Amino Acids

Collins Edward Jana, PhD

Biochemistry Division, Biomedical

Sciences Department
 Learning Outcomes

1. Know amino acids as building blocks

2. Explain classification of amino acids
3. Know basic & acidic properties of AAs
 References

1. Harper’s Illustrated Biochemistry

2. Principles of Biochemistry by Lehninger
3. Basic Medical Biochemistry: A Clinical Approach
by Marks
4. Biochemistry and Molecular Biology by Elliott
5. Introduction to Nutrition & Metabolism by Bender
6. Biochemistry 4th edition by Campbell
 What are amino acids?

• Building blocks of proteins

General structure
H
H2N C COOH
R
• 20 naturally occurring AAs
• 8 essential ones in adults (9 in infants including
histidine)
 Amino acids
Simplest amino acids

Glycine; R = H
Alanine; R = CH3
H H
H2N C COOH H2N C COOH
H CH3
Glycine Alanine
Abbreviations and symbols for amino
acids
• 3 letter abbreviation & single letter codes

Criteria for determining single-letter codes

- Unique 1st letter
- Most commonly occurring amino acids have
priority
- Phonetically suggestive codes
- Letter close to initial letter

Dr Margaret Oakley Dayhoff

 Names of the common amino acids
Name Abbreviations R polarity R acidity
Alanine Ala A nonpolar neutral
Arginine Arg R polar basic (strongly)
Asparagine Asn N polar neutral
Aspartic acid Asp D polar acidic
Cysteine Cys C nonpolar neutral
Glutamic acid Glu E polar acidic
Glutamine Gln Q polar neutral
Glycine Gly G nonpolar neutral
Histidine His H polar basic (weakly)
Isoleucine Ile I nonpolar neutral
Leucine Leu L nonpolar neutral
Lysine Lys K lar basic
 Name Abbreviations R polarity R acidity

Methionine Met M nonpolar neutral

Phenylalanine Phe F nonpolar neutral

Proline Pro P nonpolar neutral

Serine Ser S polar neutral

Threonine Thr T polar neutral

Tryptophan Trp W nonpolar neutral

Tyrosine Tyr Y polar neutral

Valine Val V nonpolar neutral

 Classification of amino acids
Based on the nature of the side chain R, which determines the
hydrophilicity and hydrophobicity of the amino acids.

- Hydrophilic aas tend to interact

with the aqueous environment,
- Mostly found on the exterior
surfaces of proteins.

- Hydrophobic aas tend to repel the

aqueous environment
- Reside mainly in the interior of proteins
- The hydrophobic interactions between their side chains in
proteins tend to stabilize the secondary and tertiary structure.
 Acidic amino acids
• Have acidic side chains (COOH)
H H
H2N C COOH H2N C COOH
CH2 CH2
COOH CH2
Aspartate COOH
Glutamate

• at physiological pH will carry negative

charge.
 Basic amino acids
• Contain basic side chains (NH2)
H H H
H2N C COOH H2N C COOH H2N C COOH
CH2 CH2 CH2
CH2 CH2 C NH
CH
CH2 CH2
HC N
NH CH2
Histidine
+
C NH2 NH2
NH2
Lysine
Arginine

• At physiological pH, basic amino acids will be positively charged

Amides of the acidic amino acids
• The acidic amino acids also exist as amides
H H
H2N C COOH H2N C COOH
CH2 CH2

CO CH2
NH2 CO
Asparagine NH2

• They are amide forms of aspartate and glutamate

Glutamine in which

side chain COOH groups are amidated.

• They are classified as neutral amino acids.
 Aromatic amino acids

Have aromatic side groups

H H H
H2N C COOH H2N C COOH H2N C COOH
CH2 CH2 CH2

NH
OH
Phenylalanine
Tryptophan Tyrosine
Sulphur-containing amino acids

Have sulphur in their side group

H H
H2N C COOH H2N C COOH
CH2 CH2
CH2 SH
S
Cysteine
CH3
Methionine
 Branched chain amino acids
(hydrophobic)
• Contains bulky hydrophobic side chains
H H H

H2N C COOH H2N C COOH H2N C COOH

HC CH3 CH2 H C CH3

CH2 H C CH3 CH3

CH3 CH3 Valine

Isoleucine Leucine

• R is alkyl hydrophobic group which cannot participate in

hydrogen bond formation
 Imino acid
• It has an imino (-NH) group rather than an
• NH2 amino group
Imino nitrogen
H

HN C COOH
Unusual bond
H2C CH2
C
H2

Proline

• -R & α-amino N form a rigid 5-membered ring structure

• -Has a 2o amino group
 Hydroxylated amino acids
• Have hydroxyl groups in the side chain

H H

H2N C COOH H2N C COOH

CH2 HC OH

OH H3C
Serine Threonine
Acid-Base properties of amino acids
• Amino acids are amphoteric, can act as a base or acid.
• All aas contain at least 2 ionizable grps, the –COOH & -NH2
which in solution forms a dipolar ion (containing
+ve & -ve charge) H
+
H3N C COO-
R

• Neutral dipolar ions are called zwitterions. (zwitter – hybrid)

• Some aas contain acidic or basic group in their side chain,
which determines the acidic or basic behavior
Acid-Base properties of amino acids
In solution, the following ionic equilibrium reactions
may be written:

R-COOH R-COO- + H+
R-NH2 + H+ R-NH3+

And because they can be ionised in aqueous

solutions, they can act as acids or bases.
Acid-Base properties of amino acids
In acidic solution, the COO- grp in the aa accepts a
proton

In more basic solution, the NH3+ donates a proton.

Therefore behaving as an acid and at other times as a
base depending on the pH of the medium.

H H O H H O H H O
+H OH-
+
HN C C +
HN C C - N C C -
H R OH O O
H R H R
at acidic pH at basic pH
+ve at physiological pH
-ve
Acid-Base properties of amino acids

The net charge of the aa molecule depends on the type

of amino acid and the pH of the medium

The pH at which the net +ve and –ve charges are equal
is the amino acid’s isoelectric point (pI). At this point
The overall charge of all amino acids in a sample is
zero.