Protein Synthesis and Structure

PROTEIN STRUCTURE AND SYNTHESIS

Proteins are polymers of a-amino acids. There are twenty amino acids that are commonly found in proteins. Each amino acid has a similar, yet unique structure. Almost all of the amino acid have a carboxyl group and an amino group. At neutral pH the natural amino acids exist as zwitterions, with a negatively charged carboxyl group and a positively charged amino group.

The a carbon of most of the amino acids is chiral. Thus there are two stereoisomers of most of the amino acids.

All proteins are made from just 20 a-amino acids all of which have the same general structure. Each amino has a different side chain.

The different side chain is labeled R above. The R group determines the name of the amino acids. The side chains vary greatly in their complexity and properties.

Amino acids are joined together by peptide bonds. The reaction involves the formation of a molecule of water in another condensation polymerisation reaction

When two amino acids join together a dipeptide is formed. Three amino acids form a tripeptide. Many amino acids form a polypeptide. e.g.:

+NH3-Gly -- Pro -- His -- Leu -- Tyr -- Ser -- Trp -- Asp -- Lys -- Cys-COO-

In a polypeptide there is always one end with a free amino (NH3) group, called the N-terminus, and one end with a free carboxyl (CO2) group, called the C-terminus.

In a protein the polypeptide chain may be hundreds of amino acids long. Amino acid polymerisation to form polypeptides is part of protein synthesis. It takes place in ribosomes, and is special because it requires an RNA template. The sequence of amino acids in a polypeptide chain is determined by the sequence of the genetic code in DNA.

Protein structure is broken down into four levels. Primary structure refers to the linear sequence of amino acids. Proteins are large polypeptides of defined amino acid sequence. The sequence of amino acids in each protein is determined by the gene that encodes it. Primary structure is sometimes called the "covalent structure" of proteins because; with the exception of disulfide bonds all of the covalent bonding within proteins defines the primary structure. In contrast, the higher orders of proteins structure (i.e. secondary, tertiary and quaternary) involve mainly non covalent interactions. This is the most basic level of protein folding, and consists of a few basic motifs that are found in all proteins.

The secondary structure is held together by hydrogen bonds between the carboxyl groups and the amino groups in the polypeptide backbone. The two most common secondary structure motifs are the a-helix and the b-sheet.

The a-helix: The polypeptide chain is wound round to form a helix. it is held together by hydrogen bonds running parallel with the long helical axis. There are so many hydrogen bonds that this is a very stable and strong structure The b-sheet: The polypeptide chain zig-zags back and forward forming a sheet of antiparallel strands. Once again it is held together by hydrogen bonds.

Tertiary structure consists of compact globular structure formed by the folding up of a whole polypeptide chain. Every protein has a unique tertiary structure, which is responsible for its properties and function. For example the shape of the active site in an enzyme is due to its tertiary structure. The tertiary structure is held together by bonds between the R groups of the amino acids in the protein, and so depends on what the sequence of amino acids is. There are three kinds of bonds involved.

Hydrogen bonds which are weak. Ionic bonds between R-groups with positive or negative charges which are quite strong and sulphur bridges - covalent S-S bonds between two cysteine amino acids, which are strong.

So the secondary structure is due to backbone interactions and is thus largely independent of primary sequence, while tertiary structure is due to side chain interactions and thus depends on the amino acid sequence.

Quarteranary structure is found in proteins containing more than one polypeptide chain, and simply means how the different polypeptide chains are arranged together. The individual polypeptide chains are usually globular, but can arrange themselves into a variety of quaternary shapes.Proteins are used in the cell for a variety of reasons. They may have a structural or a functional role, or they may act as enzymes controlling cell metabolism. Protein synthesis is a very complex process; The structures of DNA and RNA are involved in the process of protein synthesis.

DNA and RNA are nucleic acids formed from nucleotides. Individual nucleotides are comprised of three parts:

Phosphoric acid (Phosphate H3PO4). This has the same structure in all nucleotides.

Pentose sugar: These are of two types - Ribose (which occurs in RNA) and Deoxyribose (which occurs in DNA)

Organic bases: There are five different bases which are divided into two groups - Pyrimidines - these are single rings with six sides. i.e., cytosine, thymine and uracil. Purines - these are double rings comprising a six-sided and a five-sided ring, i.e., adenine and guanine.

The three components are combined by condensation reactions to give a nucleotide.

DNA is a double stranded polymer made up of two polynucleotide chains, where the pentose sugar is always deoxyribose and the organic bases are adenine, guanine, cytosine and thymine, but never uracil. Each chain has a sugar phosphate backbone on the outside with organic bases on the inside. The two chains are held together by complementary base pairing and