PROTEIN BIOCHEMISTRY

STATE THE FUNCTIONS OF PROTEIN :

1. Act as a biological catalyst (enzymes)

2. Act as a transporter and storage (haemoglobin, lipoprotein)
3. Responsible for movement (actin, myosin)
4. Maintainance of osmotic pressure (plasma protein)
5. Components of immune system (immunoglobulins)
6. Transmission of nerve impulses (receptor protein)
7. Hormones (insulin, oxytocin, vasopressin)

STATE THE CLASSIFICATION OF AMINO ACID :

Amino acid can be divided into 4 groups

1. Polar amino acids

i) Side chains which have various functional groups such as acids, amides, alcohols, and amines will
impart a more polar character to the amino acid
ii) Amide > acid > alcohol > ketone, aldehyde > amine > ester > ether > alkane
iii) Asparagine, Cystein, Glutamine, Serine, Threonine, Tyrosine

2. Non-polar amino acids

i) Side chains which have pure hydrocarbon alkyl groups (alkane branches) or aromatic (benzene rings)
are non-polar
ii) Alanine, Glycine, Isoleucine, Leucine, Methionine, Phenylalanine, Proline, Valine, Tryptophan

3. Basic amino acids

i) If the side chain contains an amine functional group, the amino acid produces a basic solution
because the extra amine group is not neutralized by the acid group
ii) Arginine, Lysine, Histidine

4. Acidic amino acids

i) If the amino acid structure contains two acid groups and one amine group, there is a net acid
producing effect.
ii) Aspartic acid, Glutamic acid

STATE THE CHARACTERISTICS OF AMINO ACIDS :

1. In aqueous solution, amino acids can exist in several ionic forms, depending on the pH of the solution.
2. Amino acids are amphoteric (acting as acids and bases)
3. Amino acids are stable at room temperature.
4. The aromatic amino acids (tyrosine and tryptophan) absorb light at λ = 280 nm.
5. The quantity of amino acid can be estimated by ninhydrin reaction.

Written by Norrifhan Akmal Ismail MBBS student of University Malaya 2010-2015

STATE THE STRUCTURES OF PROTEIN :

1. Primary structure
- Linear structure
- Consists of unbranched polypeptide chain
- Amino acid residues are bonded by peptide bond
2. Secondary structure
- Repeating parts of the 3D structure of a protein
- Exists in two form (α helix and β pleated sheet )
- Stabilised by hydrogen bond

α helix β pleated sheet

Maintained by hydrogen bond between –CO and
–NH groups of neighbouring coils
Polypeptide chain is coiled
Form from single polypeptide chain.
Triple helix (3 polypeptide chain. Eg
tropocollagen)
Maintained by hydrogen bond between –CO and
–NH groups and between polypeptide chain
Polypeptide chain is arranged parallel to each
other
Form from 2 or more polypeptide chains

3. Tertiary structure
- The 3D arrangement of all the atoms in the molecule
- Can be determined by
o X-ray crystallography (eg, myoglobin)
o Nuclear magnetic resonance (NMR)
- Stabilised by
o Hydrogen bond
o Hydrophobic interactions
o Electrostatic interactions
o Disulphide bonds
o Van der Waals forces
4. Quartenary structure
- Consists of two or more polypeptide chains
- Can be dimeric, trimeric, or tetramic
- Chains interact non-covalently
- Exhibit allosteric effect (eg. Cooperative binding properties of haemoglobin)

STATE THE PROTEIN SEPERATION METHOD :

1. Gel filtration chromatography (based on protein size difference)

2. Ion-exchange chromatography (based on protein charge)
3. Affinity chromatography (based on affinity of protein towards specific substances)

Written by Norrifhan Akmal Ismail MBBS student of University Malaya 2010-2015

 4. Electrophoresis (based on protein charge)
5. 2D electrophoresis (for complex protein)

STATE THE CHARACTERISTICS OF PROTEINS :

1. Not stable at high temperature and pH

2. Usually charged (amphoteric)
3. Globular proteins dissolve in water, fibrous protein do not.
4. Used colour reaction to estimate quantity of protein (Biuret, Lowry, Bradford reactions)
5. Contain inorganic and organic components
6. Some proteins are able to denaturate and renaturate.

WHAT IS PROTEIN CONFORMATION ?

The overall structure of a protein molecule in the 3D arrangement of each atom.

EXPLAIN THE RENATURATION AND DENATURATION PROCESS OF A PROTEIN :

1. Protein can be denatured by 8M of urea in the presence of β -mercaptoethanol.

2. The urea will break the hydrogen bond and hydrophobic interactions.
3. The β -mercaptoethanol will cleave the disulphide bond.
4. The renaturation can be done by dialysis, where the urea and β -mercaptoethanol will be removed.

DESCRIBE ABOUT COLLAGEN :

1. Fibrous protein
2. Important protein component in connective tissue.
3. Contains high amount of glycine, hydroxylysine, and hydroxyproline.
4. Has tropocollagen as basic unit
- Tropolcollagen is in triple helix form
- Has a typical sequence of glycine being the third amino acid. This is because glycine is the smallest amino
acid with no side chain. It is required at every third position because there is no space for other bigger
functional group to fit in the crowded space of the triple stranded helical cable.
5. Stabilised by the formation of cross linking covalent bond between hydroxylysine and lysine.
6. Defects in vitamin C can lead to abnormal synthesis of collagen, that eventually lead to scurvy.
7. Defects in collagen will lead to
- Ehler-Danlos syndrome / Rubber man syndrome (decreased tensile strength and intergrity of skin, joints
and other connective tissue)
- Osteogenesis Imperfecta / Brittle bone disease (some forms of dwarfism)

Written by Norrifhan Akmal Ismail MBBS student of University Malaya 2010-2015