Tuesday, March 26, 2013

Biomolecules of the Cell - Proteins

Proteins are the biomolecules which are polymers of amino acids covalently linked through a peptide bond into a chain. Before understanding the structure of proteins, lets clarify some of the terms in this context.

1. Peptide bond:

A peptide bond is the covalent bond that is formed between the carboxyl group of one amino acid and the amino group of the next amino acid. The resulting C(O)NH bond is called the peptide bond (as can be seen in the figure).  The peptide bond formation occurs as a result of the condensation reaction involving loss of a water molecule.

2. Peptide:
What is a peptide? Amino acids are covalently linked to each other with the help of the above mentioned peptide bonds and form a chain. When the length of this chain is very short, say less than 40 amino acids, it is called peptide. The shortest peptide is dipeptide (consisting of 2 amino acids joined by a single peptide bond); then there can be tripeptides (consisting of 3 amino acids with 2 peptide bonds); tetrapeptides (consisting of 4 amino acids with three peptide bonds) and so on.

3. Polypeptide:
Is peptide and polypeptide one and the same thing? NO. Polypeptide is a long chain of amino acids having around more than 40 amino acids. It is primarily a single, long, continuous, linear and unbranched peptide chain. For example, Angiotensin II is a peptide hormone (that causes vasoconstriction and increase in blood pressure) that contains only 8 amino acids (octapeptide). Another example of peptide hormone is mammalian hormone, oxytocin, which is made up of only 9 amino acids (nonapeptide).

4. Protein:
Proteins are made up of one or more polypeptides. The proteins are considered to be the 'workhorses of the cell' as they include structural and motor elements in the cell and are responsible for serving as the catalysts for literally every biochemical reaction that occur in living things. We will have a look at the structure of proteins now.

Structure of Proteins:
As mentioned above, proteins being workhorses of the cell and to understand their functions, it is necessary to determine their structure. Proteins tend to fold into one or more specific conformations which are driven by a number of interactions which we are going to see below. There are four distinct levels into which we can divide the structure of proteins as follows:

a. Primary Structure:
The linear sequence of amino acids in a protein is considered to be the primary structure of the protein. This amino acid sequence is ultimately responsible for the folding and intermolecular bonding of the linear amino acid chain which thus determines the protein’s 3-D shape. The primary structure is mainly held by peptide bonds which have been made during the process of protein biosynthesis.
b. Secondary Structure:
Secondary structure refers to the areas of local stable folding (or coiling) within a protein. These mainly include α-helix and β-sheets.
i. α-helix:  In an α-helix, the protein chain is coiled like a loosely-coiled spring (just like the telephone cable). Why it is called “alpha”? Alpha measn that if you look down the length of the spring, the coiling happens in a clockwise direction as it goes away from you. An α-helix is stabilized by hydrogen bonds between the (backbone) amino and carbonyl groups. The H-atom of amide group forms the bond with the OH atoms of carbonyl group. There is regularity in the arrangement of hydrogen atoms. All the N-H groups point upwards as against the C=O groups that point downwards (as in the figure). In an α-helix, the R-groups (side chains) of amino acids protrude out from the helically coiled polypeptide backbone. Also, each complete turn of the spiral has approximately 3.6 amino acids residues in it and the distance between two turns is 0.54nm.

ii. β-sheet: Another common secondary structure is β-sheet. In a β-sheet, strands of protein lie adjacent to one another and interact via H-bonds between backbone carbonyl oxygen and amino H atoms. There are two main kinds of arrangements as parallel and antiparallel. In parallel arrangement, all the N-termini of successive strands are oriented in the same direction whereas in an antiparallel arrangement, the successive β-strands alternate directions such that the N-terminus of one strand is adjacent to the C-terminus of the next strand (it will be more clear from the diagrams below).

c. Tertiary Structure: 
The tertiary structure refers to the three-dimensional structure of a protein. The α-helices and β-sheets are folded into compact globular structures. This results from a large number of interactions between amino acids such as:
i. Ionic Interactions: Some amino acids are basic (positively charged) while some are acidic (negatively charged). Hence, ionic bond forms between the negative and positive group if the chains folded in such a way that they are close to each other.
ii. Hydrogen Bonds: Here, we are talking about the H-bonds between the side-groups not between the groups actually in the backbone of the chain. Some amino acids contain –OH group in the side chain (eg. Serine). A H-bond can form between two different serine residues in different parts of a folded chain.
iii. Van der Waal’s forces: Van der Waal’s interaction is transient, wee electrical attraction of one atom to another. It provides an important component of protein structure. Most of the atoms in a protein are so sufficiently close to be involved in such kind of transient interaction.
iv. Disulfide bonds: Cysteine is the sole amino acids whose side-chain can form covalent bonds. When two cysteine residues in a protein comes close to one another, then the R-groups of both interacts with each other yielding disulphide bridges.
v. Hydrophobic Interactions: Certain amino acid residues possess the hydrophobic or non-polar (water-repelling) side chains. The hydrophobic amino acids are generally at the centre of the protein as against the hydrophilic amino acids which are towards the edges. Not all hydrophobic amino acids are in the interior of proteins, however.

d. Quaternary Structure: It refers to the non-covalent interactions that bind multiple polypeptides into a single, larger protein. The protein may be composed of identical polypeptides or may include different polypeptides as well. Being non-covalent interactions, quaternary structure is mainly stabilized by weak interactions between residues exposed on the surface of the polypeptides within the complex. Hemoglobin is a very good example of quaternary structure which consists of two α-polypeptide chains, two β-polypeptide chains and a prosthetic heme group (see diagram).
Here, we end the structure of proteins.