biochemistry

1. PROTEIN STRUCTURE
AND FUNCTION
Maryam Fida (o-1827)

2. INTRODUCTION
Proteins
 Protein –Term first used by Berzelius in 1838
 From the Greek work “Protos” – Primary or holding first place
 Most abundant macromolecules in living cells
 Linear polymers of Amino Acids

3. AMINO ACIDS
 > 300 amino acids (AA) known in nature
 Only 20 involved in the formation of proteins of plants as well as
animal origin
 Each of these amino acids has one or more genetic codon(s) present
in mRNAs
 These 20 amino acids are called Standard , Primary or Normal
Amino Acids

4. NON- STANDARD AMINO ACIDS
 Do not take part in protein synthesis but play important role in the
body e.g.
 Citrulline, Ornithine, Argininosuccinic acid occur in the liver and take
part in the formation of urea from ammonia (urea cycle)
 Study other non-standard amino acids

5. GENERAL STRUCTURE OF AMINO ACID
FOUND IN PROTEIN

6. PEPTIDE BOND
 Two Amino Acids are
covalently joined together
by “Peptide Bonds” to
produce a “Dipeptide”
 When many Amino Acids
are joined, the product is
called “Polypeptide”

7. CLASSIFICATION OF AMINO ACIDS
5 ways of classifying Amino Acids
1. Nutritional requirement of AA
2. Metabolic product of AA
3. Chemical nature of AA in solution
4. Structure of the side chain of AA
5. Nature or polarity of the side chain of AA

8. NUTRITIONAL CLASSIFICATION
ESSENTIAL AA
 Cannot be synthesized by the body
 Ten Essential AA
 Among the ten essential Histidine andArginine are semiessential

9. Note:
Arginine and Histidine are
semi-essential.They become
essential in diet at times of
rapid growth as in childhood
and during pregnancy
Essential AA:
PVTTIM HALL
Glucogenic and Ketogenic AA
(PIT2)

10. METABOLIC CLASSIFICATION OF
AMINO ACIDS
On the basis of their catabolic end products
 Glucogenic:Those which can be converted into Glucose
 Ketogenic:Those which can be converted into ketone bodies
(leucine & lysine)
 Both Glucogenic and Ketogenic: (PIT2) (Phenylalanine,
Isoleucine,Tyrosine andTryptophan)

11. CLASSIFICATION BASED UPONTHE
TYPE OF SIDE CHAIN
Amino Acids with Non-Polar Aliphatic Side
Chains: Their side chains are hydrophobic and tend to cluster
together
Valine
Alanine
Leucine
Isoleucine
Glycine

12. Amino Acids with Aromatic side chains:
Phenylalanine
Tyrosine
Tryptophan

13. Side Chains containing Hydroxyl (-OH) group:
Serine
Threonine

14. Sulfur (S) containing side chains:
Cysteine
Methionine
Note:The side chain of cysteine contains sulfhydry group (-SH) which is an
important component of the active site of many enzymes.

15.  The sulfhydryl (-SH) group
of two cysteine residues are
oxidized to form a dimer,
cystine which contains a
disulfide bond (-S-S-)

16. Amino Acids with Acidic Side Chains
Glutamic Acid
Aspartic Acid
They are proton donors.These are negatively charged at
neutral pH (COO-) called glutamate and aspartate.

17. Amino Acids with Basic Side Chains:
Histidine
Arginine
Lysine Their side chains accept protons. At physiological pH the
side chains are positively charged.

18. Imino Acid : Proline
Proline differs from
other amino acids in
that proline's side
chain and α-amino N
form a rigid, five-
membered ring
structure . Proline,
then, has a secondary
(rather than a primary)
amino group.

19. AMPHOTERIC PROPERTIES OF AMINO
ACID
(AMPHOLYTES/AMPHOTERIC ELECTROLYTES/ZWITTERIONS/DIPOLAR
IONS)
 Amino acids can act both as acids and bases depending upon the pH
of the medium in which they are placed
-H+
-H+
+ H+
+ H+

20.  The isoelectric point (pI) is the pH at which an amino acid is
electrically neutral, that is, in which the sum of the positive
charges equals the sum of the negative charges

21. OPTICAL PROPERTIES OF AMINO
ACIDS
The α-carbon of an amino acid (except Glycine) is attached
to four different chemical groups. It is therefor a Chiral or
Optically active carbon atom

22.  The two forms in each pair are termed stereoisomers,
optical isomers, or enantiomers.
 All amino acids found in
proteins are of the
L-configuration
 D-amino acids are found
in some antibiotics and
in plant and bacterial cell walls