Amino Acids and Peptides

Prepared by :
Justin Brian V. Chiongson, MSc. , RCh
Relicardo M. Coloso, PhD, RCh
 Amino Acid Structure –
building blocks of proteins
-variable for each amino acid
Amino Acids – three letter and one letter notation

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Amino acid classifications:
Non-polar side chains
Amino acid Three letter One letter R-group pI
abbreviation abbreviation
Glycine Gly G None 6.0
Alanine Ala A Alkyl 6.0
Valine Val V Alkyl 6.0
Leucine Leu L Alkyl 6.0
Isoleucine Ile I Alkyl 6.0
Phenylalanine Phe F Aromatic 5.5
Proline Prol P Rigid cyclic 6.3
structure
Nelson and Cox 2005. Lehninger Principles of Biochemistry
Side chains with hydroxyl group
Amino acid Three letter One letter R-group pI
abbreviation abbreviation

Serine Ser S Hydroxyl 5.7

Threonine Thr T Hydroxyl 5.6
Tyrosine Tyr Y Phenol-OH 5.7
 ,Uncharged

Nelson and Cox 2005. Lehninger Principles of Biochemistry

Nelson and Cox 2005. Lehninger Principles of Biochemistry
Side chains with sulfur
Amino acid Three letter One letter R-group pI
abbreviation abbreviation

Cysteine Cys C Thiol 5.0

Methionine Met M Methyl 5.7

sulfide
Sulfur-containing amino acids

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Side chains with non-basic nitrogen
Amino acid Three letter One letter R-group pI
abbreviation abbreviation

Asparagine Asn N Amide 5.4

Glutamine Gln Q Amide 5.7

Tryptophan Trp W Indole 5.9

 Asparagine, Glutamine, and Tryptophan

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Tryptophan (Trp) [W]

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 Acidic side chains
Amino acid Three letter One letter R-group pI
abbreviation abbreviation

Aspartic acid Asp D Carboxylic acid 2.8

Glutamic acid Glu E Carboxylic acid 3.2

Nelson and Cox 2005. Lehninger Principles of Biochemistry
 Basic side chains
Amino acid Three letter One letter R-group pI
abbreviation abbreviation

Lysine Lys K Amino 9.7

Arginine Arg R Guanidino 10.8

Histidine His H Imidazole 7.6

Basic amino acids
Nelson and Cox 2005. Lehninger Principles of Biochemistry
Nonpolar: V, L, I, F, Y, M, P; to some extent: G,
A,T

Polar: S, T, C, D, E, N, Q, K, R, H

Acidic: D, E

Basic: K, R, H
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Essential amino acids: HMATTILLVP
Amino acids that cannot be synthesized by
humans and have to be obtained from the diet

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Isoelectric point – the pH at which the net charge of
the molecule is 0

Zwitterion – the ion form of the amino acid wherein

the net charge of the molecule is zero; the ionized
form of the amino acid at its isoelectric point
pKa values of amino acids
 Ionization of aspartic acid starting with the
most protonated form (at low pH)
showing pK1 (-COOH) , pKR and pK2 (-NH2)

Net charge

+1 0 -1 -2
Properties of Amino Acids

1. Generally soluble in water, insoluble in

nonpolar solvents such as benzene and ether
2. High Melting Pt and low Vapor Pressure
3. Large Dipole Moments and High dielectric
constants
4. Chiral (except for glycine); D- and L-isomer
5. Absorb light in the UV region (aromatic
amino acids, F-260nm, W-280nm, Y-275nm)
Peptide

Peptide bonds are covalent bonds formed by

the nucleophilic addition-elimination reaction
between the carboxylic group of one amino
acid and the amino group of another amino
acid; this reaction releases a molecule of
water as the by product. 
Peptide bond formation – mechanism of
nucleophilic addition–elimination reaction

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 Naming a peptide
• 1. number of amino acids
2 amino acids – dipeptide
3 amino acids – tripeptide
4 amino acids – tetrapeptide and so on
• 2. name starting from the N-terminal end to
the C-terminal end
Ex. H2N- M-A-G-A-L-I-N-G-COOH, an octapeptide
Nomenclature- methionyl alanyl glycyl alanyl leucyl
isoleucyl asparaginyl glycine
 Exercise

1. Calculate the pI value (isoelectric point)

of the peptide
H2N- M-A-G-A-L-I-N-G-COOH

2. What is the N-terminal amino acid?

the C-terminal amino acid?

3. Predict the net charge on the peptide at pH 7.