Synthesis of Proteins (VCE SSCE Chemistry): Revision Notes

Synthesis of Proteins

Introduction to proteins

Proteins are organic biopolymers with many vital functions in living organisms. Like synthetic polymers, biopolymers are assembled from large numbers of small monomer units. However, proteins are specifically made within living organisms from monomers called amino acids.

Examples of proteins include:

• Structural proteins: Spider silk is made from fibroin, a strong fibrous protein that forms the threads of spider webs
• Transport proteins: Haemoglobin in red blood cells binds reversibly to oxygen molecules, carrying oxygen from the lungs to body cells throughout the organism

Condensation reactions in protein synthesis

All large biological molecules, including proteins, form through condensation reactions. In these reactions, small molecules (usually water) are released as byproducts when monomers join together.

Requirements for condensation polymerisation

For condensation polymerisation to occur, monomers must contain two different reactive functional groups, one at each end of the molecule. This happens in two ways:

Homopolymers form when one type of monomer has two different functional groups. For example, amino acids have an amine group ($\text{-NH}_2$) at one end and a carboxyl group ($\text{-COOH}$) at the other end. All biological polymers in this topic are homopolymers.

Heteropolymers (or copolymers) form when two different monomer types combine, each having two identical functional groups. For instance, a diol (molecule with two hydroxyl groups) can react with a dicarboxylic acid (molecule with two carboxylic acid groups).

Structure of amino acids

General features

All amino acids share the same basic structural features:

• An amino functional group ($\text{-NH}_2$)
• A carboxyl functional group ($\text{-COOH}$)
• A hydrogen atom
• All three groups attach to a central carbon atom

General formula

The amino acids used to produce human proteins have the general formula $\text{H}_2\text{N-CH(R)-COOH}$. These are called 2-amino acids or α-amino acids because the amino group bonds to the carbon atom adjacent to the carboxyl carbon (numbered as position $2$ in the chain).

The R group (side chain)

The main difference between amino acids is the R group (side chain). These side chains vary in their properties:

Three-letter abbreviations

Biochemists commonly use three-letter codes for amino acids. For example:

• Alanine = Ala
• Glycine = Gly
• Cysteine = Cys

The 20 amino acids in humans

Name	Symbol	Structure
alanine	Ala	$\text{CH}_3$ $\text{H}_2\text{N-CH-COOH}$
arginine	Arg	$\text{CH}_2\text{-CH}_2\text{-CH}_2\text{-NH-C(=NH)-NH}_2$ $\text{H}_2\text{N-CH-COOH}$
asparagine	Asn	$\text{CH}_2\text{-C(=O)-NH}_2$ $\text{H}_2\text{N-CH-COOH}$
aspartic acid	Asp	$\text{CH}_2\text{-COOH}$ $\text{H}_2\text{N-CH-COOH}$
cysteine	Cys	$\text{CH}_2\text{-SH}$ $\text{H}_2\text{N-CH-COOH}$
glutamine	Gln	$\text{CH}_2\text{-CH}_2\text{-C(=O)-NH}_2$ $\text{H}_2\text{N-CH-COOH}$
glutamic acid	Glu	$\text{CH}_2\text{-CH}_2\text{-COOH}$ $\text{H}_2\text{N-CH-COOH}$
glycine	Gly	$\text{H}_2\text{N-CH}_2\text{-COOH}$
histidine	His	$\text{CH}_2$ with imidazole ring $\text{H}_2\text{N-CH-COOH}$
isoleucine	Ile	$\text{CH}_3\text{-CH}_2\text{-CH(CH}_3\text{)-}$ $\text{H}_2\text{N-CH-COOH}$
leucine	Leu	$\text{CH}_2\text{-CH(CH}_3\text{)}_2$ $\text{H}_2\text{N-CH-COOH}$
lysine	Lys	$\text{CH}_2\text{-CH}_2\text{-CH}_2\text{-CH}_2\text{-NH}_2$ $\text{H}_2\text{N-CH-COOH}$
methionine	Met	$\text{CH}_2\text{-CH}_2\text{-S-CH}_3$ $\text{H}_2\text{N-CH-COOH}$
phenylalanine	Phe	$\text{CH}_2$ with benzene ring $\text{H}_2\text{N-CH-COOH}$
proline	Pro	Cyclic structure with $\text{COOH}$
serine	Ser	$\text{CH}_2\text{-OH}$ $\text{H}_2\text{N-CH-COOH}$
threonine	Thr	$\text{CH}_3\text{-CH(OH)-}$ $\text{H}_2\text{N-CH-COOH}$
tryptophan	Trp	$\text{CH}_2$ with indole ring $\text{H}_2\text{N-CH-COOH}$
tyrosine	Tyr	$\text{CH}_2$ with hydroxylated benzene ring $\text{H}_2\text{N-CH-COOH}$
valine	Val	$\text{CH(CH}_3\text{)}_2$ $\text{H}_2\text{N-CH-COOH}$

Note: All $2$-amino acids have the general formula $\text{H}_2\text{N-CH(R)-COOH}$, where R is the side chain shown above the main structure.

Formation of proteins

Large protein molecules form through multiple condensation reactions between amino acids. Organisms carry out these reactions in a highly organised manner to ensure the correct amino acids appear in the correct sequence. Proteins grow stepwise, starting with two amino acids forming a dipeptide, then extending to longer polypeptides, and finally to complete proteins.

Peptide bond formation

Condensation occurs between the carboxyl group ($\text{-COOH}$) of one molecule and the amino group ($\text{-NH}_2$) of another molecule. This reaction creates an amide functional group ($\text{-CONH-}$), also called a peptide link, amide link, peptide group, or peptide bond. Water is released in the process.

Since $2$-amino acids contain both functional groups, they readily undergo condensation reactions with each other.

Dipeptides

When two amino acid molecules join together, the product is a dipeptide. The peptide link connects the molecules.

Polypeptides

Polypeptides are polymers formed by further condensation reactions between amino acids, creating long chains. When three amino acids join, a tripeptide forms. A polymer made from many amino acids is called a polypeptide.

Biological synthesis

Organisms synthesise their proteins in complex structures called ribosomes. These biological machines, made from many molecules including enzymes, operate at body temperature and complete protein synthesis within minutes. This process is called translation in biological sciences.

Laboratory synthesis

Scientists can also synthesise proteins in laboratories using flow synthesis systems with solid-state catalysts at temperatures of $85-90°\text{C}$. Modern developments allow synthesis of custom proteins within a few hours.

Naming polypeptides

A shorthand notation uses three-letter abbreviations to describe the amino acid sequence in a polypeptide. By convention:

• The structure is drawn with the free amino group on the left
• The free carboxyl group is on the right

From polypeptide to protein

A polypeptide containing more than 50 amino acids is usually called a protein.

When amino acids join in a polypeptide chain:

• The amino acid at the start with a free amino group is the N-terminal amino acid
• The amino acid at the end with a free carboxyl group is the C-terminal amino acid

Example: insulin structure

Insulin is a protein hormone that regulates chemical reactions breaking down carbohydrates, fats, and proteins in the body. It is one of the smallest proteins in the human body.

This example demonstrates how a relatively small protein has a complex structure with multiple chains held together by specific chemical bonds.