topic 3

Question 1

what makes up the backbone of a polypeptide?

Answer 1

all component excluding the side chains of the amino groups

Question 2

what are the side chains? off of which carbon do they extend from?

Answer 2

the side chians come off of the beta carbon in the c-c bond.

Question 3

what is a peptide bond?

Answer 3

the bond between the Nh group and the Ca=o

note that this bond has a partial pi character due to resonance, there for the dihedral angle (omega) between these models does not change

Question 4

what is the psi angle?

Answer 4

the torision angle between the C-C=O

Question 5

what is the phi angle

Answer 5

the torision angel between the C-NH

Question 6

what are the optimal angles for phi? for psi?

Answer 6

the most common angle is found in beta sheets: phi=–60->-130, psi= 80-180

for a helix phi=-50->-170, psi=-60

another combination will result in steric clashing of the side chains

Question 7

what is the optimal torision angle for the peptide bond?

Answer 7

180, at this point, the 2 Ca=O in the backbone are trans to each other, minimizing the steric clash of their side chains

Question 8

where is the N terminus? C terminus?

Answer 8

N is at the beginning
C is at the end

Question 9

what is the molecular weight of an AA?

Answer 9

on avergae an AA weight 110g/mol
this is equivalent to a Dalton

a klio dalton = 1/10 Da

Question 10

what results in a negative torsion angle of phi or psi?

Answer 10

clock wise rotation is pos, counter clock is neg

Question 11

what is a disulfide bond, where do they occur?

Answer 11

A bond that occurs between the S groups in Cysteine, this a covalent bond that forms between the Cysteines within the same polypeptide chain