Amino Acids & Peptides

Lecture 4 and part of 4

General structure of Amino Acid

Amino group: NH3+ / NH2

• pKa = 9.5

Carboxyl group: COOG / COO-

• pKa = 2.0

R = side chain

Neutral non-polar amino acids

= aliphatic

GAVLIP

Neutral non-polar amino acids (cont.)

FWM

Neutral polar amino acids

STCYNQ

Positively charged basic amino acids

KRH

Negatively charged acid amino acids

DE

Bond between 2 amino acids in a protein

amide bond

formed between carboxylic group of amino acid (i) and the amino group of amino acid

Direction of protein sequence

N-term to C-term

Peptide nomenclature

# amino acids < 10 = peptide

# amino acids from 10-100 = polypeptide

# amino acids > 100 = protein

A

Ala

Alanine

R

Arg

Arginine

D

Asp

Aspartic Acid

N

Asn

Asparagine

C

Cys

Cysteine

E

Glu

Glutamic Acid

Q

Gln

Glutamine

G

Gly

Glycine

H

His

Histidine

I

Ile

Isoleucine

L

Leu

Leucine

K

Lys

Lysine

M

Met

Methionine

F

Phe

Phenylalanine

P

Pro

Proline

S

Ser

Serine

T

Thr

Threonine

W

Trp

Tryptophan

Y

Tyr

Tyrosine

V

Val

Valine

K, R, and H

basic

NH3+ / NH2 side chain

D, E

acidic

COOH / COO- side chain

Hydrophobic interactions

= interactions between non-polar amino acids

(Ala, Val, Ile, Leu, Trp, Phe)

• Hydrophobic aa: clustered in the core of he protein away from water

• Hydrophilic aa: exposed at the surface

Hydrogen bonds

Between the amide groups of the protein backbone

Between side chains

(Ser, Asp)

Ionic bonds

= interactions between positively charged amino acids (Lys, Arg) & negatively charged amino acids (Asp, Glu)

Disulfide bridges

= covalent bond between two cysteines

(oxidation of their thiol groups)