Protein chemistry

Learning goals

• To know different classes of proteins and their functions

• To know the structure and naming of all 20 protein amino acids

• To know the structure and properties of peptides and the particularly the structure of the
peptide bond.

• Ionization behavior of amino acids and peptides at different pH’s.

• To know the general pKa’s of amino acids: their carboxyls, aminos, the R-group weak acids.

• To know the different levels of protein structures

 Functions of Proteins
Proteins perform many different functions in the body
 Amino Acids
• are the building blocks of proteins.
• contain a carboxylic acid group and an amino group on the
alpha () carbon.

• Each AA contain a different side group (R).

• Amino acids in solution at neutral pH exist predominantly
as dipolar ions
• Also called zwitterions if the number of positive and
negative charges are equal).

• In the dipolar form, the amino group is protonated (-NH3+) and

the carboxyl group is deprotonated (-COO-).

• The ionization state of an amino acid varies with pH

Ionization of amino acids state as a function of pH
 Classification of Amino
•
Acids
There are 20 common amino acids found in human proteins.

• The 20 AA’s are classified into five groups based on polarity and charge of the R group

i. Non– polar aliphatic R- groups

ii. Polar uncharged R groups

iii. Aromatic R groups

iv. Positively charged R groups

v. Negatively Charged R groups

• Glycine in non-chiral

• Proline – imino acid (five membered ring

structure, rigid in confirmation): the amino
group is secondary not primary as other
amino acids

• The hydrocarbon R groups in Ala, Val, Leu,

Met and Ile , often involved in hydrophobic
interaction for stabilizing protein structure
+
• Disulfide bonds: SH group of two Cys in proteins can be oxidized to form a
covalent disulfide bond

• Disulfide bonds play special role in the structures of many proteins by

forming covalent links
• Phe & Tyr: Benzene rings

• Tryptophan: indole ring

• The OH- group in Tyr is an important

funtional group in proteins
(Phosphorylation, hydrogenation etc)
• NB: Phe is purely hydrophobic, whereas
Tyr and Trp are less so coz of their OH
and NH groups.
Aromatic cpds Contain conjugated planar ring systems with delocalized pi
electron clouds instead of discrete alternating single and double bonds