Molecules, Gene and
disease
Session 1
Lecture 2
Amino acids and protein
Structural Features of Amino Acids
• All 20 of the common amino acids are α-amino acids.
• They have a carboxyl group and an amino group bonded to the same
carbon atom (the α-carbon)
• They differ from each other in their side chains, or R groups
• R groups are vary in structure, size, and electric charge, and which
influence the solubility of the amino acids in water.
• The α-carbon atom is a chiral center; so,
amino acids have two possible stereoisomers,
L or D
• The Amino Acid Residues in Proteins Are L
Stereoisomers
Cells are able to specifically synthesize
the L isomers of amino acids because
the
active
sites
of
enzymes
are
asymmetric, causing the reactions they
catalyze to be stereospecific.
Classification of Amino Acids by R Group
1. Nonpolar, aliphatic R groups
2. Aromatic R Groups
3. Polar, uncharged R groups
4. Positively Charged (Basic) R Group:
5. Negatively Charged (Acidic) R Groups
Amino acids classification based on
nutritional requirement:
• Isoleusine, leusine, theronine, lysine, methionin,
phenylalanine, tryptophan, and valine are
essential amino acids. There carbon skeleton
cannot be synthesized by human being, so these
amino acids must be taken in food for normal
growth.
• Histidine and argentine are essential for growing
children not for adults so these are semiessential.
• The remaining 10 amino acids are nonessential,
because there carbon skeleton can be
synthesized by the body.
Acid- Base Behavior of Amino acids
The acid base properties of amino acids
depends on the:
*amino and carboxyl groups attached to
the α- carbon
and
*on the basic, acidic, or other functional
groups represented by R.
Acid- Base Behavior of
Amino acids
*In the physiological pH range of
7.35- 7.45, the carboxyl group of
an amino acid is dissociated and
the amino group is protonated, it is
called Dipolar ion or ampholyte, or
zwitter ion
Acid- Base Behavior of
Amino acids
Acid- Base Behavior of
Amino acids
• At low pH an amino acid is in its cationic form
with both its amino and carboxyl groups are
protonated (NH3+ and COOH).
• As the pH rises, the carboxyl group loses its
proton and the ampholyte form appear at
about pH 6.
• With a further increase in pH the amino group
(NH3+ ) is deprotonated, resulting in the
anionic form of the molecule.
Alanine
Titration of amino acids:
Amino acids with ionizable R
groups have additional ionic
species, depending on the pH of
the medium and the pKa of the
R group.
•
Iso electric point of amino acids
• The pH at which amino acid bears no
net charge and therefore does not
move in an electric field, is called
isoelectric pH (pI).
• The characteristic pH at which the
net electric charge is zero is called
the isoelectric point or isoelectric
pH, designated pI. For glycine, which
has no ionizable group in its side
chain, the isoelectric point is simply
the arithmetic mean of the two pKa
values:
• One of the most Important
Reactions of Amino Acids is
the formation of peptide bond
24
Peptide Bonds Are Planar. In a pair of
linked amino acids, six atoms (C α , C, O, N,
H, and C α ) lie in a plane. Side chains are
shown as green balls.
25
Trans and Cis Peptide Bonds. The trans
form is strongly favored because of steric
clashes that occur in the cis form
26
Key feature of the peptide bond:
• All the atoms of the bond are in the same
plane
• No rotation about the peptide binds due to
double bond characteristics
• Carbonyl oxygen and Amide hydrogen are in
the trans orientation
The peptide has a direction
28
The pentapeptide
serylglycyltyrosylalanylleucine,
Peptides are named beginning with
the aminoterminal residue, which by
convention is placed at the left.
29
Peptides Can Be Distinguished by Their
Ionization Behavior
30
Example: Alanylglutamylglycyllysine. This
tetrapeptide has one free -amino group,
one free -carboxyl
group, and two
ionizable R groups. The groups ionized at
pH 7.0 are in red
31
Proteins
 Proteins are polypeptides
Linear chains of 20 different amino acids, in a
sequence encoded by the gene
 The polypeptide chain folds into a complex
and highly specific three-dimensional
structure, determined by the sequence of
amino acids
 The folding of proteins depends on the
chemical and physical properties of the
amino acids
. Chemical Nature and function of
proteins
• The amino acids that make up a protein
contribute to the folding and function of
that protein. The side chains those of the
amino acids are more important in a
polypeptide as they contribute to the
charge seen on the protein.
The isoelectric point (pI) of protein
• The isoelectric point (pI) is the pH at
which a protein has no overall net
charge.
• Acidic proteins contain many negatively
charged amino acids and have a low pI
• Basic proteins contain many positively
charged amino acids and have a high pI
Proteins play crucial roles in virtually all
biological processes, as :
 Catalysts - enzymes
 Machines – e.g., muscular contraction and motion
 Structural support (e.g., collagens in skin and bone)
 Immune protection (e.g., immunoglobulins)
 Ion channels
 Receptors (for hormones, neurotransmitters, etc.)
 Ligands in cell signalling (growth factors etc.)
 Transporters (e.g. O2, Fe)
Summary