PROTEINS PART I

AMINO ACIDS AND

PEPTIDES
PROTEINS
⚫ are polymers of amino
acids.

Polymers –
macromolecules that are
formed from simpler
molecules called
Polymers and Monomers
•Amino acids are the
monomers of
proteins.
•PROTEINS – are
polymers of amino
acids.
AMINO ACIDS
⚫ There are 20 types of
genetically encoded amino
acids in peptides and
proteins.
⚫ Usually abbreviated either
in “one letter” or “three
letters” symbol.
GENERAL FORMULA OF AMINO
ACIDS
H

R – C – COOH

NH2

• COOH (Carboxyl group)

imparts acidity
• NH2 (Amino group) imparts
basicity
FORMS OF AMINO ACIDS
⚫ Anionic form (negatively
charged)
⚫ Cationic form (positively
charged)
⚫ Zwitterionic form (positive
and negatively charged)
because of internal
neutralization.
FORMS OF AMINO ACIDS
1. At high pH (7 above) basic environment
H H

R – C – COOH + Base R -C–

COO-
(accepts H+ from)
NH2 COOH group NH2

Amino acids become negative

or in anionic form.
FORMS OF AMINO ACIDS
2. At low pH (7 below) acidic environment
H H

R – C – COOH + Acid R -C–

COOH
(donates H+)
NH2 NH3 +

Amino acids become positive

or in cationic form.
FORMS OF AMINO ACIDS
3. At pH 7 (physiological condition)
internal neutralization occurs,
H H

R – C – COOH R - C – COO-

NH2 NH3+

Amino acids become

zwitterionic form.
STEREOCHEMISTRY OF AMINO
ACIDS
H

⚫ R – C – COOH

NH2

• α (alpha) Carbon is bonded to four

different groups, so being termed
as Chiral Carbon
Chiral Carbon exhibits optical
activity
STEREOCHEMISTRY OF AMINO
ACIDS
H

⚫ R – C – COOH

NH2

• For each Chiral Carbon there are

two distinguishable stereoisomers.
• These stereoisomers are non
superimposable mirror images of
one another called
ENANTIOMERS.
The Stereochemistry of Amino Acids
Chiral molecules existing in two forms

http://www.imb-jena.de/~rake/Bioinformatics_WEB/gifs/amino_acids_chiral.gif
Two types of Enantiomers
1) D (Dextrorotatory)
- solutions that rotates plane of
polarized light in the clockwise
direction.
2) L (Levorotatory)
- solutions that rotates plane of
polarized light in the
counterclockwise direction.
FACT:
All amino acids incorporated by
organisms into proteins are all of the
L form/enantiomers.
 Structure and Stereoisomerism of a-Amino Acids
Ca : a-carbon (chiral) NH + : amino group - R : functional group
3 COO : carboxyl group
(side chain)

Absolute Configuration : S Absolute Configuration : R

Left, Counter-Clockwise Right, Clockwise

Only L-amino acids

are constituents of
proteins.
TWENTY (20) COMMON AMINO
ACIDS
TWENTY (20) COMMON AMINO
ACIDS
TWENTY (20) COMMON AMINO
ACIDS
 One Letter Abbreviation of
Amino Acids
1. Glycine - G
2. Alanine - A
3. Valine - V
4. Leucine - L
5. Isoleucine - I
6. Methionine - M
7. Phenylalanine- F
 One Letter Abbreviation of
Amino Acids
8. Tryptophan - W
9. Proline - P
10. Aspartic Acid - D
11. Glutamic Acid - E
12. Asparagine - N
13. Glutamine - Q
14. Lysine - K
 One Letter Abbreviation of
Amino Acids
15. Histidine - H
16. Arginine - R
17. Cysteine - C
18. Serine - S
19. Threonine - T
20. Tyrosine - Y
PEPTIDES AND PEPTIDE BOND
Peptide Bonds – are amide
linkages between the α- amino
group of one acid and the α-
carboxyl group of another
amino acid.

The products formed by such

linkage are called PEPTIDES.
•Amino acids are joined together when a
dehydration reaction removes a hydroxyl group
from the carboxyl end of one amino acid and a
hydrogen from the amino group of another.
PEPTIDES AND PEPTIDE BOND
⚫ If the linkage is consists of two
amino acid residues it is called
DIPEPTIDE.
⚫ Few amino acid residues (4, 5..)
are collectively referred to as
OLIGOPEPTIDES.
⚫ If the chain is very long it is
then called POLYPEPTIDES.
PEPTIDES AND PEPTIDE BOND
⚫ Most oligopeptides and
polypeptides retain an
unreacted amino group at one
end called the N-terminus and
an unreacted carboxyl group at
the other end called the
C-terminus.
NAMING PEPTIDES
⚫ Amino acid in the N-terminus
side is written and named first.
⚫ All amino acids lying to the left
of the C-terminus in “yl”
ending while the C-terminus
amino acid is named as is.
Serotonin
⚫ The scientific
name
for serotonin is
5-hydroxytrypt
amine, or 5-HT.
It is mainly
found in the
brain, bowels,
and blood
Dopamine
⚫ Its
chemical
name is
4-(2-amin
oethyl)ben
zene-1,2-d
iol.
Oxytocin
⚫ has the chemical
formula C43H66N12O12S2. It is
a relatively short polypeptide,
being composed of only
nine amino acids (a
nonapeptide). The sequence
is cysteine - tyrosine - isoleuc
ine - glutamine - asparagine -
cysteine
Oxytocin
Examples:
⚫ Draw the structure of the
peptide having the following
amino acid sequence:.Also
provide names for the
peptides.
a) E-G-A-K
b) Y-K-W-M
c) K-V-A-R-L