Cellular Biology

Amino Acids and their Structure and Function



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Amino acids are the main constituents that are used to make up proteins in cells and as we know proteins are absolutely crucial to the continuation of life: it is the unique properties of each amino acid that can be used in order to achieve this. For example amino acids can help to catalyse reactions via and alternative mechanism, transport ions across an otherwise impermeable membrane or even act as a signaling device in the cell. Here i will try to show hoe these amino acids are crucial to life itself using specific examples.

There are 20 naturally occurring amino acids in proteins (not including fMet in prokaryotes)that are coded for in the DNA genome of each organism: this is converted into a protein message using mRNA as a template with each three letter codon representing an amino acid that is incorporated at the ribosome. It is important to note with the four different bases there are 64 combinations and only 20 amino acids: this is explained by the fact that multiple codons code for each amino acid as well as the three codons that indicate the termination of protein synthesis.

Each amino acid itself contains an amine (-NH2) and a carboxylic acid (-COOH), linked by an alpha carbon with another hydrogen as well as the R group attached: it is this R group that determines the identity and property of the amino acid. Most of the amino acids used in nature are l-amino acids, which means that when compared to l-glyceraldehyde they are similar in conformation. Chemists would describe 18 of the amino acids as being of S stereocentres at the alpha carbon with cysteine being R due to the heavy sulfur in the R group and so stereochemistry is inverted and glycine has no stereocentre as it has two hydrogen atoms attached to the alpha carbon and so does not exist as two enantiomers (Here it may be advisable to look up the Cahn-Ingold Prelog rules that are used to determine stereochemistry). However isoleucine and threonine have a second stereocentre due to the beta (second) carbon being differently substituted; these are S and R respectively.

The twenty amino acids have vastly different R groups due to the different properties they are required to have. Here I will not discuss all the amino acid as it is a waste of time as in my opinion it is best to see them drawn and discussed in detail and so should be looked up in a text book or using the internet; however i will discuss some general properties such as the way that there are amino acids that are charged or have hydrogen bonding capabilities and so can form interactions; others have groups that make them reactive to other molecules; some have rigid groups (such as proline) that can adopt only a few conformations so restricting movement of the protein and finally the are R groups that can hide away from water and so effect a protein's overall shape.

Now I will move onto the examples i will use in order to describe the way that amino acids are used in biology. Firstly these amino acids are used in enzyme active sites as catalytic agents. In the serine proteases a serine residue (containing an -OH group) is used as a nucleophile to attack the carbonyl of a peptide bond between amino acids, which leads to the overall hydrolysis of the bond. This is a good example to use as the serine is not the only amino acid of importance as histidine acts as a base to remove the proton from serine and so is a good example of acid-base catalysis that is a common biological theme. Aspartate is also present and also aids this reaction by forming a favourable hydrogen bond with histidine's hydrogen atom attached to the other side chain (R group) nitrogen as well as aiding in the orientation of the active site amino acids that means that the nucleophile is more effective.
Amino acids are hugely important in stabilising protein structure as each amino acid contains at least one carbonyl and N-H that can form hydrogen bonds and so are hugely important in local secondary structures such as alpha helices and beta sheets. The R groups themselves often help to maintain a protein's tertiary structure i.e. its shape due to numerous interactions like ionic interactions between charged side chains as well as weaker Van der Waal's interactions. By far the most important "interaction" is the hydrophobic effect that sees hydrophobic side chains such as phenylalanine (an alanine-linked benzene ring) and tryptophan avoiding water due to entropy (if any more information is needed on this topic it should be looked up). Disulphide bonds are also formed between cysteine residues (after this they are known as cystine)in an oxidation reaction; however this is generally only seen in extracellular proteins as the disulfides are reduced back and so do not form.
Proteins can also undergo what is known as post-translational modifications that see the addition or removal of various constituents. The most important example in my opinion is phosphorylation reactions that see the addition of a phosphate group to a protein usually from ATP (the cell's "energy currency"). This can lead to a change in activity of an enzyme or can even act as a signal in the cell:
Serine and threonine phosphorylation is usually reserved for the control of enzymes and other similar actions and is present in all organisms; however tyrosine phosphorylation arose later as the signaling pathway and is generally only seen in multicellular (eukaryote) organisms: this is as unicellular organisms do not require signaling between different cells. These signals can be in this way converted from a stimulus at the cell membrane to a difference in gene expression and in particular protein synthesis.

This essay could effectively be endless if we included all the examples of amino acids in a protein; however there is one more point that i feel must be mentioned. This point is the fact that proteins can contain various non-amino acid groups: the amino acids are responsible for interacting with the groups and so are hugely important: a good example to use in this instance is hemoglobin with its iron (II) containing heme group that is responsible for oxygen binding, it is a histidine residue that acts as the fifth ligand and so aids in the stabilisation of the complex.

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