Protein Biochemistry

Question 1

Amino acids

Answer 1

20 amino acids (human synthesize 11, essential amino acids 9)

Amino group, carboxylic acid group, R group (varying) defines chem of amino acid

Order of amino acid=nature/structure/function of protein

Question 2

Classes of amino acid (R group)

Answer 2

Nonpolar: R group w/ CH2 or CH3

Polar uncharged: R group w/ oxygen or EN atom

Charged: R group w/ acid or bases (ionize)

Aromatic: aromatic ring

Special Character: Cysteine (disulfide bridge - SS)

Question 3

Primary structure

Answer 3

1) Sequence of amino acids within protein
2) Dehydration synthesis (peptide bonds amino acids)

3) 2 amino acids: dipeptide
- multiple amino acids: polypeptide

4) free amino group (N-terminal) & free carboxylic acid group (C-terminal)
- Amino acids added to C-terminal

Question 4

Secondary structure (NO R group relevant)

Answer 4

Protein backbone (peptide group, not R group) - interact (H-bonds)

Patterns: alpha-helices (cylindrical region) & beta-pleated sheets (planar region)

Patterns in many proteins: motifs
Helix turn helix motif, beta barrel motif (photo)

Domains: regions of large proteins (specific function within protein)

Question 5

Tertiary structure

Answer 5

Interactions b/w R groups (structure from 2nd structure patterns)

Final 3D structure, determines function of protein

H-Bonds, disulfide bridges, ionic bonds, van der Walls interactions, hydrophobic exclusions/interactions 
Test question (photo)

Question 6

Quaternary structure

Answer 6

3D structure: Association of several individual polypeptides (subunits)

Recap: photo

Question 7

Denaturation

Answer 7

Protein lose 3D structure = lose function

Causes: heat, treatment w/ acid, ionizing radiation, reducing agents, etc.

Chaperones: proteins that help folding of proteins