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Protein Structure

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Amino acids; Peptide bond

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Side chains

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Protein Structure


Proteins are made up of chains of amino-acids that are connected by covalent bonds formed by the loss of a water molecule. The sequence of amino-acids gives the primary structure.

There are two types of secondary structures possible. Hydrogen bonds between amino-acids within a polypeptide strand give alpha-helices, and between adjacent polypeptide chains give beta-pleated sheets.

These are further folded to give tertiary structures, by hydrogen bonds, ionic and van deer Waals interactions, and disulphide bonds to give a three-dimensional form. Quaternary proteins are macromolecules with many polypeptide chains.

Definition of Protein

Proteins are polymers made of chains of amino acids. Proteins can have hundreds or thousands of amino-acids. These are combinations of 20 different kinds of amino-acids.


amino-acidAmino-acids all have a basic simple structure composed of an alpha, or central, carbon linked to a carboxyl (COOH), an amino group (H3N), and a hydrogen atom. In addition, there is a fourth group called the R-group, that can vary, and forms the side chain. The simplest amino-acid, glycine, has a hydrogen atom as the R-group. Each of the 20 amino-acids has an unique side-chain. The structural formula of an amino-acid always shows the R-group on the side. For example:

              H                                        CH3

              │                                          │

NH2—CH— COOH            NH2—CH— COOH                             

            Glycine                          Alanine

It is only the L-isomers of amino-acids that combine to form proteins. L-isomers are stereoisomers, or organic compounds that rotate polarized light to the left, or in a counter-clockwise direction. These can also be called S-isomers [S from sinister (left-handed)].

Structure of Proteins

There are four levels in which protein is structured, and they are called primary, secondary, tertiary and quaternary structure. The structure of proteins decides their function.

Primary structure

The exact sequence of amino acids connected by covalent peptide bonds gives the primary structure of proteins. The sequence of amino-acids is given in the genetic code of  DNA and passed on to RNA for protein synthesizes.

Peptide bonds are formed between the the amino group of one amino-acid and the carboxyl group of another amino-acid by the loss of a water molecule. Since the proteins are formed from what is left of amino-acids after the loss of water, proteins are called a chain of amino-acid residues. The last free carboxyl group is shown on the right side of the chain, and the last amino group is depicted on the left end of the chain.

Two amino-acids can join in two different sequences. For example, Glycine and alanine can be joined as Glycine — alanine or Alanine— glycine. A chain of two amino-acids is called a dipeptide, and a chain of three amino-acids is tripeptide. A chain of several amino-acids is called oligopeptide, and a chain of many is called a polypeptide. A protein usually has 50-500 amino-acids.

Secondary structure

There are two types of secondary structures, where the long chain is folded into stable structures. This happens in the form of alpha-helices and beta-pleated sheets. In both cases, hydrogen bonds between amino-acids along the chain occur between the carboxyl group (C=O) and amino group (H-N) group. It is the oxygen atom that binds with the hydrogen atom.


The backbone of the polypeptide chain containing the carboxyl group and amino group spiral in an clockwise direction, so that all the R-groups are located on the outside of the spiral. The hydrogen bonding occurs between the C=O and H-N groups of the same strand.

The positioning of the two groups forming the hydrogen bonds is always the same, so that the H-N group are pointing upwards and the C=O are pointing downwards in the spiral. Cytochrome C has all α-helices.

β-pleated sheets

Here the hydrogen bonds are formed between two separate adjacent polypeptide chains. The R-groups are alternately pointing up and down the pleats. The sheets can be arranged parallel, that is with the carboxyl ends on the same side, or be anti-parallel, where adjacent strands run in opposite directions. Plastocyanin is a protein made entirely of β–sheets.

In a protein, the folding can be completely in the form of α-helices, or β-strands, or a mixture of the two types.The Triosephosphate Isomerase (TIM), a glycolytic enzyme, has polypetide strands that are mixed.

Tertiary structure

Tertiary StructureHere the α-helices or β-strands are further folded to give the protein a three-dimensional form. The form holds due mainly to non-covalent bonds between the R-groups or side-chains of the different strands. The sequence of the amino-acids decides where the folding occurs.

a) Hydrogen bonds can form between hydrophobic side-chains. Bonds can occur between -OH groups, or -COOH groups on one side, with -CONH2groups, or -NH2groups on the other side in many combinations. These bonds are stronger than those in the secondary structure.

b) Ionic bonds are formed because the amino-acid can carry positive or negative charges because it has an extra -NH2group or -COOH respectively. For example aspartic acid is negative and lysine is positively charged, so they are attracted and form bonds.

 c) van der Waals interactions occur between hydrophobic side-chains and depend on attraction and repulsive forces between the side-chains.

d) Disulphide bonds are the only instance of covalent bonds influencing tertiary structures, and happen only between the side-chains of the amino-acid cysteine.

Quaternary structure

This is the most complex form of structuring, and involves many different polypeptide chains or sub-units. For example, the protein Hemoglobin in blood has four sub-units- two alpha and two beta.Protein structure


Proteins are made up of amino acids bonded to each other covalently. The DNA code, translated through mRNA at the ribosome, determines a protein's primary structure. The secondary structure occurs when the long chain of amino acids is folded either into either alpha-helices or beta-pleated sheets. These proteins are then folded again to give them a three dimensional form and their tertiary structure. Some of the most complex proteins, like hemoglobin, also have quaternary structures made up of many different polypeptide chains, or sub-units.


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