Amino Acid

Structures and Function

Amino acid Functions

Components of peptides and proteins
Amino acids or their derivatives are also form components
of lipids
Serine in phospholipids and glycine in bile salts
Several amino acids function as neurotransmitters
themselves
Precursors of neurotransmitters, mediators, or hormones
Specific amino acids form precursors for other
metabolitese. g., for glucose in gluconeogenesis, for
purine and pyrimidine bases, for heme, and for other
molecules.

BASICS
Lets start with the basics. All amino acids have a common structural
unit that is built around the alpha carbon (click 1). Lets call this the core
structure. The figure shows the core with one of the bonds on the -carbon
unassigned. A group in this location is represented by the letter R (click 1).

H3N

COOH
C
R

H
R

R groups are the only variable groups in the structure. Consider R the only
unknown and focus on this group to learn the structures. Hence, Rule (1) is
amino acids are composed of a core group and an R group. Rule (2) is the R
group gives an amino acid its structural identity. Thus, if you insist on using flash
cards, draw them as shown above (click 1) with the box representing the core.
Click to go on.

Building an R Group
You saw the importance of the R group. Now, you will see how R
groups build and interrelate. Four that illustrate this point are glycine, alanine,
phenylalanine and tyrosine. The R groups of each will be shown below (click 1).
Glycine

Alanine

CH3

Phenylalanine

CH2

Tyrosine

CH2

OH
With an H, glycine is the simplest amino acid, so named because of its sugary taste
(click 1). Alanine with a methyl group is the next simplest (click 1). The red color
helps you see how each R group structure differs from the preceding. Phenylalanine
arises when a phenyl group replaces an H on alanines methyl group (click 1).
Tyrosine evolves by adding an OH group to the para position on the phenyl ring of
phenylalanine (click 1). Click to go on.

Acidic and Amide Amino Acids

The acidic amino acids have () charges in their R group. There are
two, aspartic acid and glutamic acid (click 1). Note their similarity. Glutamic acid
has one more CH2 group (click 1). Note that both have a COO group which
gives the negative charge.
Aspartic
acid

CH2
COO
Aspartate

Glutamic
Acid

Glutamine

Asparagine

CH2

CH2

CH2

COO
C=O

COO

NH2

Glutamate

CH2

CH2
C=O
COO
NH2

The COO can exchange a proton with the solvent and hence behave as an acid.
The suffix ate is used to designate an ionized acid (more properly called a salt).
Hence, you will see aspartic acid and glutamic acid referred to as aspartate and
glutamate (click 1). By forming the amide derivatives of aspartate and glutamate
you give rise to asparagine and glutamine (click 1). Note name and structure
similarities between the open and the corresponding amide amino acids. Click
to go on.

The (+) charged amino acids are represented by lysine, arginine and
histidine. Unfortunately, R structures for basic amino acids have little resemblance
to one another. But each is characterized by a (+) N in the R group.
Lysine

Arginine

CH2

CH2

CH2

CH2

CH2

CH2

CH2

NH

NH

+
3

Epsilon amino

H2N=C

Histidine

CH2

HN

NH+
Imidazole

NH2

Guanidinium

It will help you to remember that each (+) N is part of a group. For lysine this
group is called the epsilon amino group (click 1). In arginine its the
guanidinium group and for histidine its the imidazole group. Remember these
group names and you will remember the structures of the basic amino acids.
Click to go on.

Serine,Threonine, Cysteine and Methionine

Start with serine. Serine has a simple CH2OH for it R group (click 1).
Threonine is serine with a methyl group (click 1). And, if you replace the O in
serine with an S, you generate cysteine (click 1).
Serine

CH2OH

Threonine

H-C-OH
CH3

Cysteine

CH2SH

Methionine

CH2
CH2
S
CH3

Methionine appears to combine cysteine with threonine. The name tells you
methionine has a sulfur (thio) and a methyl group in the structure. Like
threonine methionine has a 2 carbon chain attached to the alpha carbon (click
1). This is followed by sulfur and ends with a methyl on the sulfur. Click to go
on.

Valine, Leucine, Isoleucine

These 3 branched-chain hydrophobic amino acids have only C and H in
their R groups. Valine is easy to remember because the carbon chain is
arranged as the letter V (click 1). Leucine and isoleucine both have a 4 carbon
R group. Leucine resembles valine but with a -CH2 before the V (click 1).
Isoleucines side chain resembles the letter L, just the opposite of what you
would predict from the name (click 1). To distinguish the 3, focus only on the
branched chains in the R structure. Valine and leucine have only methyl groups,
whereas isoleucines branches are one methyl and one ethyl group (click 1).
Click to go on.
Leucine

Valine

C
C

C
C

Isoleucine

C C

C
C

Ethyl group

Tryptophan and Proline

The last 2 amino acid to consider are tryptophan (pronounced trip-toefane) and proline. Tryptophan is unique in having an indole ring (click 1). Attach
this ring to the core via a CH2 group and you complete the structure of tryptophan
(click 1). Proline also has a ring, but this ring is saturated. In fact prolines ring
looks like home plate in baseball (click 1). Note proline does not have a core
structure. This is because the alpha amino group is incorporated into the ring.
Tryptophan
Proline

CH2

H2C

CH2
C

H2 C

Indole

N
H

N
H

H
COO

This completes all the amino acids.

Review this lesson as many times as necessary.
Use paper and pencil to draw out the structures.
Soon you will have mastered amino acid structures.
Click to go on to quiz.

 The aliphatic amino acids (class I) include glycine,

alanine, valine, leucine, and isoleucine.
These amino acids do not contain hetero atoms (N, O, or
S) in their side chains and do not contain a ring system.
Their side chains are markedly apolar.

 The
sulfurcontaining
amino
acids cysteine and methionine
(class II), are also apolar.
Ability to form disulfide bonds,
cysteine plays an important role in
the stabilization of proteins
Two cysteine residues linked by a
disulfide bridge are referred to as
cystine

 The aromatic amino

acids (class III) contain
resonance
stabilized
rings.
In this group, only
phenylalanine
has
strongly
apolar
properties.
Tyrosine and tryptophan
are moderately polar,
and histidine is even
strongly polar.

neutral
The
amino
acids
(class IV) have
hydroxyl
groups
(serine, threonine)
or amide groups
(asparagine,
glutamine).
their
Despite
nonionic
nature,
the amide groups
of asparagine and
glutamine
are
markedly polar.

 The carboxyl groups

in the side chains of
the acidic amino
acids aspartic acid
and glutamic acid
(class V) are almost
completely ionized at
physiological
pH
values.

 The side chains of the

basic
amino
acids
lysine and arginine are
also fully ionizedi. e.,
positively
chargedat
neutral pH. Arginine, with
its
positively
charge
guanidinium group, is
particularly
strongly
basic,
and therefore
extremely polar.
Histidine, which is only
aromatic in protonated
form can therefore also
be classified as a basic
amino acid.

 Proline (VII) is a special

case. Together with the
-C atom and the -NH2
group, its side chain
forms a five membered
ring. Its nitrogen atom is
only weakly basic and is
not
protonated
at
physiological pH.
Due to its ring structure,
proline causes bending
of the peptide chain in
proteins

Essential Amino acids

Essential amino acids - that the human body is not
capable of producing on its own.
Amino acids, including cysteine and histidine, are not
absolutely essential, but promote growth in children.
Some amino acids are able to substitute for each other
in the diet.
Humans can form tyrosine, which is actually essential, by
hydroxylation from phenylalanine, and cysteine from methionine.

Proteins that lack several essential amino acids or only

contain small quantities of them are considered to be of
low value.
Pulses only contain small amounts of methionine, while wheat
and corn proteins are poor in lysine. In contrast to vegetable
proteins, most animal proteins are high-value