Exam 1b Chem 4511/6501 Spring 2019 January 31, 2019 Name______________

1) [15] Draw a parallel b-sheet with 2 strands and 5 amino acids per strand. Draw all hydrogen bonds, indicate correct stereochemistry at all the Ca’s. Use the letter R for each sidechain.

2) [10 points] List all the molecular interactions in a) liquid helium and b) crystalline xenon.

a) Short range repulsion, dispersive interactions (London Forces) b) Short range repulsion, dispersive interactions (London Forces)

3) [5 points] List all the molecular interactions the central core of an a-helix formed by polyalanine.

a) short range repulsion b) London Interactions (Dispersive Interactions) c) dipole-dipole d) dipole-induced dipole e) hydrogen bonding

4) [20 points] Using correct stereochemistry at the a-position, and the predominant ionization states of the sidechains at pH 5.5, draw the peptide PCRHV. Draw a box around 2 sets of co-planer backbone atoms and label one phi/psi pair. In one sentence state what happens if the pH increases to 9.0. This is the sequence LCHRP. The H on the N of proline is not correct and should be omitted.

When the pH is lowered from 9.0 to 5.5 the histidine protonates and becomes cationic and the cysteine anion protonates and becomes neutral. 5) [5 points] Draw the two most important resonant structures of a peptide.

Exam 1b Chem 4511/6501 Spring 2019 January 31, 2019 Name______________

6) [10 points] Give the three letter code and one letter code of all the amino acids whose sidechains contain: a) branched aliphatic groups Val, V; Ile, I; Leu, L b) functional groups that bind to metals Cys,C; Met, M; His, H; Asp, D; Glu, E (any three of these) c) hydroxy groups Ser, S; Thr, T; Tyr, Y d) b-branching (b-substitution) Thr, T; Val,V; Ile, I

e) functional groups that absorb in the near UV His, H; Phe F, Tyr,Y; Trp, W 7) [9 points, circle one] For the transfer of one mole of hydrocarbon (for example CH3-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH3) from the neat (pure) state to water at 20° C:

a) DG < 0 T F can’t predict b) DH < 0 T F can’t predict c) TDS < 0 T F can’t predict

8) [6 points] Label the handedness (left-handed or right-handed) of these helices.

left right right 9) [10 points] Draw the Newman projections (i.e., the views along the central bond) of both f and j, at the angles observed in a b-sheet.

120°, +120° ok 10) [10 points] Using only the amino acids V and K, write out the sequence of

a) an amphathic a-helix (16 amino acids long). VKKVKKVVKKVKKVVK abcdefgabcdefgab

b) an amphipathic b-strand (8 amino acids long) VKVKVKVK