Bio 111 Exam #2. Version A 11/13/06. Question Value Score 1 23 TOTAL: 100. Your Name: Solutions can be found in the Biochemistry 5 handout.

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1 Bio 111 Exam #2 Version A 11/13/06 Your ame: TA's ame: Lab Section Write your initials on every page in the space provided. This exam has 11 pages including this coversheet. heck that you have pages 111. This exam has five questions. You may want to read all questions before starting to write. Make your answers as clear and precise as possible. Answer all questions in the space provided. Solutions can be found in the Biochemistry 5 handout. Question Value Score TTAL: 100 A1

2 Question 1: hemistry (23 points) ote that a summary of chemistry can be found on page 10 of this exam. onsider the following three molecules: Molecule #1 Molecule #2 Molecule #3 S 3 a) Rank the three molecules in order from the most hydrophobic to the most hydrophilic. ote that they are not amino acids. Write your answers in the blanks below (9 pts.) Most ydrophobic Most ydrophilic b) Draw a molecule in the space below which is similar to the molecules above and is more hydrophilic than the most hydrophilic molecule you indicated above. Make sure that your molecule obeys the bonding rules described in lecture and includes all hydrogen atoms. ote that there are many possible correct answers here. (8 pts) A2

3 Question 1, continued: c) Shown below is a molecule of betamercaptoethanol. Draw a single water molecule making a single hydrogen bond to an appropriate part of the betamercaptoethanol molecule. Indicate the hydrogen bond with a dashed line ( ). (6 pts) S A3

4 Question 2: rotein Structure I (19 points) ote that structures of amino acids can be found on page 11 of this exam. You are designing a protein to bind to a small molecule, Molecule X. Molecule X is shown below with three parts circled: art A art B art 3 a) onsider art A. hoose an amino acid that has a sidechain that can only form a van derwaals bond with art A of Molecule X. If more than one is possible, give only one. Explain why these two can only form a van der Waals bond. (7 pts) Amino acid Explanation: b) onsider art B. hoose an amino acid that has a sidechain that can form a noncovalent bond with art B of Molecule X. Give the amino acid and the bond that could form between its side chain and art B. If more than one is possible, give only one. (6 pts) i) Amino acid ii) ircle the strongest bond that could form between the side chain and art B. ionic hydrogen hydrophobic van der Waals bond bond interaction bond c) onsider art. hoose an amino acid that has a sidechain that can form a noncovalent bond with art of Molecule X. Give the amino acid and the bond that could form between its side chain and art. If more than one is possible, give only one. (6 pts) i) Amino acid ii) ircle the strongest bond that could form between the side chain and art. ionic hydrogen hydrophobic van der Waals bond bond interaction bond A4

5 Question 3: rotein Structure II (18 points) These structures are relevant to this question: alanine aspartic acid 3 2 serine 3 2 phenylalanine a) onsider an enzyme with a hydrophobic core. Amino acid #212 is alanine and is part of this hydrophobic core. (6 pts each) i) A mutation that changes amino acid #212 to serine results in an enzyme that is completely inactive. Based on the structures of the two amino acids, provide a plausible explanation for why the mutation results in an inactive enzyme. ii) A mutation that changes amino acid #212 to phenylalanine results in an enzyme that is completely inactive. Based on the structures of the two amino acids, provide a plausible explanation for why the mutation results in an inactive enzyme. iii) onsider a mutation that changes amino acid #212 to aspartic acid. Based on the data given so far, what do you think the effect of this mutation would be? ircle one and explain your reasoning. Inactive Enzyme Active Enzyme Explanation: A5

6 Question 4: Thermodynamics (15 points) Given that the reaction is spontaneous, answer the following questions. a) Rank the following states of hydrogen and oxygen in order from the highest free energy to the lowest free energy. (8 pts) State Description 1 free and atoms not bonded to anything 2 the products ( 2 molecules) 3 the reactants ( 2 and 2 molecules) 4 the transition state between reactants and products ighest free energy Upper Middle free energy Lower Middle free energy Lowest free energy b) What type(s) of bonds are being broken when going from state (3) to state (1)? ircle all that apply. (3 pts) ionic hydrogen covalent hydrophobic van der Waals bonds bonds bonds interactions bonds c) Suppose that you added a catalyst for this reaction. What effect would adding the catalyst have on the energy of each of the following states? ircle the correct answer. (4 pts) i) State 1: free energy free energy free energy increases unchanged decreases ii) State 2: free energy free energy free energy increases unchanged decreases iii) State 3: free energy free energy free energy increases unchanged decreases iii) State 4: free energy free energy free energy increases unchanged decreases A6

7 Question 5: Enzymes, athways, Glycolysis, & Fermentation (25 points) The reaction pathway for glycolysis and fermentation are shown on pages 8 and 9. Each reaction is indicated by a number. a) Answer the following questions using the numbers from the reactions on pages 8 and 9. There may be more than one right answer to each question; give only one. (4 pts each) i) Give a number corresponding to a reaction where a phosphate () is transferred from another molecule to AD to make AT. ii) Give a number corresponding to a reaction where a single covalent bond connecting two carbon atoms is broken. b) onsider enzyme (1) in the glycolysis pathway. Suppose that there are two forms of this molecule encoded by two different alleles of the gene: allele enzyme (1) encoded G fullyfunctional enzyme (1) g nonfunctional enzyme (1) i) omplete the following table with numbers as appropriate: (6 pts) Genotype % of Enzyme (1) that is functional % of Enzyme (1) that is nonfunctional GG gg Gg ii) Individuals with the genotype gg are dead. Explain why this genotype would be lethal. (5 pts) ii) What is the most likely phenotype of a Gg individual? (circle one) live dead Explain your reasoning. (6 pts) A7

8 Reactions of Glycolysis & Fermentation I glucose AT (1) AD (2) glucose6phosphate i 2 fructose6phosphate dihydroxyacetone phosphate 2 AD AD AD AT 2 (5) 2 2 (6) (borrow an "" for each piece) (move to AD) AT (3) (7) (4) AD 2 fructose1,6diphosphate 3phosphoglyceraldehyde 3phosphoglyceraldehyde 3phosphoglyceraldehyde AD AD 1,3diphospho glycerate AD AT 3 phospho glycerate i A8

9 Reactions of Glycolysis & Fermentation II 2 3phospho glycerate (8) 2 2phospho glycerate 2 2 AD AT (9) (save 's as 's return the 's) (10) (pick up 's as needed) 2 phosphoenolpyruvate AD AT carbon dioxide 3 (11) (pick up 's as needed) pyruvate carbon dioxide AD AD 3 (12) (pick up 's as needed) acetaldehyde AD AD 3 ethanol A9

10 Summary hart: If you see.. art of molecule You should think... roperties nonpolar phobic no no yes nonpolar phobic no no yes polar philic ª no polar philic ª no S nonpolar phobic no no yes polar philic ª yes no polar philic ª yes no polar philic ª no S nonpolar phobic no no yes S polar philic ª no philic no yes no S philic yes no no philic no yes no philic yes yes no phobic no no yes otes: * Assuming a suitable partner is nearby. ª If the or is charged, yes ; if not no. Yes, if the or has a lone pair available. Since this is an atom, not a bond, it is neither polar nor nonpolar. A10

11 STRUTURES F AMI AIDS 3 3 ALAIE (ala) ARGIIE (arg) ASARAGIE (as) 2 3 ASARTI AID (asp) 2 S 3 YSTEIE (cys) GLUTAMI AID (glu) GLUTAMIE (gl) 2 3 GLYIE (gly) 2 3 ISTIDIE (his) ISLEUIE (ile) 2 3 LEUIE (leu) LYSIE (lys) 2 2 S 3 3 METIIE (met) 3 3 TREIE (thr) EYLALAIE (phe) TRYTA (trp) RLIE (pro) TYRSIE (tyr) 2 3 SERIE (ser) VALIE (val) A11

12 A12

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