Organic Chemistry

Section 23.13 Secondary Structure of Proteins 989

PROBLEM 33

Determine the primary structure of an octapeptide from the following data:

Acid hydrolysis gives 2 Arg, Leu, Lys, Met, Phe, Ser, Tyr.

Carboxypeptidase A releases Ser.

Edman’s reagent releases Leu.

Cyanogen bromide forms two peptides with the following amino acid compositions:

1. Arg, Phe, Ser 2. Arg, Leu, Lys, Met, Tyr
   Trypsin forms the following two peptides and two amino acids:


2. Arg 3. Arg, Met, Phe


3. Ser 4. Leu, Lys, Tyr

23.13 Secondary Structure of Proteins

Secondary structuredescribes the conformation of segments of the backbone chain of

a peptide or protein. To minimize energy, a polypeptide chain tends to fold in a repeat-

ing geometric structure such as an or a sheet. Three factors deter-

mine the choice of secondary structure:

• the regional planarity about each peptide bond (as a result of the partial double-
  bond character of the amide bond), which limits the possible conformations of
  the peptide chain (Section 23.7)


• maximization of the number of peptide groups that engage in hydrogen bonding
  (i.e., hydrogen bonding between the carbonyl oxygen of one amino acid residue
  and the amide hydrogen of another)


• adequate separation between nearby R groups to avoid steric hindrance and
  repulsion of like charges

-Helix

One type of secondary structure is the In an the backbone of the

polypeptide coils around the long axis of the protein molecule (Figure 23.8). The helix

is stabilized by hydrogen bonds: Each hydrogen attached to an amide nitrogen is

A-helix. a-helix,

A

a-helix b-pleated

C

HN

NH

R

R

R

R

O HN

O

O

hydrogen bonding

between peptide

groups

a. b. >Figure 23.8

(a) A segment of a protein in an

(b) Looking up the

longitudinal axis of an a-helix.

a-helix.

BRUI23-959-998r2 29-03-2003 1:37 PM Page 989