AMINO ACIDS
The commonest amino acids are -amino acids, which are found in most living
systems. They have a primary amino group bonded to the -carbon atom of a
carboxylic acid and have the general formula:
R
H2N.CH.COOH
The 20 naturally occurring amino acids differ only in the nature of the R group.
Except when R=H (glycine), the -carbon atom is asymmetric, and the amino acid
shows optical activity. It is usual for living systems to contain only one enantiomer.
Name
glycine
alanine
serine
aspartic acid
asparagine
valine
leucine
isoleucine
threonine
cysteine
methionine
glutamic acid
lysine
phenylalanine
tyrosine
Abbreviation
Gly
Ala
Ser
Asp
Asn
Val
Leu
Ile
Thr
Cys
Met
Glu
Lys
Phe
Tyr
R=
H
CH3
CH2OH
CH2COOH
CH2CONH2
CH(CH3)2
CH2CH(CH3)2
CH(CH3)CH2CH3
CH(CH3)OH
CH2SH
CH2CH2SCH3
CH2CH2COOH
CH2CH2CH2CH2NH2
CH2C6H5
CH2C6H4OH
Acid & Base Properties
Amino acids contain both an amino group, which is basic, and a carboxyl group,
which is acidic. Because of this, amino acids never exist in the form of an uncharged
compound. At a pH of 7.3, which is found in living systems, the carboxyl group
protonates the amino group to form a dipolar ion known as a zwitterion. The
zwitterion has no overall charge.
R
+
H3N.CH.COO
The presence of the zwitterion increases the strength of the bonding in amino acid
crystals. They therefore have much higher melting points than similar compounds
which lack this ionic character.
For example,
glycine H2NCH2COOH melts at 290oC, whereas
2-hydroxyethanoic acid HOCH2COOH melts at 80oC
In a strongly acidic solution, the carboxyl group is undissociated and the amino group
is protonated. In a strongly alkaline solution, a proton is removed from the carboxyl
group and the amino group is uncharged.
R
+
H3N.CH.COOH
strongly acidic
R
+
H3N.CH.COO
neutral
TOPIC 13.9: AMINO ACIDS & PROTEINS 1
R
-
H2N.CH.COO
strongly alkaline
Proteins
Proteins are naturally occurring polymers formed by the joining together of up to
4000 amino acids. The amide bond CO-NH which forms between amino acids is
usually called a peptide link. Proteins are frequently referred to as polypeptides.
R’
R
R”
+
H2N.CH.COOH
+
H2N.CH.COOH
R
R’
H2N.CH.CO
NH.CH.CO
H2N.CH.COOH
R”
NH.CH.COOH
peptide link
The amino acid sequence in a protein is referred to as its primary structure. The way
that the amino acid chain is shaped, into for example a -helix, is referred to as the
secondary structure.
Hydrolysis of a peptide link
Proteins can be hydrolysed into their constituent amino acids in the presence of a
strong acid catalyst, such as HCl, or by using a protease enzyme.
R
R’
H2N.CH.CO
NH.CH.CO
R”
NH.CH.COOH
H+/H2O
R’
R
+
H2N.CH.COOH
R”
+
H2N.CH.COOH
H2N.CH.COOH
The primary structure of a protein can be determined by breaking the protein down in
a stepwise manner from one end and identifying each amino acid as it is released.
TOPIC 13.9: AMINO ACIDS & PROTEINS 2
Hydrogen Bonding in Proteins
Hydrogen bonding plays an important role in the secondary structure of proteins and
is responsible for holding together ordered structures such as the -helix and the pleated sheet. Although individually hydrogen bonds are weak, the large number of
bonds present in proteins gives rise to a stable structure. In the commonest form of
hydrogen bonding in proteins, the carbonyl oxygen atom of one peptide group forms
a hydrogen bond with a hydrogen atom in another peptide group:
NH.C=O
H-N.CO
H
N
C
O
H
N
R
C
O
C
H
N
R
C
C
R
C
H
N
O
C
R
C
O
H
N
C
O
H
N
R
A peptide chain of a protein coiled
to form a -helix. The configuration
of the helix is maintained by
hydrogen bonds, shown as dotted
lines.
C
O
C
H
N
R
C
C
H
O N
C
R
C
C
O
H
N
R H
N
C
O
C
C
O
TOPIC 13.9: AMINO ACIDS & PROTEINS 3
R
R
H
O
H
C
C
N
N
O
H
H
H
O
H
N
C
H
R
H
C
N
C
C
C
N
R
O
H
H
R
O
R
H
O
H
R
H
C
C
N
C
C
N
N
C
C
R
H
O
H
R
H
O
H
O
H
R
H
O
H
C
N
C
C
N
O
H
H
H
O
H
N
C
C
H
H
N
C
N
O
H
C
N
C
C
C
R
H
R
C
C
N
C
C
C
N
R
O
H
H
R
O
R
H
O
H
R
H
N
C
C
N
C
H
O
C
H
R
C
C
H
O
The hydrogen-bonded structure of silk fibroin. The structure is
called an antiparallel -pleated sheet: the peptides run in
different directions in alternate chains.
TOPIC 13.9: AMINO ACIDS & PROTEINS 4
N
N
Asn
Asp
Leu
Tyr Arg Gly Tyr Ser Leu
Gly Asn
Trp Val
Val Asp
Gln
Thr
Gly
Lys
Lys
Phe
Arg
Gly
Asn
Ile
Lys
Ala
S
Cys
Trp
Arg
Ala
S
Gly
Ala
His
Cys
Arg
Arg
Gly
Met
Cys
Ala
Ala
Arg
Ala
S
Leu
Glu
Cys
Trp
Leu
COO
S
-
Asn
Ala
Phe
Val
Asn
Trp
Arg
+
H3N
Ser
Thr
Ala
Gly
Lys Val Phe
Gln
Asn
Gly
Gly Asp
Ser Asp
Met
Ala
Thr
Val
Asn
Ile
Arg
Lys
Lys
Arg
Asn
Ser Gly
Pro
Asn
Thr
Ala
Thr
Leu
Asp
Cys
Asn
Arg
Cys
S S
Gly
Asn
Val
Thr
Cys
Ile
S S
Ser
Asp
Ser
Thr
Asn
Pro
Ala
Ser
Asp
Ile
Ser
Gly
Ala
Leu
Ser Leu
Asp
Cys
Tyr
Trp
Gly
Trp
Ile
Leu
Arg
Ser
Asn Ile
Gln
The structure of lysozyme from hen egg-white, showing the
primary structure and the four intrachain disulphide bridges.
TOPIC 13.9: AMINO ACIDS & PROTEINS 5