PROTEINS PART I

AMINO ACIDS AND PEPTIDES

PROTEINS
are polymers of amino acids.

Polymers – macromolecules that are

formed from simpler molecules
called monomers.
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) NH3+ : amino group COO- : carboxyl group R : functional 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-
hydroxytryptamine
, or 5-HT. It is
mainly found in the
brain, bowels, and
blood platelets.
Dopamine
 Its chemical
name is 4-(2-
aminoethyl)be
nzene-1,2-
diol.
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 - isoleucine -
glutamine - asparagine - cysteine -
proline - leucine -
glycine (CYIQNCPLG).
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