BoC proteins

Question 1

Give eg of amino acid with hydrophobic sidechain?

Answer 1

Valine (see notes for diagram)

R is CH(CH2)2

Question 2

No sidechain amino acid

Answer 2

Glycine (non-chiral)

Question 3

positive sidechain

Answer 3

lysine (see notes for diagram)

R is C4H8NH2

Question 4

negative sidechain

Answer 4

aspartate (see notes for diagram)

R is ethanoate

Question 5

polar sidechain

Answer 5

Asparagine (has amide group where N is polar)

R is CH2CONH2

Question 6

sulphur-containing sidechain

Answer 6

cysteine (can form disulphide bridges)
(see notes for diagram)
R is CH2SH

Question 7

Amino acid with non-ionisable sidechain titration curve explain

Answer 7

see notes

Question 8

How many times more readily do amino acids lose a proton than acetic acid, and why?

Answer 8

300, because neighbouring positively charged amino group withdraws electrons from carbonyl stabilising carboxyl form

Question 9

If R contains an ionisable group…

Answer 9

Titration curve has a third PKa

Question 10

Which enantiomers of amino acids are found in natural proteins

Answer 10

L

Question 11

Draw L and D amino acid

Answer 11

see notes

Question 12

L based on…

Answer 12

similarity to glyceraldehyde again

Question 13

By convention amino acids in a polypeptide chain are written…

Answer 13

N to C terminus

Question 14

How much double bond character does a peptide bond have?

Answer 14

40%, is a resonance hybrid

Question 15

Is peptide bond usually cis or trans and why?

Answer 15

Trans with alpha carbons on opposite sides because if it were cis side chains on adjacent residues would clash

Question 16

Why are disulphide bridges rare in intracellular proteins?

Answer 16

Because of reducing cytoplasmic environment

Question 17

Proteins that bind to DNA likely to be…

Answer 17

Rich in positively charged amino acids like lysine to bind to negatively charged phosphate backbone

Question 18

What are phi and psi?

Answer 18

see notes

Question 19

What are phi and psi restricted by? Why does glycine have less restrictions?

Answer 19

steric hindrance between main chain and side chains of adjacent residues, therefore as glycine sidechain is just H more combinations allowed

Question 20

Draw a ramachandran plot

Answer 20

see notes

Question 21

H bond donors and acceptors in interior of proteins…

Answer 21

bond each other

Question 22

In exterior H bonds are with…

Answer 22

Water

Question 23

What are 4 criteria for secondary structures?

Answer 23

1) peptide bond planar with favourable length and angle, 2) each carbonyl O and amide N involved in H bonds, 3) H-bonded atom in straight line, 4) sidechains project out with minimum steric inteference

Question 24

Describe and draw alpha-helix

Answer 24

see notes
H bonds between i and i+4
3.6 residues per 360 degree turn

Question 25

Draw and describe beta sheet

Answer 25

see notes
Beta strands connected by ladders of H bonds to other strands
Antiparallel = strands run in opposite directions
In both sheet types sidechains alternately project

Question 26

Describe reverse beta turn

Answer 26

Puts secondary structure elements together
Allows polypeptide chain to reverse direction
Turn is min of 4 residues
Glycine and proline commonly occur in the turn