BioPHYSICAL chemistry

These groups have distinctive properties such as charge and polarity. The
structure of the 20 standard amino acids are shown in Figure 1.8.
There are five amino acids with aliphatic side chains – glycine, alanine,
valine, leucine, and isoleucine – as shown in Figure 1.8. These side chains
are generally hydrophobic and will be usually found clustered in the
interior of the protein. Glycine has the simplest structure, with a single
hydrogen serving as the side chain. Alanine is next with a methyl
group, with larger hydrocarbon side chains found on valine, leucine, and
isoleucine. As the side chains become more extended the amino acids
become more hydrophobic.
Three amino acids have aromatic side chains. Phenylalanine contains a
phenyl ring attached to a methylene (-CH 2 -). The aromatic ring of tyrosine
contains a hydroxyl group. This group makes tyrosine less hydrophobic
than phenylalanine and also more reactive as the hydroxyl can form a
hydrogen bond. Tryptophan has an indole ring joined by a methylene

CHAPTER 1 BASIC THERMODYNAMIC AND BIOCHEMICAL CONCEPTS 17

COO

H 3 N C H

CH 2

CH 2

C

O NH 2

Glutamine

(Gln, Q)

COO

H H 3 N C H

CH 2

CH 2

C

O O–

Glutamate

(Glu, E)

COO

H 3 N C H

CH 2

C

O NH 2

Asparagine

(Asn, N)

COO

H 3 N C

CH 2

C

O O–

Aspartate

(Asp, D)

H

COO

H 3 N C

CH 2

Cysteine

(Cys, C)

H

COO

H 3 N C

CH 2

CH 2

CH 3

Methionine

(Met, M)

SH

S

H

COO

H 2 N C

CH 2

CH 2

H 2 C

Proline

(Pro, P)

Amino acids with amido and carboxylate groups

Amino acids containing sulfur Amino acid with a cyclic structure

Figure 1.8(Cont’d)