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Stamford University Bangladesh


Course title: Biomolecular Pharmacy

Course code: BPH-234

Submited to:

Shah Marzia Mahjabin Lina

Assistant Professor
Stamford University Bangladesh

Summited by:

SL Name ID Topics Page

02 Nazrul Islam BPH- 3
03 Abdul Wadud BPH- 4
04 Samima BPH- 5
05 Masud Sadik BPH- 6

1. Amino acids are building blocks of proteins

2. Proteins are composed of 20 different amino acids.

3. Their chemical structure influences three dimensional structure of protein.

4. They are important intermediates in metabolism.

5. They can have hormonal and catalytic function.

An organic compound containing an amino group (NH2),a carboxylic acid
group(COOH),and any of various side groups, especially any of 20
compounds that have the basic formula NH2CHRCOOH,and that link together
by peptide bonds to form proteins or that function as chemical messengers
and as intermediates in metabolism.

Classification of amino acid

On the basis of R group the most helpful point is to separate amino acids

1. Non-polar ((Hydrophobic)

a. Aliphatic side chain

b. Aromatic side chain

2. Polar (Hydrophilic)

a. Positively charged R group

b. Negatively charged R group

c. Un-charged R group

1. Non-polar amino acids:

a. Only carbon and hydrogen in their side chain


b. Generally unreactive.

c. Determining 3-D structure of proteins

Glycine is the simplest amino acid having single H atom as its side chain
Alanine, Valine, Leucine and Isoleucine have saturated hydrocarbon R
groups. Leucine and Isoleucine are isomers of each other.

Proline is rather an amino acid than amino acid because its side chain is
bonded to the backbone Nitrogen as well as to the alpha carbon Phenylalanyl
and Alanine with an extra benzene group on the end side times called phenyl

Phenylalanine is highly hydrophobic and is found buried within globular


Tryptophan is highly hydrophobic and structurally related to alanine but with

2 ring Indole group added in the place of the single aromatic ring found in

2. Polar hydrophilic R- group:

polar, uncharged R groups

Tyrosine is polar, very weakly acidic phenylalanine with an extra OH


Serine and Threonine play important role in enzymes which regulate

phosphorylation and energy metabolism.

Cysteine has Sulphur containing side group . It tends to be more

reactive. It is not very polar.

Asparagine and Glutamine are amide derivatives of Aspartate(Aspartic

acid)and Glutamine(Glutamic acid)

Negatively charged R group:

Two amino acids with negatively charged side chains Aspartate

(Aspartic acid) and Glutamate(glutamic acid)

They confirm a-ve charge on the protein of which they are a part.

Positively charged R group:

Lysine and Arginine are positively charged at neutral ph.

Histidine can be uncharged or positively charged depending on its local

environment. It has important role in catalytic mechanism of enzymes.

Classification based on chemical constitution

Small amino acids : Glycine and Alanine

Branched amino acids : Valine ,Leucine and Isoleucine

Hydroxyl amino acids : Serine and Threonine

Sulphur amino acids : Cysteine and Methionine

Aromatic amino acids : Phenylalanine , Tyrosine and Tryptophan

Acidic amino acid and their derivatives :Glutamate , Glutamine

Basic amino acids : Lysine , Arginine and Histidine

Essential amino acid

Required in diet

They must come from food or amino acid supplements

1. Isoleucine

2. Leucine

3. Lysine

4. Methionine

5. Phenylalanine

6. Threonine

7. Tryptophan

8. Valine

Food source: Fish, meat, poultry-cottage cheese, peanuts-lentils


Branched-chain amino acids all import ants in muscle.

Non-essential amino acid

Required in diet

The body can make these amino acids from the above essential amino acids.

1. Alanine

2. Arginine

3. Asparagine

4. Aspartic acid

5. Cysteine

6. Glutamic acid

7. Glutamine

8. Glycine

9. Histidine

10. Proline

11. Serine

12. Tyrosine

These are essential for infant, since their bodies cannot produce them yet.

Definition of peptide bond:

The peptide is formed between the amino group (-NH2) of the first amino acid
and carboxyl group (-COOH) of the second amino acid by eliminating one
molecule of water. The amino acids are held together in a protein by covalent
peptide bonds or linkage. The peptide bonds are a type of amino acids.

Importance of peptide bond:

Peptide bonding is one of the most important reaction in biochemistry as it is the
bond used by amino acids to form proteins. Amino acid form peptide bond with
other amino acids when the amino group of the first amino acid bonds with the

carboxyl group of the second amino acid. The dipeptide formed is followed by the
loss of water. A chain of amino acids are connected by peptide chain while each
individual amino acid is referred to as a residue. These chain then fold due to
various internal and external forces in order to become proteins.

Reaction mechanism:
This reaction to form peptide bonds involve reacting the amine group of one amino
acid to the carboxyl group of another amino acid .A peptide bond is dehydration
reaction or condensation reaction meaning it releases a molecule of water though
the cause of the reaction. The molecule formed by a peptide bond is called an

Protein denaturation:
Denaturation is a process in which proteins or nucleic acids lose the quaternary
structure, tertiary structure and secondary structure which is present in their native
state by application of some external stress or compound such as a strong acid or
base, a concentrated inorganic solvent. Denaturation the breakdown the bond
forming the quaternary , tertiary and secondary structure of proteins and nucleic

Functional proteins have four levels of structural organization

1. Primary structure: The linear structure of amino acids in the polypeptide chain

2. Secondary structure: Hydrogen bonds between peptide group chain in an alpha

helix or beta sheet.

3. Tertiary structure: Three dimensional structure alpha helix and beta helixes

4. Quaternary structure: Three dimensional structure of multiple polypeptides and

how they fit together.

Enzyme kinetics:
Enzyme kinetics is the study of the chemical reaction that catalyzed by enzyme. In
enzyme kinetics the reaction rate is measured and the effects of varying the
condition of the reaction are investigated. Its role in metabolism how its activity is
control, how a drug or an agonist might inhibit the enzyme. Enzymes are usually

protein molecules that manipulate other molecules the enzymes substrate.

Summited by: