Amino Acids, Peptides &

Proteins Part 2
carboxyl group
amino group

side chain

-carbon

Harliansyah, PhD
(Doctor of Philosophy in Medical Biochemistry)

Dept. of Biochemistry. FKUY

Amino group of an AA combines with

the carboxyl group of another AA
A dipeptide will have 2 AA and one
peptide (not two) bond
Peptides containing more than 10 AA
(decapeptide)

polypeptide

Characteristics of Peptide
Bonds
1.
2.
3.
4.
5.

Rigid
Planar
Partial double bond in character
Generally exists in transconfiguration
Both _C = O and _NH2 groups of
peptide bonds are polar
6. Involved in hydrogen bond formation

Writing of Peptide
Structures

The peptide chains are written with the

free Amino end (N terminal residue) at
the left, and the free carboxyl end (C
terminal residue) at the right.
The AA sequence is read from N
terminal end to C terminal end
Incidentally the protein biosynthesis
also starts from the N terminal Acid.

Shorthand to read peptides

The AA in a peptide or protein are represented by the 3 letter or one

letter abbreviation.
This is the chemical shorthand to write proteins.

Naming of Peptides
For naming peptides, the AA suffixes
ine (glycine), - an (tryptophan) ate
(glutamate) are changed to yl with
the exception of C terminal AA.

A tripeptide composed of an N
terminal glutamate, a cysteine and a
C terminal glycine is called:
glutamyl cysteinyl - glycine

Polypeptide Chains
- The linking together of many AA by
peptide bonds produces polypeptide
chains.

a.Residues - AA, when in

polypeptide chains, are
customarily referred to as
residues.

b.Large peptide chains - protein

polypeptide chains are typically
more than 100 AA residues long.

Biuret Reaction

Peptides of Physiologic
Importance
1. Glutamine (Glutathione)
- a tripeptide composed
of 3 AA
- gamma glutamyl
cysteinyl glycine
- wildly distributed in
nature
- exists in reduced or
oxidized states

Functions:
a) As a coenzyme for certain enzymes as
prostaglandin PGE2
synthase
glycoxylase
b) Prevents the oxidation of sulfhydryl groups of
several proteins to disulfide groups
c) In association with glutathione reductase
participates in the formation of correct disulfide
bonds in several protiens
d) In erythrocytes
- maintains RBC membrane structure and
integrity
- protects hemoglobin from getting oxidized by
agents such as H2O2

e) Involved in the transport of AA in the

intestine and kidney tubules via delta
glutamyl cycle or Meister cycle
f) Involved in the detoxification process
g) Toxic amounts of peroxidases and
free radicals produced in the cells are
scavanged by glutathione peroxidase
( a selenium containing enzyme).

2. Thyrotropin Releasing Hormone (TRH)

- a tripeptide secreted by hypothalamus
Function:
Stimulate pituitary gland to release
thyrotropic hormone
3. Oxytocin
- contains 9 AA (nonapeptide)
- hormone secreted by posterior
pituitary gland
Function:
Stimulate contraction of the uterus muscle
during delivery
Stimulate contraction of muscle in breasts
for milk ejection

4. Vasopressin (ADH antidiuretic hormone)

- also a nonapeptide
- produced by posterior pituitary gland
Function:
Stimulates kidneys to retain water and
thus increases the blood pressure
5. Angiotensins
- Angiotensin 1 a decapeptide (10AA)
which is converted to angiotensin II (8AA)
Function:
For the release of aldosterone from
adrenal gland

6. Methionine Enkephalin
- a pentapeptide found in the brain and
has opiate like function.
Function:
It inhibits the sense of a pain.
7. Bradykinin and Kallidin
- nona and decapeptides respectively
- produced from plasma proteins by
snake venom enzymes
Function:
Powerful vasodilators

8. Peptide Antibiotics
- Antibiotics such as Gramicidin, Bacitracin,
tyrocidin and Actinomysin
peptide in nature
9. Dipeptide aspartame
- Consists of aspartate and phenylalanine
- acts as Sweetener ~ used by diabetic
patients
10. Gastrointestinal Hormones
- Gastrin, Secretin & etc.
- gastrointestinal peptides serving as
hormones

Identifying the amino acid

sequence
a. Edman Reaction
1. Description
Phenylisothiocyanate reagent
- developed for a technique that allows
repetitive sequencing of a peptide

2. Process
a. Phenylisothiocyanate reacts in alkali with
the N terminal group to form a

phenylthiocarbamyl derivative of the peptide

In the presence of a strong

anhydrous
acid,
the
phenylthiohydantoin derivative of
the 1st AA is cleaved from the
peptide and can be identified
chromatographically.
b. The remainder of the peptide is left intact with the
next residue in the chain bearing a free amino group.
This can in turn react with fresh reagent , and the
reaction continues until the impurities produced by
incomplete reactions build up and prevent further
repetition of the reaction.

c. The procedure has been

automated and can be used
to
determine
the
AA
sequence of peptides 50 to
60 residues in length. Longer
peptides must be broken into
smaller
fragments
for
sequencing.

B. Sequencing of peptide
fragments
1. The direct sequencing of proteins > than
100 residues is difficult
- the analysis is considerably aided by
first breaking (i.e. cleaving) the protein
chain into short fragments
- this cleavage is performed by using
chemical reagents or enzymes that sever
the peptide chain at specific sites
- the sequence of these shorter peptide
fragments is then determined by the
Edman reaction, using an automated
sequenator

2. Arranging the peptide fragments in

their true order
is a problem that also can be
overcomed by fragmenting the
original protein with several reagents
that act at different sites
3. Reagents used to obtain peptide
fragments include proteolytic
enzymes & chemical reagents

a) Proteolytic enzymes:
i. Trypsin preferentially cleaves
peptide bonds on the carboxylic
side of basic AA (Arginine, lysine)
ii. Chymotrypsin preferentially
cleaves on the carboxyl side of
aromatic AA (Phenylalanine,
tyrosine, tryptophan)
iii. Staphylococcal protease
- preferentially cleaves on
the carboxyl side of the acidic AA
(Aspartate, glutamate)

b) Chemical Reagents
i. Cyanogen bromide cleaves on the
carboxyl side of methionine residues
ii. Hydroxylamine cleaves at
asparagine glycine bonds.