Amino acid structure

Amino acids are the monomers, or building blocks, from which proteins are made. Each amino acid has a central carbon atom bonded to four groups: an amino group, a carboxyl group, a hydrogen atom and a variable side chain.

The general structure can be represented as:

In this representation, the central carbon is the $$\ce{C}$$ in $$\ce{CH}$$. It is bonded to:

• an amino group, $$\ce{NH2}$$;
• a carboxyl group, $$\ce{COOH}$$;
• a hydrogen atom, $$\ce{H}$$;
• a side chain, represented by $$R$$.

The twenty amino acids commonly found in proteins share this general structure but have different side chains. Side chains differ in properties such as charge and attraction to water. These differences contribute to the properties of the proteins containing them.

Peptide bond formation

Amino acids can join together when the carboxyl group ($$\ce{COOH}$$) of one reacts with the amino group ($$\ce{NH2}$$) of another. An $$\ce{OH}$$ from the carboxyl group and an $$\ce{H}$$ from the amino group combine to form water ($$\ce{H2O}$$). The bond formed between the two amino acids is a peptide bond.

Because the amino acids join while releasing water, this is a condensation reaction. Joining two amino acids produces a dipeptide.

Further condensation reactions can add more amino acids, producing a chain called a polypeptide. A functional protein may consist of one polypeptide or more than one polypeptide.

Protein structure and function

A protein’s function depends on its shape and chemical properties. These arise as one or more chains of amino acids fold and, in some proteins, assemble together. Protein structure can be described at four levels.

Primary structure: amino acid sequence

A polypeptide is a chain of amino acids joined by peptide bonds. Its primary structure is the order of amino acids in the chain. A protein may contain one polypeptide chain or several, each with its own amino acid sequence.

Amino acids have different side chains. Their sequence matters because different side chains can form different interactions as the polypeptide folds.

Secondary structure: local folding

Parts of a polypeptide fold into regular shapes, including alpha helices and beta-pleated sheets. These local arrangements make up its secondary structure. Hydrogen bonds between parts of the polypeptide backbone stabilise them.

Tertiary structure: overall shape of a chain

Further folding gives a polypeptide its overall three-dimensional shape, called its tertiary structure. Interactions involving side chains help to stabilise this shape. These include hydrogen bonds, ionic bonds and disulfide bridges between certain side chains.

Because the amino acid sequence determines which side chains are present and where they occur, it influences the interactions that can form and therefore how the chain folds.

Quaternary structure: arrangement of chains

Some proteins contain more than one polypeptide chain. Their quaternary structure is the arrangement of these chains relative to one another. A protein with only one polypeptide chain does not have quaternary structure.

How structure supports function

The folded shape and chemical properties of a protein determine how it interacts with other molecules. For example, an enzyme’s shape and chemical properties allow it to interact with particular molecules and catalyse a reaction. A transport protein has a structure suited to interacting with the substance it transports, while a structural protein has properties that help it provide support.

Different amino acid sequences produce proteins with different structures and properties, allowing proteins to carry out these varied functions.

Biuret test for proteins

The biuret test is used to test a sample for proteins. It detects peptide bonds, which link amino acids together in proteins.

Carrying out the biuret test

1. Add sodium hydroxide solution to the sample to make it alkaline.
2. Add copper sulfate solution and observe the colour.

A lilac or purple colour is a positive result, indicating that peptide bonds are present. If the mixture remains blue, the result is negative.