molecules when they absorb a photon of light?  Light can be absorbed, transmitted, or reflected  The light that is transmitted or reflected gives the object it’s color  Photosynthesis is the only interaction in which energy is captured to be used in biological systems  Electrons in pigment molecules become excited when they absorb a photon of light 9) What is a photosystem, where are they located, and how do they respond to solar energy?  A photosystem is a light harvesting complex that captures and absorbs light energy, and consists of pigments and a primary electron acceptor  Located in the thylakoid membrane  When a photon of light is absorbed, it passed from pigment to pigment, then excites an electron, which jumps up to the primary electron acceptor, which passes the electron on to an electron transport chain 10) Describe the proper sequence of events of how electrons are excited, flow, and are replaced in photophosphorylation.  11) What are the products of photophosphorylation, and what role do electron transport chains play in this process?  12) Explain in detail how ATP molecules are formed in a chloroplast by chemiosmosis. (What types of gradients are formed, where, and how?_  13) What is ATP synthase, and what role does it play in chemiosmosis? How does it work?  ATP synthase is an enzyme embedded in a membrane. In chemiosmosis, H+ protons flow back down the gradient through ATP synthase. This spins a motor in the ATP synthase which enables it to attach a third phosphate group to ADP, thus creating ATP 14) Compare and contrast cellular respiration and photosynthesis. 

15) What is the connection between the light reactions and the Calvin cycle? (What is produced in the light reactions and required for the Calvin cycle?)  The CO2, ATP, and NADPH produced in the light reactions is required for the Calvin cycle to take place 16) What is the location and what are the requirements for the Calvin cycle?  The Calvin cycle occurs in the stroma of the chloroplast  Requires CO2, ATP, and NADPH 17) Be able to give a general description of the Calvin cycle (what are the four steps and what occurs in each of them?) In the stroma of the chloroplast: 1) Carbon fixation o CO2 binds to RuBP sugar with help from Rubisco, 6-C splits into two 3-C PGA molecules 2) Reduction Phase o 3-PGA is converted into G3P with help of ATP and NADPH from light reactions 3) Carbohydrate formation o G3P turned into carbohydrates with ATP from light reactions 4) Regeneration Phase o G3P + ATP used to make RuBP, which starts the cycle again 18) What is the fate of G3P molecules that are produced at the end of the Calvin cycle reactions? Can they only form one type of macromolecule?  One G3P molecule leaves the cycle to be stored in glucose and other compounds  Other 5 G3P molecules are reused in the cycle...