Exam 2 Chem 4511/6501 Spring 2014 February 25, 2014 a1 Name______________

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1) [15 points] Draw a C-G base pair.

a) Include the sugars and 3’ phosphates, b) Label the major groove and the minor groove, c) Label all the atoms of both bases (1’C, 2’C, N3, etc.), d) Indicate the lengths of all the hydrogen bonds (H---O and H---N distances).

2) [10 points] Draw the reaction for the reduction of a disulfide bond to form two cysteines. Draw both cysteines completely, in their correct ionization states at pH 7.8.

3) [15 points] Draw the peptide PVHRQWK

a) indicate stereochemistry of all of the Cα-positions, b) indicate the predominant ionization states of the sidechains at pH 7.5, c) draw boxes around the first 2 sets of six co-planer atoms, d) Label φ and ϕ on the 4th and 5th amino acids, e) draw the hydrogen bonds if the peptide is an α-helix.

Exam 2 Chem 4511/6501 Spring 2014 February 25, 2014 a1 Name______________

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4) [10 points] Draw a helical wheel for this sequence: EAVRKLDEAVKR

4a) [2 points] Indicate any hydrophobic and/or hydrophilic faces of this α-helix. 5) [8 points] Draw the Newman projections (i.e., the views along the central bond) of both φ and ϕ, at the angles observed in an α-helix. 6) [14 points] Give the three letter codes of any amino acids whose sidechain contains a) a charge at any physiological pH Arg, Lys, Glu, Asp, His b) a branched aliphatic group Val, Leu, Ile

c) a hydroxyl group Ser, Thr, Tyr, Asp, Glu

Exam 2 Chem 4511/6501 Spring 2014 February 25, 2014 a1 Name______________

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d) β-substition (β-branching) Val, Ile, Thr e) an aromatic ring Phe, Trp, Tyr f) a sulfur atom Cys, Met g) -CH2-CH2-NH3

+ Lys 7) [15] Draw a parallel β-sheet with 2 strands and 5 amino acids per strand. Draw all hydrogen bonds, indicate correct stereochemistry at all the Cα’s. Use the letter R for each of the sidechains.

8) [3 points] Is this helix right-handed or left-handed (underline the correct answer).

9) [4] From the list below (the numbers are molecular weight in Daltons): D Runs fastest in an SDS polyacrylamide gel. B Runs slowest in an SDS polyacrylamide gel. a) Liver alcohol dehydrogenase, 41,000 b) Human transferrin, 80,000 c) Bovine serum albumin, 68,000 d) Carbonic anhydrase, 29,000 10) [4 points] Who determined the structure of DNA? a) Romeo and Juliet b)  Lewis and Clark c) Watson and Crick d) Hall and Oats e) Asterix and Obelix

Exam 2 Chem 4511/6501 Spring 2014 February 25, 2014 a1 Name______________

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