Amino Acids and Peptides
An Introduction to Protein
Chemistry
Beta
chain
Alpha
chain
2 α and 2 β chains = the
globin part
4 heme groups in RED
Representation of hemoglobin
structure
Functions of Proteins
• The word proteins is derived from a Greek
word meaning “of the first order”. The
following list clarifies that:
• As enzymes they are needed for every
reaction.
• Structural proteins support every living cell.
• Contractile proteins are behind every cellular
motion.
Functions of Proteins
• Transport and storage of nutrients in aqueous
fluids needs certain proteins.
• In addition to these, proteins may also
function as:
– Hormones, receptors
– Clotting factors
– Buffers
– Regulators of gene expression
– Defense means against foreign bodies
Definitions
• Proteins are polymeric biomolecules made up
of one or more polypeptides. A polypeptide is
composed of amino acids linked together by
peptide bonds.
• An amino acid is an organic compound having
the following formula:
H
NH3+–C–COOR
• A peptide bond is an amide linkage formed by
a condensation reaction involving the
carboxyl group of one amino acid and the
amino group of another.
Formation of a peptide bond
2 amino acids
Water
N-terminus
C-terminus
The Standard Amino Acids
• Hundreds of amino acids are found in nature;
20 of these are found as monomers of protein.
• In addition to their role as the building blocks
of proteins, amino acids are also involved in:
– Synthesis of specialized non-protein products such
as purines, pyrimidines, heme, some hormones,…
– Energy production
• Amino acids found naturally in proteins adopt
an L configuration
What are D and L isomers
• A carbon atom attached to four different atoms or
groups is called an asymmetric carbon or a chiral
centre.
• Chiral compounds show optical activity; the ability to
deviate the path of plane-polarized light either to the
left or to the right in a polarimeter.
• Organic compounds are either D (dextrorotatory) or
L (levorotatory).
• The reference compound in this system is the CHO
glyceraldehyde
Chirality of Amino Acids
CHO
H
OH
CH2OH
D-glyceraldehyde
COOH
H2N
H
CH3
L-alanine
Remember: carbohydrates exist in the D-form,
Naturally occurring amino acids exist in the L-form
Classification of Amino acids
• Amino acids are classified based on the nature
of R into polar and nonpolar groups.
• The polar amino acids could be charged (+ve
or –ve) or uncharged (containing mainly
hydroxyl and amide groups)
• The positively charged group (containing two
amino groups) are called basic amino acids.
• The negatively charged ones (containing two
carboxyl groups) are called acidic amino acids.
Non-polar Side Chains
• When all or most of the side chain is a hydro-carbon,
the amino acid is non-polar or hydro-phobic.
Name
Abbrev.
R
Name
Abbrev.
R
Alanine
Ala, A
-CH3
Glycine
Gly, G
-H
Valine
Val, V
-CH-(CH3)2
Tryptophan
Trp, W
Leucine
Leu, L
-CH2-CH(CH3)2
Phenylalanine
Phe, F
Isoleucine
Ile, I
-CH
(CH3)CH2-CH3
Tyrosine
Tyr, Y
-CH2CH2-SCH3
Proline
Pro, P
Methionine Met, M
Polar Uncharged Amino acids
When the side chain contains amide, sulfhydryl or hydroxyl groups, the
amino acid is polar uncharged
Name
Abbreviation
R
Serine
Ser, S
-CH2-OH
Threonine
Thr, T
-CH (OH) –CH3
Glutamine
Gln, Q
-CH2-CH2-CO-NH2
Asparagine
Asn, N
-CH2CO-NH2
Cysteine
Cys, C
-CH2- SH
Polar Charged Amino acids
Name
Abbreviation
Lysine
Lys, K
Histidine
His, H
Arginine
Arg, R
Aspartate
Asp, D
Glutamate
Glu,E
Other Descriptions of R
• Aromatic side chains are seen in three amino
acids.
• Sulfur-containing amino acids are two.
• Imino acid (more correctly secondary amino
acid).
Other Classification Schemes
• Based on nutritional requirements amino
acids are either: essential or non-essential.
• Essential amino acids are those amino acids
which our cells cannot synthesize, and must
therefore be supplied by the diet.
• PVT TIM HALL
• Non-essential amino acids can be synthesized
by our cells from CHO or other intermediates.
Other Classification Schemes
• Based on metabolic fate, the amino acids are
either glucogenic or ketogenic (or both).
• A glucogenic amino acid may give rise to
glucose, while a ketogenic one produces
ketone bodies ( lipid derivatives)
• Some amino acids may be metabolized to
glucose and ketone bodies.
General structure of a tetrapeptide
N – terminus
+
H2N
C - terminus
O
H
N
N
H
O
O
N
H
COO-
The Peptide Bond
• The peptide bond is a strong covalent bond that
maintains protein structure.
• The difference in electronegativity between the
atoms making the peptide bond makes it polar.
• Polarity of the peptide bond allows hydrogen
bonding between the –CO of one amino acid and the
–NH of another amino acid.
• A hydrogen bond is defined as the sharing of a
hydrogen atom between two electronegatives
The Peptide Bond
• The peptide bond is described as being planar,
meaning that all atoms CONH lie on the same
plane.
• It is also said to be trans in configuration,
meaning on opposite directions of the bond
axis
Home Work (HW)
• Define pK. Find out the pK values for the charged
amino acids. Which amino acid pK value is expected
to be physiologically important? Explain.
• Give examples of medically important peptides (less
than 10 amino acid residues).
• Why is an amino acid in peptide linkage called an
amino acid residue?