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1 Biol 205 Exam 1 TEST FORM A Spring 2008 NAME Fill out both sides of the Scantron Sheet. On Side 2 be sure to indicate that you have TEST FORM A The answers to Part I should be placed on the SCANTRON SHEET. The answers to Part II should be written directly on the exam. NO CALCULATORS OR CELL PHONES ALLOWED Part I: Multiple choice Questions. 2 pts. each. ONE POSSIBLE CORRECT ANSWER for questions 1-11 Answers shown in blue 1. A number of physiological changes occur when an animal hybernates. Its body temperature drops and the membrane composition of its cells changes. To maintain membrane fluidity, the lipid bilayers in a hybernating animal would show a(n) in the amount of unsaturated fatty acids and a(n) in the length of the hydrocarbon tails. a. increase, increase b. decrease, decrease c. increase, decrease d. decrease, increase 2. Which statement is incorrect with respect to passive transport facilitated by carrier proteins: a. the movement of an individual solute can occur in either direction, but the net flow of solutes is down the concentration gradient (from higher to lower) b. the conformation change in the carrier that is required to move the solute across the membrane is triggered by binding of the solute to a pocket in the protein c. carrier transporters are very specific with respect to the solute that they transport d. an energy source is not required 3. Custom genome sequencing is currently available for individuals who are willing and able to ante up a considerable sum of money: ~$300,000. How much per base pair does this price represent? Note: use the size of a single genome copy in this calculation. You do not need a calculator to answer this question. a. $1 b. 10 cents c. 1 cent d. 1/10 of a cent e. 1/100 of a cent 4. Which of the following would move through the lipid bilayer of a plasma membrane most rapidly (unaided by transporters)? a. O 2 b. an amino acid c. a nucleotide d. K + e. a very large hydrophobic molecule 5. A protein domain 1

2 a. is another term for the primary sequence of a protein. b. refers to a subunit in a multi-subunit protein (i.e., one that has quaternary structure). c. refers to the pattern of α-helices and β-sheets in particular parts of a protein. d. is a segment of a protein that can fold independently of the rest of the protein into its tertiary structure or conformation and is usually associated with a specific function of the protein 6. Most reactions in cells require enzymes because a. the free energy of the products is higher than the reactants. b. the free energy of the products is less than the reactants. c. their spontaneous (uncatalyzed) rates of reactions occur too slowly for cells to survive. d. they are more complex than other reactions in nature, such as the combustion of gasoline. e. they could never possibly occur without the action of a catalyst. 7. Some enzymes lower the activation energy for a reaction a. by bringing substrates close together in the active site. b. by bringing reactants close together between two different protein domains in the enzyme. c. by using the hydrolysis of ATP to provide the energy for a reaction to occur. d. by coupling the hydrolysis of ATP to a reaction requiring energy. e. by readily releasing the products of a reaction. 8. In order for a specific ligand to bind to a protein found in the cytosol, a. the protein must have a specific binding site in its tertiary structure in which the ligand fits. b. the protein must have a specific binding site in its secondary structure in which the ligand fits. c. the protein must have a specific binding site in its primary structure in which the ligand fits. d. the ligand must be hydrophobic to interact with the core, or central part, of the protein. 9. The α helix and β sheet are found in many different proteins because they are formed by a. hydrogen bonding between the amino acid side chains most commonly found in proteins. b. noncovalent interactions between amino acid side chains and the polypeptide backbone. c. ionic interactions between charged amino acid side chains. d. hydrogen bonding between atoms of the polypeptide backbone. e. hydrophobic interactions between the many nonpolar amino acids. You have purchased a filtration unit off the internet. It is supposed to purify water of any contaminating biological agent. When you read the fine print included with the product, you discover that the pore size is 10 µm. 10. What does µ (micro) mean? a b c c With this pore size, your water is likely to be contaminated with a. single-celled eukaryotes only b. viruses only c. both prokaryotic and eukaryotic cells d. viruses and prokaryotic cells 2

3 e. None of the above the product performs as advertised. QUESTIONS MORE MULTIPLE CHOICE BUT THERE MAY BE MORE THAN ONE CORRECT ANSWER. INDICATE ALL CORRECT ANSWERS 12. Prokaryotic cells differ from eukaryotic cells in that they a. use RNA as their genetic material. b. use DNA as their genetic material. c. do not have a membrane-bound nucleus. d. have a plasma membrane that is permable to some solutes but not to others e. have cytoplasm 13. Which of the following statements is(are) FALSE? a. Peptide bonds are the covalent bonds that link together two amino acids in proteins. b. The polypeptide backbone is free to rotate about each peptide bond. c. Nonpolar amino acids tend to be found in the interior of cytosolic proteins. d. The sequence of the atoms in the polypeptide backbone varies between different proteins. 14. Given what you know about the differences between procaryotic cells and eucaryotic cells, study of the model organism E. coli might provide a general (universally applicable) understanding of which of the following processes: answers given the full two points: b only, c only or b and c a. formation of the endoplasmic reticulum b. DNA replication c. how cells decode their genetic instructions to make proteins d. how mitochondria get distributed to cells during cell division 15. Which of the following statements about hydrogen bonds are TRUE? a. They are weak covalent bonds that are easily disrupted by heat. b. They are weak bonds formed between hydrocarbons in water. c. They are weak bonds formed between nonpolar groups. d. They are weak bonds involved in maintaining the conformation of macromolecules. 16. Which of the following statement(s) about amino acids is(are) TRUE? a. Twenty-two amino acids are commonly found in proteins. b. Most of the amino acids used in protein biosynthesis have charged side chains. c. Amino acids are often linked together to form branched polymers. d. All amino acids contain an NH 2 and a COOH group. 3

4 CHOOSE TRUE OR FALSE. ANSWER FALSE IF ANY PART OF THE STATEMENT IS INCORRECT. 2 PT EACH. 17. One "lesson" from the study of prions is that although the amino acid of a polypeptide will determine its shape, a given primary structure can result in more than one stable secondary and tertiary structure. This statement is TRUE 18. Even though it doesn t have cytoplasm, the mimivirus is thought to be more like a living organism than a typical virus because its genome is similar in size to a prokaryotic cell. This statement is TRUE PART II: WRITE YOUR ANSWERS TO THESE QUESTIONS DIRECTLY ON THE EXAM 1. (3 pts.) a b DNA mrna protein c DNA Next to each letter indicate the name (proper term for the process shown above. a transcription (copying a DNA sequence into RNA) b translation (converting the information in RNA into protein) c replication (copying an entire genome) 2. (3 pts.) Which of the two bases on the right will form the most hydrogen bonds with the base on the left? Circle: TOP or BOTTOM. Then defend your answer by showing H-bonds and indicating the critical difference between the top and bottom structure. The base pairing surfaces are facing each other. Don t worry about distance between atoms. The top purine forms two H-bonds and the bottom 3 H bonds with the pyrimidine 3. ( 8 pts.) 4

5 (3 pts.) Write out the complete formal name for this macromolecule: (Do not use its acronym and be sure to include the relevant number.) 2 deoxyribonucleic acid Pick from the list of term below an fill in the blank ( 5 pts total) The structure indicated by arrow # 1 is deoxyribose The structure indicated by arrow # 2 is a purine The functional group indicated by arrow # 3 is an amino or amine The general category of bond indicated by arrow # 4 covalent bond The general category of bond indicated by arrow # 5 non-covalent bond purine pyrimidine methyl hydroxyl carbonyl phospholipid carboxyl ribose deoxyribose phosphate amino acid ligand fatty acid steroid cholesterol phosphate amino methyl hydrophobic bond non-covalent bond covalent bond 5

6 4. (15 pts.) Non-mutated version of the gene codes for a leucine Mutated version of the gene codes for an aspartic acid aspartic acid 3 a. On one of the structures above, circle a carboxyl group and label it with a C 3 b. Circle the R-group on aspartic acid and label R 3 c. A researcher discovers that mutation (change) in the DNA sequence of a gene causes replacement of an isoleucine by an asparatic acid in the polypeptide coded for by the gene. The researcher isolates the mutant protein, examines its structure and says: "Oh my gosh, this cytosolic protein has been turned inside out." Using protein folding/structure terminology, briefly explain what she meant by this comment. Be sure to briefly discuss the bonding forces. 3 sentences (maximum) OR Draw a vcry clearly labelled diagram (schematic) to show what has happened. Label your diagram and include a one sentence caption 6

7 5. (15 pts) One of the themes that we will continue to explore this quarter is how specific cellular processes are controlled by modulating the activity level of specific proteins. In lecture we talked about a couple of mechanisms (see below) by which the function of a plasma membrane ion channel could be regulated such that it is either open or shut. Draw a detailed, schematic diagram which illustrates one of these strategies. Use simple symbols to illustrate the structure of the channel protein, the lipid bilayer (show generic components in a very schematic form) and the regulatory molecule. Indicate the extracellular and cytoplasmic face of the membrane. Be sure to provide a detailed key to your symbols (example: = regulatory molecule) You do not need to draw out any specific chemical structures (atoms, bonds etc.) PROVIDE a two sentence caption for your diagram to help the viewer understand the regulatory process. Use proper terminology Circle the mechanism that you choose to illustrate (and fill in the long blank if you choose #3): Mechanism 1: involved allosteric regulation of a channel protein that exhibited quaternary structure Mechanism 2: involved regulation of the cystic fibrosis channel which doesn t show quaternary structure but does a number of specific functional domains Mechanism 3: a hypothetical regulatory mechanism that you will propose that respects the properties of membranes and proteins and has some basis in biological reality: 7

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