BioPHYSICAL chemistry

regions of the lipids are exposed to aqueous environments and the hydro-
phobic regions are buried. Proteins are embedded within the bilayer, usually
forming long helices connected by loops that lie outside of the bilayer. In
eukaryotic cells, carbohydrates may be attached to the exposed portions
of the lipids and proteins. The membrane mosaic is fluid as the lipids and
proteins are able to move within the membrane.

Amino acids

Proteins are built from amino acids. Each amino acid has the fundamental
unit of a carbonyl group (COOH) and an amino group (NH 2 ) bonded to
a central carbon atom that is designated as Cα(Figure 1.6). The amino
acids differ from each other by the presence of the side chain. There are
20 different side chains found in proteins and these differ in the struc-
ture, size, and charge. Each atom of an amino acid is uniquely identified,
with the atoms of the side chain being designated by the Greek letters β,
γ, δ, and εproceeding from the αcarbon
(the oxygen, nitrogen, and other carbon
do not have letters assigned). There are two
possible stereoisomers of each amino acid
that are mirror images of each other, but
only the L-amino acids are found in pro-
teins (Figure 1.7). The presence of only one
isomer allows cells to synthesize proteins
that are asymmetric, causing reactions to
be stereospecific.

Classification of amino acids by their side chains

An understanding of the properties of proteins requires knowledge of
the chemical properties of the amino acids. The amino acid residues can
be classified into groups according to the properties of the side chains.

CHAPTER 1 BASIC THERMODYNAMIC AND BIOCHEMICAL CONCEPTS 15

Side chain

Cα

H

Amino group

(a)

H

N

H

Carboxyl group

O

OH

C

R

(b)

Cα

H H

N

nn 1

O

H

Peptide bond

H O

C

N

Cα

C

R 1

R 2

Figure 1.6(a) The basic structure of an amino acid with the side chain represented by R.
(b) Amino acids can be covalently joined through a peptide bond to form a peptide.

COO

CH 3

L-Alanine

H 3 N C H

COO

CH 3

D-Alanine

HNC H 3

Figure 1.7

Of the two possible

stereoisomers,

L-amino acids are

found in proteins.