Biochemistry of Protein to be Enzymes

1. ENZYMES-2
Protein structure

3. Dipeptide

4. Tetrapeptide
Tripeptide Pentapeptide
Oligopeptide
Polypeptide

5. SINGLE DOUBLE
BOND BOND
It do not allow free
It allow free rotation of
rotation of functional
functional attached to it
attached to it

6. Partial Double bond

7. • C and N atoms participate in a π bond.
• Which makes lone e- pair on the oxygen.
• There is no free rotation around C-N bond
(Peptide bond).

8. Consequences of Peptide bond as Partial
double bond
1. It restricts free rotation around the peptide bond
2. Six atoms of peptide bond forms amide plane.
3. C−N bond length -----------------> 0.133 nm
Normal C−N bond lengths------> 0.145 nm
Typical C=N bonds----------------> 0.125 nm
4. The peptide bond is estimated to have 40% double-bond
character.

12. Homomultimeric
Multimeric
Protein Heteromultimeric
Monomeric
Protomer

13. Primary Structure

14. Secondary
structure
β-Sheet α-Helix

15. STERIC
HINDERENCE

16. STERIC
HINDERENCE

17. STERIC
HINDERENCE

18. STERIC
HINDERENCE

19. Ramachandran Plot

22. 1. One turn of the helix represents 3.6 a.a.
residues.
2. Each amino acid residue extends 1.5 Å
3. With 3.6 residues per turn i.e. 3.6 × 1.5 Å = 5.4 Å
This is translation distance/pitch
4. All H-bonds are parallel to helix
5. All the carbonyl groups points in one direction
6. N-H groups are pointing in the opposite
direction.

23.  Each peptide bond have dipole moment.
 Dipole moment is because of N-H and C=O
 Such groups lie as helix axis.
 Therefore Helix has dipole moment.
 N-terminus have partial positive charge &
C-terminus have partial negative charge.

24. 0.325 nm
0.347 nm

26. Hydrophobic side chains
Hydrophobic side chains
• H bonds in this structure are interstrand (not intrastrand)
• Parallel sheets are large(more than five strands).
• Antiparallel sheets have few strands (not more than two)
Hydrophobic side chains

29. Tertiary structure