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UVM BCOR 103 - Unit 1 Study Guide

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Questions BCOR 103/MMG 196/BIOL108Lecture 1: Intro to the CourseNothing to review here. Lecture 2: Origins and Biomolecules. 1. Describe Stanley Miller’s experiment.2. What is the “RNA World Hypothesis?”3. Describe the evolution of metabolism? 4. What process is believed to brought about the existence of mitochondria and chloroplasts in eukaryotic cells? 5. Compare/contrast prokaryotes and eukaryotes.6. Be able to describe covalent, ionic and hydrogen bonds? 7. What is the difference between hydrophilic, hydrophobic, and amphipathic molecules? 8. What is the main function of: a) carbohydrates, b) lipids, c) nucleic acids, and d) proteins? 9. What is the general structure of carbohydrates? What bond joins the monomers together?10. Be able to count carbons in a sugar molecule11. Name at least 2 complex sugars and describe their main role.12. What are some common features of all phospholipids?13. Describe the most common components of phospholips. 14. If a lipid head group contains a glucose instead of a phosphate group, what is it called? 15. Compare/contrast DNA and RNA16. Be able to name the reaction AND bond that holds nucleotides together.17. Know the difference between a nucleic acid, a nucleotide and a nucleoside?18. Be able to name the purines and pyrimidines and know how they pair together.Lecture 3: Amino Acids, Proteins, and Enzymes1. What are the three common features of all amino acids? 2. Be able to list some common functions of proteins.3. Be able to draw and label the parts of an amino acid4. How is the structure of hydrophobic and hydrophilic amino acids different? Be able to label an amino acids as hydrophobic, hydrophilic, acidic, or basic.5. Name the bond that holds amino acids together and describe which parts of the amino acid interact to form this bond.6. What are the differences between a primary, secondary, tertiary, and quaternary proteinstructure? 7. What type of bond underpins the structure of the alpha helix as well as the beta sheet? 8. What is a prion? 9. Why are enzymes important?10. What are to important properties of all catalysts? 11. How does an enzyme speed up a reaction?12. What is the difference between lock and key and induced fit models of enzyme function? 13. What are cofactors?14. Feedback inhibition of isoleucine on threonine deaminase is an example of what? 15. Where on the enzyme do substrates bind? Is this different than where coenzymes or enzyme inhibitors bind? 16. What can phosphorylation of an enzyme do? Lecture 4: Membrane Structure1. What property of lipids allow them to spontaneously form membranes when exposed toan aqueous environment? 2. Be able to list some of the important roles proteins play in a cell3. In what ways can and can’t lipids move in a membrane? 4. Describe the structure of a phosphoglyceride, a sphingolipid, and a glycolipid.5. How does cholesterol fit into a membrane? 6. Why is cholesterol considered a fluidity buffer? 7. What factors can affect membrane fluidity?8. Describe what lipid rafts are and why scientist think their role is.9. What membrane components are only found on the outside of the cell? 10. What are the main differences between: a) integral membrane proteins, b) peripheral membrane proteins, and c) lipid-linked membrane proteins? 11. Why is it important that an alpha-helix anchored membrane protein has consecutive hydrophobic amino acids? 12. Which class of integral membrane proteins can form channels through the cell membrane? 13. How many transmembrane domains does a G-protein coupled rector (GPCR) have? Does this structure form a channel? 14. What are two ways that a peripheral protein can associate with the membrane? 15. What must a lipid-linked protein contain that allows it to associate with the inside of the phospholipid bilayer? 16. Why does it make sense to sometimes limit the mobility of membrane proteins? Lecture 5: Membrane Transport1. At rest, is in the inside of the cell negatively charged or positively charged? 2. At rest, what is the concentration gradient of Na+ and of K+? If we allow these ions to move, where will they move? 3. What are the three types of membrane transport? Which ones require energy?4. Why can’t everything diffuse across the membrane? 5. Do channels require energy? How about pumps?6. What are the three different ways that we can control when a channel is open or closed (i.e. gating)?7. What component of a voltage-gated channel structure creates a selectivity to specific ions? 8. What component of a voltage-gated channel structure responds to a voltage change in the cell? How does this work? 9. Can you provide an example of a functioning protein in the form of a tertiary structure? Quaternary structure? 10. How is a channel different from a carrier? 11. How can a carrier move something against its concentration gradient without using energy? 12. Can you describe the structure of each of the channels and transporters described in class and how they work?13. What is the difference between the T domains and the A domains on an ABC pump? Why is it important that the A site faces the intracellular space? 14. Why does the Na+/K+ pump require energy? If the Na+/K+ uses so much energy, then why is it important that this protein is always functioning? Lecture 6: Metabolism 1. What does it mean when G is negative? Positive? 2. How can a reaction proceed in the unfavorable direction? What is the best example of how this is done? 3. Can you list 3 reasons why the hydrolysis of ATP is a favorable reaction, even if it involved the breakdown of bonds? 4. What is the main role of activated carrier molecules? What are the two examples that you need to know for this section? 5. What enters glycolysis? What is the end product of glycolysis? How many ATP molecules are required to perform glycolysis? How many ATP molecules are produced as a result of glycolysis? So what is out NET gain? 6. What is the difference between aerobic and anaerobic processes? 7. What are common products of 1) glycolysis, 2) the citric acid cycle, and 3) fatty acid oxidation? Why are these products important? 8. How does the citric acid cycle function as a “cycle?”9. What happens to the extra carbons atoms in the citric acid cycle? 10. In the electron transport chain, what is the role of complexes 1-4? 11. What is the purpose of having a double membrane in mitochondria? 12. In the electron transport chain, what is the role of complex 5 (the ATP Synthase)?

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