Name: ___________________________ 1 7.013 Exam One -- 2007 Exam starts at 11:05 am and ends at 11:55 am. There are 12 pages including this cover page. Please write your name on each page. Only writing on the FRONT of every page will be graded. (You may use the backs, but only as scratch paper.) Topic 1 22 pts________ Topic 2 30 pts________ Topic 3 28 pts________ Topic 4 20 pts________ TOTAL out of 100_______Name: ___________________________ 2Topic 1. A researcher in your lab has developed a way to tag specific proteins in cultured cells to make the proteins fluoresce green. Now when she looks at cells under the microscope, she finds that, depending on which protein is tagged, only certain parts of cell fluoresce green. When the following proteins are tagged, which organelle or part of the cell is most likely to fluoresce green? 1a. (2 points) DNA polymerase: 1b. (2 points) Primase: 1c. (2 points) A protein involved in appending carbohydrates to other proteins: 1d. (2 points) Collagen: 1e. (2 points) A protein involved in metabolizing simple sugars to make ATP: 1f. (2 points) A protein involved in digesting food particles that have been taken up by phagocytosis: 1g. (4 points) She then tags a cellular protein whose function is unknown. When she looks under the microscope, she finds that the cells don’t fluoresce at all. However, there is a greenish glow to the liquid in which the cells had been growing. Assuming the protein was correctly tagged and expressed, what might have caused this result? Provide you answer in 15 words or less.Name: ___________________________ 31h. (2 points) An error occurs during division of cells that make up the lining of the intestines such that daughter cells inherit an abnormal number of parental chromosomes. Is this more likely to be an error in mitosis or in meiosis? Explain your choice in 15 words or less. 1i. (2 points) A child is born with three copies of chromosome #21 in nearly every cell in its body. This is a disorder commonly called Down Syndrome. Does this disorder most likely reflect an error that occurred during a mitotic cell division or during a meiotic cell division? Explain your choice in 15 words or less. 1j. (2 points) During which type of cell division would you expect to see chiasmata? Explain your choice in 15 words or less.Name: ___________________________ 4Topic 2. Xylose is a 5-carbon sugar that can be enzymatically converted to xylitol, a low calorie, diabetic-safe sweetener that is used in products such as chewing gum. 2a. (2 points) In nature, long polymers made of xylose are major structural components of wood. Would you classify a polymer of xylose as a protein, a lipid, a polypeptide, a nucleic acid, a polysaccharide, a polyethylene, or a polyester? Xylose reductase (XR) is the enzyme that is used to convert xylose into xylitol. Figure 1 illustrates this reaction OOHOHHOOHOOHOHHOOHHXROOHOHHOOHOOHOHHOOHHOOHOHHOOHOOHOHHOOHHXR Figure 1. Xylose reductase (XR) converts xylose to xylitol. Other molecules involved in this reaction have been omitted for simplicity. 2b. (4 points) As with other enzymes, xylose reductase changes some of the thermodynamic properties of the chemical reaction in which xylose is converted to xylitol. Of the following properties of this reaction, circle all that are changed by the enzyme. • Rate of the reaction • ΔG • Activation energy • Equilibrium of the reactionName: ___________________________ 5 Figure 2 is a diagram of the xylose molecule in the active site of xylose reductase. Although the enzyme is composed of many amino acids, only those closest to the xylose molecule are indicated. AA-113AA-309AA-51AA-23AA-50OOHOOHOHHNNHNOH2OHNO-OAA-113AA-309AA-51AA-23AA-50OOHOOHOHHOOHOOHOHHNNHNOH2OHNO-O Figure 2. Xylose in the active site of xylose reductase. “AA-#” refers to individual amino acids. Adapted from Kratzer et al., 2006, Biochem, J. 393:51-58 2c. (8 points) Based on the description of the chemical reaction provided in Figure 1, which two amino acids are positioned to interact most strongly with the portion of the xylose molecule that will be chemically modified? List the two amino acids by their “AA-#” here. Indicate how each is most likely to interact with the substrate as it is shown in Figure 2 (you choices are: hydrophobic interaction, hydrogen bond, ionic bond, covalent bond). Amino Acid Numbers Interaction TypeName: ___________________________ 6 2d. (8 points) Only the side groups have been shown for each of the amino acids in Figure 2 and their common portions have been indicated as boxes. Using the table on the last page of this exam, identify each of the following amino acids, and indicate whether each is hydrophilic or hydrophobic. Amino Acid Numbers AA-23 AA-50 Amino Acid Names Hydrophobic or Hydrophilic 2e. (2 points) In terms of primary structure, which of the five amino acids shown in the figure of the enzyme’s active site is closest to the C terminus of the protein chain? 2f. (2 points) Assuming xylose reductase is a single subunit enzyme, what is the highest order protein structure one would need to describe the enzyme? Your choices are “primary”, “secondary”, “tertiary”, or “quaternary.” Triglycerides are common fats produced by a variety of organisms, including bacteria, fungi, plants, and animals. The common structure of triglycerides is as shown in Figure 3. CHHHOCOR1CHOCOR2CHOCOR3CHHHOCOR1CHOCOR2CHOCOR3 Figure 3. Triglyceride structure 2g. (2 points) Many organisms produce triglycerides in which all three R-groups are 15-17 carbons in length. These R-groups are similar in length to those of the lipids found in cell membranes. However, triglycerides are almost never found in cell membranes. What property of such triglycerides makes them unsuitable for incorporation into normal cell membranes? Answer in 15 words or less. 2h. (2 points) Some bacteria adapt to lower temperatures by increasing the fluidity of their cell membranes. Would you expect increasing the fluidity of a cell membrane to involve increasing or decreasing the number of double bonds in the fatty acids that make up the membrane lipids? Explain your choice in 15 words or less.Name: ___________________________ 7Topic 3. You’ve taken over the family business of breeding heffalumps. You
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