BioPHYSICAL chemistry

group. Phenylalanine and tryptophan are highly hydrophobic and usually

buried within proteins. Tyrosine is less hydrophobic due to the hydroxyl

group, which can form hydrogen bonds. Because of the delocalized πelec-

tron distribution of these aromatic rings, these amino acid residues have

an optical absorption spectrum in the ultraviolet region that can be used

to characterize proteins containing these residues.

Four amino acids have hydroxyl or sulfur-containing side chains. Two

amino acids, serine and threonine, have aliphatic hydroxyl side chains.

The hydroxyl groups on serine and threonine make them more hydro-

philic and reactive than alanine and valine. Two amino acids contain

sulfur atoms: cysteine has a terminal sulfhydryl group (or thiol group) and

methonine has a thioether linkage. Because of the sulfur-containing side

chains, these residues are hydrophobic. The sulfhydryl group of cysteine

is highly reactive and will often be found forming a disulfide bond with

another nearby cysteine.

There are two groups of residues that can be charged, rendering them

highly hydrophilic. Lysine and arginine are positively charged at neutral

pH. The side chains of lysine and arginine are the longest ones of

the 20 amino acid residues. Histidine can be uncharged or positive,

depending upon the local environment, and is often found at the active

site of proteins due to the reactivity of the imidazole ring. Aspartate

and glutamate are amino acids that are almost always negatively

charged. Asparagine and glutamine have very similar structures to

aspartate and glutamate respectively except for a terminal amide group

in place of the carboxylate group.

Finally, one amino acid, proline, has an aliphatic side chain but

differs from the other 19 amino acids because it has a cyclic structure.

The side chain shares many of the properties of the aliphatic amino

acids but has the rigidity of the ring compared to the flexibility of the

other amino acids. Proline is often found in bends and turns of pro-

teins because of the uniqueness of its character.

DNA and RNA

Deoxyribonucleotides make up the basic units of deoxyribonucleic

acid, DNA, whereas ribonucleotides form the basis for ribonucleic acid,

RNA. A nucleotide consists of a nitrogenous base, a sugar, and one or

more phosphate groups (Figure 1.9). In DNA the sugar is deoxyribose

and the bases in DNA are either purines, adenine (A) or guanine (G),

or pyrimidines, thymine (T) or cytosine (C). In DNA, the nucleotides

are linked together in a defined chain. The 3′-hydroxyl of the sugar of

one deoxyribonucleotide is joined to the 5′-hydroxyl of the adjacent

sugar by a phosphodiester bridge. With this arrangement a backbone

is created consisting of the deoxyriboses linked by the phosphate groups.

18 CHAPTER 1 BASIC THERMODYNAMIC AND BIOCHEMICAL CONCEPTS

O

O

O

O

H 2 C^5 

3 

1 

HH

H

OH

H

O P O

Base

O P O

H 2 C

O

HH

H

OH

H

Base

O

O

P O

H 2 C

HH

H

OH

H

Base

Figure 1.9The chemical
structure of a DNA chain.