Final Chem 4511/6501 Spring 2011 May 5, 2011 b Name

Transcription

1 Key 1) [10 points] In RNA, G commonly forms a wobble pair with U. a) Draw a G-U wobble base pair, include riboses and 5 phosphates. b) Label the major groove and the minor groove. c) Label the atoms of the G, including the ribose. d) Indicate the lengths of the hydrogen bonds and of the N-H bonds. N-H = 1.0 Å N----H = 1.8 Å 2) In A-form RNA, the base pairs stack. a) [5 points] List all the molecular interactions between stacked base pairs. Short Range Repulsion / London Dispersion / Dipole-Dipole / Dipole-Induced Dipole b) [5 points] List all the molecular interactions between a base pair and the surrounding water. Short Range Repulsion / London Dispersion / Dipole-Dipole / Dipole-Induced Dipole / Hydrogen Bonding 3) [5 points] For a spontaneous forward process: a) ΔH TΔS > 0 T F can t predict b) ΔH/TΔS = 0 T F can t predict c) ΔG > 0 T F can t predict d) ΔH > 0 T F can t predict e) TΔS > 0 T F can t predict 1

2 4) [5 points] For the transfer of one mole of grease (for example CH 3 -CH 2 -CH 2 -CH 2 -CH 2 - CH 2 -CH 2 -CH 2 -CH 2 -CH 3 ) from the neat (pure) state to water at 20 C: a) ΔS uni < 0 T F can t predict b) ΔG < 0 T F can t predict c) ΔH < 0 T F can t predict d) TΔS < 0 T F can t predict e) TΔS = 0 T F can t predict 5) [10 points] The image above is B-form DNA. a) Draw a circle around a phosphate group b) Label each atom of one of the deoxyriboses. c) Indicate the directionality of both strands with 5 and 3 labels. d) Indicate a glycosidic bond with g-b. e) Label a guanine base with a G. 2

3 6) [10 points] Consider the following peptide Leu-His-Ile-Arg-Trp (N->C) Using correct stereochemistry at the α-position, and the predominant ionization states of all the sidechains, draw the peptide (at ph 7.0). Draw boxes around adjacent sets of coplanar atoms of the peptide backbone. 7) [5 points] Give the three letter code of all the amino acids whose sidechains contain a) hydroxyl groups Ser, Thr, Tyr b) carboxylic acids Asp, Glu c) sulfur atoms Cys, Met d) β-substition Val, Thr, Ilu e) amide groups Asn, Gln 3

4 8) [5 points] Draw a β-sheet, with two strands and 5 amino acids in each strand. The sheet must be antiparallel. Draw correct stereochemistry at the Cα s. The sidechains should all be R. 9) Hemoglobin [10 points] True or False a) The tertiary structure of myoglobin is similar to the tertiary structure of one subunit of hemoglobin [T or F]. b) Hemoglobin binds one molecule of oxygen per heme group [T or F]. c) Myoglobin binds one molecule of oxygen per heme group [T or F]. d) Hemoglobin is allosteric [T or F]. e) Myoglobin is allosteric [T or F]. 4

5 10) [10 points] Identify the following on the graph above: 1) ΔG rxn 2) ΔG rev 1 3) ΔG for 1 4) ΔG rev 2 5) ΔG for 2 i) product(s) ii) transition state 1 iii) intermediate iv) transition state 2 v) reactant(s) 5

6 11) [5 points] Draw Fischer projections for the linear forms of D-glucose and D- fructose. 12) [5 points] Draw the reaction for conversion between the α and β anomers of D- glucose, including the linear intermediate. 6

7 13) [5 points] Sketch a membrane that is associated with an integral membrane protein and with a lipid-linked protein. For the membrane, use spheres to indicate polar head groups and double wavy lines to indicate lipophilic tails. Use blobs to indicate the proteins. Just draw the Integral protein and the lipid-linked protein 7

8 14) [20 points] Sketch the mechanism of a serine protease. Indicate the electron flow, the oxyanion hole and label the tetrahedral and acyl enzyme intermediates. It is not necessary to give amino acid labels (as in the first panel) 8

9 Consider the following mechanism of an enzymatic reaction: k 1 E +S k -1 ES k 2 E + P 15) [10 points] Give the equation describing how the concentration of the Michaelis Complex changes over time. d[es]/dt = k 1 [E][S] k - 1 [ES] k 2 [ES] d[es]/dt =0 : - 3 points (this is true only under steady state, not in general) 16 [20 [points] Derive the Michaelis-Menten equation (below), giving all the assumptions. v = v max[s] K M +[S] d[es]/dt = k 1 [E][S] k - 1 [ES] k 2 [ES] = 0 (steady state assumption, solve for [ES] [ES] = [E][S] k 1 /(k k 2 ) Define K M (the Michealis Constant) K M = (k k 2 )/k 1 [ES] = [E][S]/K M rearrange to give K M = [ES]/[E][S] substitute [E] = [E] 0 [ES] ([E] 0 [ES])[S] = K [ES] M multiply both sides by [ES] K M [ES] = ([E] 0 [ES])[S] solve for [ES] [ES] = [E] 0 [S] K m +[S] multiply both sides by k 2 (this gives get the velocity of the reaction) dp dt = v = k [ES] = k [E] [S] K M +[S] and remember that k 2 [E] 0 = v max v = v max [S] K M +[S] Michaelis Menten Equation 9

10 17 [10 points] State the significance of kcat, Km and kcat/km. [full credit if any correct description is given] K M the apparent dissociation constant of the ES complex. K M is a measure of a substrate s affinity for the enzyme (if k 1,k -1 >>k2, the K M =K D.) the substrate concentration required to reach half-maximal velocity (v max /2). A small K M means the substrate binds tightly to the enzyme and saturates (max s out) the enzyme. k cat For the simplest possible mechanism, where ES is the only intermediate, and dissociation is fast, then k cat =k 2, the first order rate constant for the catalytic step. If dissociation is slow then the dissociation rate constant also contributes to k cat. If there are multiple catalytic steps (see trypsin) then each of those rate constants contributes to k cat. If one catalytic step is much slower than all the others (and than the dissociation step), than the rate constant for that step is approximately equal to to k cat. k cat is the turnover number : indicates the rate at which the enzyme turns over, i.e., how many substrate molecules one catalytic site converts to substrate per second. k cat /K M the catalytic efficiency. the apparent second order rate constant (v=k cat /K M [E] 0 [S]) gives an estimate of the reaction velocity from the total enzyme concentration ([E] 0 ). the specificity constant. It is used to distinguish and describe various substrates. 10

11 18 [11 points] Fill in the boxes. [see next page] 11

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13 19 [17 points] (a) List the four steps of transcription. (b) Draw the transcription reaction, indicating the sense strand, the antisense (template) strand, the incoming NTP, the nascent strand, and the electron flow. Initiation Promoter Clearance Elongation Termination 13

14 20 [17 points] Draw the translation reaction (i.e., transpeptidation), indicating the reactants (the trna-nascent peptide in the P-site, the charged trna in the A-site) and the products (the trna in the P-site, the trna-nascent peptide in the A-site) and the electron flow. 14