Amino acids Compiled and Edited by

Dr. Syed Ismail Associate Professor, SSAC

College of Agriculture, VN MKV Parbhani

Amino Acids: Building Blocks of Protein

1. Proteins are heteropolymers of -amino acids

2. Amino acids have properties that are well suited to carry out a

variety of biological functions

Functions:

1. Capacity to polymerize

2. Useful acid-base properties

3. Varied physical properties

4. Varied chemical functionalities

Most -Amino Acids are Chiral

The -carbon has always four

substituents and is tetrahedral

All (except proline) have an

acidic carboxyl group, a basic

amino group, and an alpha

hydrogen connected to the -

carbon

Each amino acid has an

unique fourth substituent R

In glycine, the fourth

substituent is also hydrogen

4 Compiled & Edited by Dr Syed Ismail,

MKV Parbhani

Amino Acid Enantiomers

•Steroisomers / enantiomers

•Biological system only synthesize

and use L-amino-acids

5 Compiled & Edited by Dr Syed Ismail,

MKV Parbhani

Amino Acid Classification

• Aliphatic

• Aromatic

• Sulfur containing

• Polar/uncharged

• basic/acidic

Hydrophobic

Hydrophilic

6 Compiled & Edited by Dr Syed

Ismail, MKV Parbhani

7

Am

ino

Acid

Typ

es

Name R-Group Properties

Glycine G Gly Hydrophobic

Alanine A Ala Hydrophobic

Valine V Val Hydrophobic

Leucine L Leu Hydrophobic

Isoleucine I Ile Hydrophobic, two chiral carbons

Proline P Pro Cyclic, not terribly hydrophobic

Phenylalanine F Phe Hydrophobic, bulky

Tyrosine Y Tyr Less hydrophobic (than Phe), bulky

Tryptophan W Trp Hydrophobic, bulky (indole ring)

Cysteine C Cys Hydrophobic, highly reactive (S-S link)

Methionine M Met Hydrophobic (start a.a.)

Serine S Ser Hydrophilic, reactive

Threonine T Thr Hydrophilic, reactive, two chiral carbons

Lysine K Lys Highly hydrophilic, positively charged

Arginine R Arg Highly hydrophilic, positively charged

Histidine H His Highly hydrophilic, positive or neutral

Aspartate D Asp Highly hydrophilic, negatively charged

Glutamate E Glu Highly hydrophilic, negatively charged

Asparagine N Asn Uncharged

Glutamine Q Gln Uncharged

Aliphatic (alkane) Amino Acids

•Proline (pro, P)- cyclic “imino acid”

•Glycine(gly, G)-only non-chiral amino acid, not hydrophobic

•Alanine (ala, A) – R-group = methyl-group

•Valine (Val, V) –

•Leucine (Leu, L) –

•Isoleucine (Ile, I) -2 chiral carbons

Hyd

rop

ho

bic

ity

8

Aromatic Amino Acids • All are hydrophobic

• All contain aromatic group

• Absorb UV at 280 nm

• Phenylalanine (Phe, F)

• Tyrosine (Tyr, Y) – -OH ionizable (pKa = 10.5), H-Bonding

• Tryptophan (Trp, W) – bicyclic indole ring, H-Bonding

Phe Tyr

TRP 9

Sulfur Containing Amino Acids

• Methionine (Met, M) – “start” amino

acid, very hydrophobic

• Cysteine (Cys, C) – sulfur in form of

sulfhydryl, important in disulfide

linkages, weak acid, can form

hydrogen bonds.

10 Compiled & Edited by Dr Syed

Ismail, MKV Parbhani

• Contain carboxyl groups (weaker acids than a-carboxyl-group)

• Negatively charged at physiological pH, present as conjugate

bases (therefore –ate not –ic acids)

• Carboxyl groups function as nucleophiles in some enzymatic

reactions

• Aspartate –

• Glutamate –

Acidic Amino Acids

11 Compiled & Edited by Dr Syed Ismail,

MKV Parbhani

Basic Amino Acids • Hydrophillic nitrogenous bases

• Positively charged at physiological pH

• Histidine – imidazole ring protonated/ionized, only amino acid

that functions as buffer in physiological pH range.

• Lysine - diamino acid, protonated at pH 7.0

• Arginine - guianidinium ion always protonated, most basic amino

acid

12

Histidine Lysine Arginine

• Polar side groups, hydrophillic in nature, can form hydrogen bonds

• Hydroxyls of Ser and Thr weakly ionizable

• Serine (Ser, S) – looks like Ala

• Threonine (Thr, T) – 2 chiral carbons

• Asparagine (Asn, N) – amide of aspartic acid

• Glutamine (Gln, Q) – amide of glutamic acid

Polar Uncharged Amino Acids

13 Compiled & Edited by Dr Syed

Ismail, MKV Parbhani

Essential/Non-Essential Amino Acids

14 Compiled & Edited by Dr Syed

Ismail, MKV Parbhani

Peptides and Peptide bonds

Peptide bond in a

di-peptide

“Peptides” are

small

condensation

products of amino

acids

They are “small”

compared to

proteins (di, tri,

tetra… oligo-)

17 Compiled & Edited by Dr Syed Ismail,

MKV Parbhani

Peptide Ends are Not the Same Numbering starts from the amino terminus

AA1 AA2 AA3 AA4 AA5

18 Compiled & Edited by Dr Syed Ismail,

MKV Parbhani

Compiled & Edited by Dr Syed

Ismail, MKV Parbhani

19

Pro

tein

Pri

mary

Str

uctu

re

Note the

Polarity of

the

sequence

(amino

carboxy)

Note also the disulfide

linkages (cys-cys S-S

bonds; actually considered

a component of tertiary

structure)

Proteins are:

• Cofactor is a general term for functional non-amino acid component – Metal ions or organic molecules

• Coenzyme is used to designate an organic cofactors – NAD+ in lactate dehydrogenase

• Prosthetic groups are covalently attached cofactors – Heme in myoglobin

• Polypeptides (covalently linked -amino acids) + possibly –

• cofactors,

• coenzymes,

• prosthetic groups,

• other modifications

20 Compiled & Edited by Dr Syed

Ismail, VN MKV Parbhani

Protein Nomenclature

• Peptides 2 – 50 amino acids

• Proteins >50 amino acids

• Amino acid with free -amino group is the amino-terminal or N-terminal residue

• Amino acid with free -carboxyl group is the carboxyl-terminal or C-terminal residue

• Three letter code – Met-Gly-Glu-Thr-Arg-His

• Single letter code – M-G-E-T-R-H

21 Compiled & Edited by Dr Syed

Ismail, MKV Parbhani

Compiled & Edited by Dr Syed

Ismail, MKV Parbhani

22

Fiv

e C

ate

go

rie

s

Note 20

(naturally

translated)

amino acids