protein (idea)

Protein Structure

Introduction

Proteins are polymers whose molecules are made from many amino acid molecules linked together. Proteins have a very wide range of different functions in living organisms. Some proteins, such as haemoglobin, enzymes and antibodies are involved in metabolic reactions, while others, such as collagen and keratin form the structure of living organisms. The function of any particular protein is related to its shape. Proteins themselves have four levels of structural organization. Each of these levels is associated with particular types and patterns of bonding, which combine to result in the overall shape of the protein.

Amino Acids

There are twenty different, naturally occurring amino acids. amino acids can link to form polypeptide chains and these can associate with one another to form proteins. All amino acids contain a central carbon atom, known as C_α, to which four different groups are bonded. One of these is a hydrogen atom, which plays no part in the amino acid's function; the others are an amine group (-NH₂), a carboxylic acid group (-COOH) and the "R-group". It is this variable R-group which is different between amino acids.

In fact, while amino acids are in solution they are not in this form: the proton from the carboxylic acid group reacts with the basic amine group, to form a -COO^- group and a -NH3⁺ group. When an amino acid is in this form, it is called an internal salt or zwitterion.

Since the C_α carbon has four different groups bonded to it, it can exist in two different three-dimensional spatial arrangements. This is known as optical isomerism or chirality. However, in nature only one of the forms, known as enantiomers, is ever found. This is because once one system had been chosen in a 'frozen accident' it was easiest for new molecules to fit the same pattern: any difference would be lethal, or at least very strongly selected against.

Primary Structure

The twenty different amino acids which exist in nature can be combined in any combination to make a protein. However, this order is of tremendous significance as a change in just one amino acid can drastically change the behaviour of the protein formed. The number and sequence of amino acids in a polypeptide is known as its primary structure. The primary structure of a protein determines its overall shape and therefore its function.

The amino acids are linked by peptide bonds, which are the result of enzyme-catalysed condensation reactions. A hydrogen atom from the amine group of one amino acid joins with a hydroxyl group from the carboxylic acid group of another amino acid. A molecule of water is formed and expelled from the molecule.

Secondary Structure

The chain of amino acids which makes up a polypeptide chain does not remain perfectly straight but twists into a shape known as the secondary structure. This is determined by the strength and direction of hydrogen bonding within the polypeptide chain. The combination of these bonds results in the formation of one of two kinds of secondary structure: the α-helix and the β-pleated sheet.

In an α-helix, the chain twists into a regular spiral similar to a telephone cord. The helix is held together by hydrogen bonds between the (-NH) group of one amino acid and the (-CO) group of the amino acid four places ahead of it in the chain. Most proteins have at least part of their structure in the form of an α-helix.

In a β-pleated sheet, on the other hand, the chain is not tightly coiled, but lies almost straight. Often, several â strands lie side by side, and form hydrogen bonds with one another. Again, these bonds are between (-NH) groups and (-CO) groups but this time they are from different polypeptide chains. The result is a group of polypeptide chains which form a sheet. β-pleated sheets form part of the structure of most proteins.

Tertiary Structure

The tertiary structure is the overall, three-dimensional structure of a polypeptide chain or protein. The amino acid chain, which is already in the form of an α-helix or β-pleated sheet, coils again to form a very precise shape which is characteristic of the specific protein. The shape is held firmly in place by bonds between amino acids which lie close to each other in the three dimensional structure. There are four types of bonds: van der Waals forces, hydrogen bonds, ionic bonds and disulphide bridges.

In some proteins, the tertiary structure forms a long, super-coiled chain, usually with a very regular repeating pattern. These proteins are called fibrous proteins. They are used for producing various structures in organisms such as keratin in nails, or fibrin, which causes blood clots to form.

In other proteins, the tertiary structure is more spherical, forming a globular protein. Globular proteins are usually soluble and are involved in metabolic reactions inside and outside cells. Some examples include haemoglobin, enzymes and some hormones.

Quaternary Structure

Finally, in proteins with more than one polypeptide chain, there is a fourth level of organization. In proteins such as insulin, hydrogen and ionic bonding cause two or more polypeptide chains curl together to form a complete protein molecule. This is known as the quaternary structure of the protein. The different polypeptide chains are held together by the same types of bonds which are responsible for the tertiary structure.

Glossary

alanine

one of the twenty naturally occurring amino acids, its "R-group" is –CH₃

α-helix

a regular spiral of amino acids which is one of two common secondary structures in a protein

β-pleated sheet

a flat sheet of polypeptide chains which is one of two common secondary structures in a protein

condensation reaction

a chemical reaction in which two molecules combine with the expulsion of a smaller molecule

Disulphide bridges

chemical bonds formed between the sulphur atoms on adjacent cysteine amino acids

Enantiomer

one of a pair of optical isomers

enzyme

a biological catalyst

haemoglobin

the red pigment which is used to transport oxygen in the blood

Insulin

a polypeptide hormone secreted in the islets of Langerhans which is used to regulate the metabolism of carbohydrates and fats

Keratin

a fibrous protein which is present in nails, hair and horn

Metabolic

relating to the chemical processes occurring within a living cell or organism that are necessary for the maintenance of life

peptide bond

the chemical bond formed by the condensation reaction between two amino acids

polymer

any of a number of natural and synthetic compounds consisting of many repeated linked units, each a relatively simple molecule itself

Polypeptide

a polymer consisting of amino acids joined by peptide bonds

Van der Waals' forces

weak electrostatic forces of attraction between protons and electrons in different molecules

zwitterion

a molecule carrying both a positive and a negative charge

Bibliography

Friedli Georges-Louis (1999). Proteins at URL: www.friedli.com/herbs/phytochem/proteins.html
Birbeck College Biology Dept. (1998). The Principles of Protein structure at URL www.cryst.bbk.ac.uk/PPS/
Taylor, D. Jones, M. (1994). Foundation Biology. Cambridge University Press
Jones, M. Jones, G. (1997). Advanced Biology. Cambridge University Press