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UCI BME 50B - xiangl9_Exam 1 answer key

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NAME: ID #: BME50A – Exam 1 – January 22, 2016 – 45 minutes – 4 questions – 65 points total (Please use a pen. Use your scratch paper to work out your answer before writing it on the test. If you must cross out an answer on the test, you can write the answer on the back of that page, provided you note it clearly.) Question 1 (20 points) a) Is this a parallel or antiparallel beta sheet? (2.5 pts) Parallel b) What type of interaction, shown as red dotted lines, is keeping the two strands in part a) together? (2.5 pts) Hydrogen bonds c) Does cholesterol increase or decrease the fluidity of membranes? (2.5 pts) Decrease d) Which element is more electronegative, sulfur or oxygen? (2.5 pts) Oxygen e) True or false: A strand of RNA is more stable against self-cleavage than an analogous strand of DNA. (2.5 pts) False f) Name an amino acid whose sidechain can form a salt-bridge with the sidechain of arginine. (2.5 pts) Aspartic acid or glutamic acid g) How many hydrogens are in a molecule of the amino acid valine? (2.5 pts) 11 h) True or false: the proteins making up your right hand and the proteins making up your left hand are mirror images of each other. (2.5 pts) FalseQuestion 2 (20 points) As you know, complementary DNA forms a duplex: two strands base pair with each other in antiparallel orientation to give the double helix structure. Instead of two DNA strands, the above image shows the structure of a PNA-DNA duplex, where we have replaced one strand with PNA. As you can see, the sequences of the strands are still complementary, since PNA uses the same nucleobases as DNA. However, PNA has a different chemical backbone than DNA. a) For the DNA strand, please draw an arrow on the figure pointing in the 5’ to 3’ direction. (2 pts) See figure. b) It has been observed that PNA-DNA duplexes are stronger (i.e., harder to separate into single strands) than corresponding DNA-DNA duplexes. Based on your knowledge of intermolecular forces, please explain why. (2 sentences max, 6 pts) PNA-DNA duplexes are stronger than DNA-DNA duplexes, because PNA-DNA duplexes contain less electrostatic repulsion in their backbone than DNA-DNA duplexes.c) The strength of a DNA duplex depends on salt concentration. For example, when DNA is dissolved in water containing some NaCl, the DNA duplex is stronger than if the same DNA were dissolved in water alone. Based on your knowledge of intermolecular forces, please explain why. (2 sentences max, 6 pts) Na2+ ions shield the negative charges of the phosphate backbone of one strand from the other, thereby stabilizing the duplex. d) Will the strength of the PNA-DNA duplex be more or less sensitive to salt concentration than a DNA-DNA duplex? (2pts) Why or why not? (4 pts) Less, because a PNA-DNA duplex contains less charged groups in its backbone than a DNA-DNA duplex.Question 3 (15 points) Cells need to constantly regulate the concentration of protons (H+) in their cytoplasm. However, as you’ve read in the book, protons cannot passively diffuse across the phospholipid bilayer of the cell membrane. Bacteriorhodopsin is a membrane protein that actively pumps protons out of the cell. a) Bacteriorhodopsin contains alpha-helices that span across the membrane. These alpha-helices are amphipathic, meaning that one side of the helix is hydrophobic and the other side is hydrophilic (see image to the right, where red represents the hydrophobic side and blue represents the hydrophilic side). Recalling that an alpha-helix has an average of 3.6 amino acids per turn, which of the following sequences is most likely an alpha-helix in bacteriorhodopsin? (5 pts) Seq 1: Arg-Ser-Lys-Arg Seq 2: Val-Leu-Arg-Asn-Val-Thr-Val-Val-Leu-Trp-Ser-Ala-Tyr Seq 3: Val-Leu-Arg-Asn-Pro-Thr-Val-Val-Leu-Trp-Ser-Ala-Tyr Seq 4: Val-Arg-Leu-Ser-Ala-Lys-Ala-Asn-Ile-Glu-Ala-Ser b) Reasoning from the function of bacteriorhodopsin described above, circle the structure from the three below that is bacteriorhodopsin. Please note that the color in the images is shown just for clarity. (3 points) Why? (Three sentences maximum, 7 pts) To transport protons across the phospholipid bilayer, bateriorhodopsin has six amphipathic alpha helices that span across the membrane. These alpha helices form a stable hydrophilic pore that is large enough for protons to pass through.Question 4 (10 points) While on a scientific expedition in Yellowstone national park, Grant and Tessa each isolate a water sample teaming with different bacteria. Grant’s sample was isolated from a hot spring that has an average temperature near boiling. Tessa’s sample was isolated from a stream with an average temperature of 15 degrees C (a few degrees below room temperature). Unfortunately, when Grant and Tessa return to their lab, the realize they forgot to label the test tubes that they stored their samples in. So now they don’t know which sample of bacteria came from which location. You suggest to Grant and Tessa that they should isolate the double-stranded DNA genomes of the bacteria in each sample and then, with some simple chemistry and a spectrophotometer, they should measure the percentage of G in the total DNA isolated from their samples. You claim this will likely allow them to figure out which sample was Grant’s and which was Tessa’s. They like your idea and carry it out. For the first sample (Sample 1), Grant and Tessa find that 12% of the nucleobases in the isolated DNA genomes is G. For the second sample (Sample 2), they find that 35% of the nucleobases in the isolated DNA genomes is G. a) What percentage of the nucleobases in Sample 1 is T? (3 pts) 38% b) What percentage of the nucleobases in Sample 2 is A? (3 pts) 15% c) Is Sample 1 Grant’s isolate or Tessa’s isolate? (4 pts)


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