SUBTOPIC: PROTEIN

Introduction
1) Natural polymer, which is also known as polyamides
2) Proteins can be divided into 2 categories
a. Fibrous/Structural proteins
b. Globular proteins

2) Protein contains building blocks known as amino acids

3) Amino acids are monomers in protein

Amino acids
1) Amino acid (AA) contains a carboxyl group and amino group in the same molecule
2) General structural formula of AA

3) There are 20 different R groups in AA, which would give rise to 20 different AAs in nature
4) Solid at room temperature- has a property of ionic cpds.
5) Soluble in water but insoluble in non-polar organic solvent
6) Zwitterion or dipolar ion
a. AAs would form zwitterions in neutral environment (in aqueous solution at pH 7)

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7) AA in low pH solutions

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8) AAs in high pH solution

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Proteins
1) AAs polymerize to form protein (polypeptide) in condensation reaction

2) Proteins are large molecule (macromolecule), in which peptide groups link AA units.

3) Proteins contain many peptide groups, thus it is polyamide.

4) Therefore, proteins are naturally occurring polyamides
5) There is no repeating unit in protein because each AA has different R group.

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 6) Proteins have polar amide groups, which provide the sites that allow hydrogen bondings between
a. sections of polypeptide chains

b. the polypeptide chain and water molecules

Structures of proteins
1) Primary structure
a. The sequence of AAs in a polypeptide chain

2) Secondary structure
a. AAs sequence in polypeptide chain is folded or twisted into a particular shape through
extensive hydrogen bondings between amide/peptide groups
b. There are 2 conformations
i. Alpha-helical structure- hydrogen bondings between amide/peptide groups in a
single polypeptide chain

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 ii. Beta-pleated sheet- hydrogen bondings between amide/peptide groups in 2 or
more different polypeptide chains

3) Tertiary structure
a. The secondary structure is folded or bent in a particular manner that is characteristic of a
particular protein and is essential to its function
b. The tertiary structure is held by the bondings btw R groups on the side chains
c. These bondings could be
i. Primary bonds
1. ionic bonds, disulfide links(covalent)
ii. Secondary interactions
1. hydrogen bonds, DDI, DF

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 4) Quaternary structure
a. More than 1 tertiary structure proteins may come together to form a composite structure
with a particular shape and function

Denaturation of protein

1) Proteins are biological catalysts

2) Biological function of a protein is a consequence of its unique spatial arrangement (shape of active
site)
a. If its spatial arrangement is altered, its biological function is also altered

2) Denaturation of protein refers to the situation where the protein changes its secondary, tertiary or
quaternary structure hence loses its capacity to perform its biological function (catalytic function).

The effect of pH change on the protein structure

1) In low pH

– H+ from acid protonates carboxylate group forming carboxyl side group.

2) In high pH

– OH- from alkali deprotonates ammonium ion group into amino side group.

The effect of temperature on the protein structure

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 High temp breaks secondary interactions formed between peptide groups in secondary str & R
side groups in tertiary & quaternary structure of protein.