Old Midterm1 (Sp 2023) for practice

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MCB 100A/CHEM 130 : MIDTERM 1 : Spring 2023 NAME_________________________________ UNIVERSITY OF CALIFORNIA, BERKELEY CHEM C130/MCB C100A MIDTERM EXAMINATION #1 FEBRUARY 17, 2020 INSTRUCTORS: David Wemmer and Ke Xu Question point value Your Total 1 28 2 12 3 20 4 30 5 10 total 100 Page 1

MCB 100A/CHEM 130 : MIDTERM 1 : Spring 2023 NAME_________________________________ Question 1 (28 points). Multiple choice and True/False questions. Circle the correct option or circle either TRUE or FALSE. +2 points for each correct answer, -2 points for each wrong answer. To get the maximum score you do not need to answer all the questions, so be careful not to answer questions incorrectly. Maximum points: 28. Minimum points: 0. (i) The hydrophobic e ff ect stabilizing folded proteins is very similar in its basis to the base stacking interaction in nucleic acids. TRUE/ FALSE (ii) There are three amino acids that one expects to be negatively charged at pH 11. TRUE / FALSE (iii) The width of the minor groove in a B-form double helix varies somewhat with sequence but is normally in the range of (circle the correct answer): (a) 4–8 Å (b) 8-12 Å (c) 12-16 Å (d) 16-20 Å (iv) For an amide to carbonyl hydrogen bond in a protein the distance between the N and C is approximately : (a) 2.2 Å (b) 2.7 Å (c) 3.2 Å (d) 3.7 Å (v) Glycans occupy a larger volume of space per residue than most amino acids and nucleotides. TRUE / FALSE (vi) The residues used to synthesize glycans are directly encoded in genomic DNA sequences. TRUE / FALSE (vii) Modified bases can stabilize the fold of tRNA. TRUE / FALSE (viii) The Ramachandran diagram is based on the steric interactions of sidechains with the backbone of a protein. TRUE / FALSE (ix) Circle the amino acid substitution that results in the greatest change of polarity of the sidechain: (a) N → Q (b) S → T (c) Y → F (d) L → I (x) In RNA double helices G-U base pairs have a very di ff erent geometry from Watson-Crick base pairs. TRUE / FALSE (xi) A transmembrane segment of a protein can be recognized unambiguously because it contains a long run of essentially all hydrophobic residues. Page 2

MCB 100A/CHEM 130 : MIDTERM 1 : Spring 2023 NAME_________________________________ TRUE / FALSE (xii) D-isomer amino acids, such as D-Ala, do occur in bacteria but are not incorporated into proteins. TRUE / FALSE (xiii) Large proteins are usually comprised of several domains that fold independently. TRUE / FALSE (xiv) The interaction energy of a charge with a dipole at moderate distance falls o ff as ≈ 1/r n , where: (a) n =1 (b) n = 3 (c) n = 6 (d) n=12 (xv) The hydrophobic e ff ect is a long-range interaction between large sidechains in a protein. TRUE / FALSE (xvi) Phospholipid membranes always have a negatively charged surface due to the presence of the phosphate group. TRUE / FALSE Page 3

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MCB 100A/CHEM 130 : MIDTERM 1 : Spring 2023 NAME_________________________________ Question 2. (12 points) In “loop E” 5S RNA from ribosomes the base sequence suggests regions of Watson-Crick base pairing at the ends, with a internal “loop” region with two possible A-U base pairs but otherwise mismatched (i.e. not Watson-Crick pairs) (i) (6 points) Looking from a distance the loop E looks remarkably like a duplex RNA. What two principles lead to the bases not sticking out into solution? (ii) (6 points) To study structures like the loop E RNA scientists sometimes join the two strands of RNA into one, and also add one of the common tetraloop sequences at the end. Why does it make sense to use such a tetraloop sequence? Page 4

MCB 100A/CHEM 130 : MIDTERM 1 : Spring 2023 NAME_________________________________ Question 3. (20 points) The figure below is a small region of the structure of an RNA riboswitch. This is a folded RNA structure that recognizes one specific natural nucleic acid component. The molecule being recognized is darker in the structure below. Hydrogen atoms are not shown. (i) (4 points) Identify the molecule being recognized. Write the name of it on the blank line provided. (ii) (6 points) Label all of the N and O atoms of the base on the drawing below. (iii) (5 points) The molecule recognized makes hydrogen bonds to the surrounding residues from the riboswitch (lighter gray). Add a dotted line for each hydrogen bond, label the identities of atoms on the RNA riboswitch in contact with the base. Put an H where the hydrogens would be, and draw solid line for a covalent bond between the appropriate N or O atom and the hydrogen atom involved in the hydrogen bond. (iv) (5 points) The bases show form a planar base triple. Does this correspond to a base triple that you might find in a DNA triplex? (explain) Page 5 recognized = _____________

MCB 100A/CHEM 130 : MIDTERM 1 : Spring 2023 NAME_________________________________ Question 4. (30 points) (i) (6 points) What amino acid is most likely to undergo a change in charge when the solution it is in is changed from pH 5 to pH 7? Draw the amino acid sidechain structure in both states and label which occurs at which pH. (ii) (6 points) What amino acid can form a covalent cross-link between segments of the polypeptide chain? Draw the structure of the cross-linked form showing backbone and sidechains. (iii) (6 points) Specify two amino acids that can form two hydrogen bonds between the sidechains and also would be a salt bridge (ionic interaction). Give one and three letter codes and draw the hydrogen bonded parts: (iv) (6 points) Explain why the distribution of observed ࠵? , ࠵? values in real proteins deviates significantly from the distribution predicted by Ramachandran. (v) (6 points) What pattern of hydrophobic amino acids would you look for that would suggest a segment of protein is a beta strand in a typical beta sheet? Page 6

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MCB 100A/CHEM 130 : MIDTERM 1 : Spring 2023 NAME_________________________________ Question 5. (10 points) An image is shown below of a circular plasmid DNA. (i) (5 points) Estimate the value of writhe for this DNA (include the sign). Assume that this plasmid was produced in a cell by normal biological processes. writhe = ________ (ii) (5 points) Intercalators bind to DNA by slipping between base pairs, and reducing the twist at the binding site to ≈ 0° rather than the standard ≈ 36°. For the DNA shown will the writhe INCREASE or DECREASE as the intercalator is added? (circle one) Explain briefly why you chose your answer. Page 7

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