Lecture 1, Biochemistry

1st course\ 3rd stage Dr. Suhad

Biomolecules: Amino Acids and Peptides
 Amino acids constitute the building blocks of proteins and are precursors in the
biosynthesis of numerous nonprotein, nitrogen-containing compounds, including
heme, purines, pyrimidines, and neurotransmitters (e.g., glycine, glutamate).

 All peptides and polypeptides are polymers of alpha-amino acids.

 There are 20 -amino acids that are relevant to the make-up of
mammalian proteins.
 Several other amino acids are found in the body free or in combined
states (i.e. not associated with peptides or proteins).
Each amino acid has an amino group and a carboxyl group , joined by a single
Carbon atom. In addition, each amino acid has a characteristic "side chain" (often
called the -R group) as shown in Figures 1.1 .

Amino acids side chain vary in:

Size
Shape
Polarity
At physiological pH’s (7.0-7.4), both the carboxyl and amino groups are
charged.
Amino acids have two possible stereochemical configurations -D
and L.
L-Amino acids are the forms that are found in biological proteins. D-
Amino acids are found in rare proteins, such as the bacterial cell
wall polypeptides, where they are thought to protect against protease
digestion .
 pH dependent properties
• Zwitter ionic structures contain both N-H+ and COO-.
• At low pH, protonate COO-.
• At higher pH : lose H on N
• Isoelectric pH: differs for each amino acid (due to structural
differences)

D-amino acids are found in

a few small peptides,
including some peptides
of bacterial cell walls and
certain antibiotics (such
as penicillin).
D-Glu
D-Ala
 Chirality of Amino Acids
• A chiral center has four different functional groups.
• All naturally occurring -amino acids, except glycine (R=H), are chiral and the ‘L’
stereoisomer .

• The stereochemical reference for amino acids is the Fischer

projection of L-serine.

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Enantiomers of alanine :Since they are non superimposable
mirror images of each other, the two forms represent a class
of stereoisomers called enantiomers .

Figure : D or L enantiomers

a b
Classification Based on Essentiality:
All 20 types of amino acids are required for protein synthesis.
These amino acids can be derived from digesting dietary protein and
absorbing their constituent amino acids or, alternatively, by synthesizing
them.
There are 10 amino acids that cannot be synthesized in humans and
thus must be provided from dietary sources. These are called the
essential amino acids.
Arginine is required only during periods of growth or positive nitrogen
balance.
 Tetrahedral arrangement of bonding orbitals around the α-carbon atom

Tetrahedral arrangement of bonding orbitals around the α-carbon atom.

For all the common amino acids except glycine, the α-carbon is bonded to 4
different groups: a carboxyl group, an amino group, an R group and an H atom.
The α-carbon is therefore a chiral center; the four different groups can occupy
two unique spatial arrangements (Figure 1.6).
 Amino Acids Classification:
The amino acids can be classified as hydrophobic or hydrophilic, depending on the ease
with which their side chains interact with water. In general, proteins fold so that amino
acids with hydrophobic side chains are in the interior of the molecule where they are
protected from water, while those with hydrophilic side chains are on the surface.

Amino Acids Amino Acids 

BASIC AMINO ACIDS

ACIDIC AMINO ACIDS

• Each of the 20  -amino acids found in proteins can be distinguished by the
R-group substitution on the alpha-carbon atom.
• Two broad classes of amino acids based upon whether the R-group is
hydrophobic or hydrophilic.
– The hydrophobic amino acids reside predominantly in the interior of
proteins. This class of amino acids does not ionize nor participate in the
formation of H-bonds.
– The hydrophilic amino acids tend to interact with the aqueous
environment, are often involved in the formation of H-bonds and are
predominantly found on the exterior surfaces proteins or in the reactive
centers of enzymes.
– These side chains are non polar and hydrophobic. Ala, Val, Leu and Ile
tend to cluster together within proteins, stabilizing protein structure via
hydrophobic interactions.
 Histidine
• Contains an imidazole ring that is partially protonated in
neutral solution
• Only the pyridine-like, doubly bonded nitrogen in
histidine is basic. The pyrrole-like singly bonded nitrogen
is nonbasic because its lone pair of electrons is part of
the 6  electron aromatic imidazole ring.

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 Acid-Base Properties of the Amino Acids

 The -COOH and -NH2 groups in amino acids are

capable of ionizing (as are the acidic and basic R-groups
of the amino acids).
 At physiological pH (around 7.4) the carboxyl group will

be unprotonated and the amino group will be

protonated.
 As a general rule the amino terminal has a pKa~9.8 and

carboxy-terminal is at pKa~2.3

When the net charge of an amino acid or protein is zero the pH

will be equivalent to the isoelectric point: pI.

pI=(pKa1+pKa2)/2
Table below lists the 20 amino acids used to make proteins, the one-letter code used to
designate them, and some of their chemical properties. Figure 2 shows the structures of the 20
amino acids in proteins.
 Zwitterionic property
A zwitterion is a molecule with functional groups, of which at least one has a
positive and one has a negative electrical charge.
The net charge of the entire molecule is zero. Amino acids are the best-known
examples of zwitterions. They contain an amine group (basic) and a
carboxylic group (acidic). The -NH2 group is the stronger base, and so it
picks up H+ from the -COOH group to leave a zwitterion. The (neutral)
zwitterion is the usual form of amino acids that exist in the solution .

 Amphoteric property
Amino acids are amphoteric in nature that is they act as both acids and base due to
the two amine and carboxylic groups present.
 Henderson-Hasselbach Equation
 pH=pKa + log [base]/[acid]