Instant Protein Notes
(simply remove water)
Proteins are made up of polypeptides. Polypeptides are a chain of amino acids connected together. Amino acids have the general formula NH2-CH(R)-COOH, where R is anything (e.g. if R = H then the amino acid is glycine, if R = CH3 then the amino acid is alanine.). Polypeptides are made up of combinations of 20 different amino acids (There are lots of others that don't occur in proteins). Glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, tyrosine, tryptophan, aspartic acid, glutamic acid, lysine, arginine, histidine, asparagine, glutamine, serine, threonine, cysteine and proline. The nature of the 'R' group determines how hydrophilic or hydrophobic the amino acid is. Glycine doesn't care. Alanine, valine, leucine, isoleucine and methionine have aliphatic, non-polar side chains and are therefore hydrophobic. Phenylalanine, tyrosine and tryptophan have aromatic (ring) side chains and are very hydrophobic. The rest are hydrophilic. Cysteine is a bit odd but very useful. Cysteine has an SH group in its side chain which can link to SH groups in other cysteine residues and thus link two parts of a polypeptide (see tertiary structure).
When amino acids are connected together to make a polypeptide molecule OH is removed from the COOH group of one amino acid and H from the NH2 group of the other to give H2O and NH2-CH(R)-CONH-CH(R)-COOH, a dipeptide (the middle bit of the amino acid in a polypeptide is now called an amino acid residue). This is a condensation reaction, so called because water is released in the joining process (condensation reactions don't occur in cells in a single step). Hydrolysis is the opposite process, water is added and a molecule is broken. Literally, hydro (water) lysis (splitting or breaking). Hydrolysis reactions do occur in a single step within cells. The process of condensation and joining amino acids together may be repeated ad infinitum to give tripeptides (NH2-CH(R)-CONH-CH(R)-CONH-CH(R)-COOH)and tetrapeptides and so on. Any chain <25 amino acids is called an oligopeptide, a chain containing >25 amino acids is a polypeptide. The largest polypeptide contains 5000 amino acids. Most polypeptides contain less than 2000. No matter how many amino acids are added together, the polypeptide will always have NH2 at one end, the N terminus and COOH at the other, the C terminus. A protein may be composed of a single polypeptide or it may be made up of several subunits (e.g. the α, β and γ subunits of G-proteins).
So far as function is concerned, it is not only the arrangement (the primary structure) of amino acids into a polypeptide that is important. Proteins also have a secondary structure (the orientation of the amino acids to their nearest neighbours e.g. α-helix), a tertiary structure (the folding of the polypeptide back on itself ) and a quaternary structure (the arrangement of several subunits held together by weak forces)