Amino acids

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Amino acids are the building blocks of proteins. There are 20 naturally occurring amino acids. Amino acids exist in proteins as L-optical isomers, however they can extist as D-isomers in isolated examples, e.g. some bacterial cell walls contain D-isomers.

Amino Acids are made up of 3 bases called a codon.

Amino acids can also be characterized as polar or non-polar and these dictate the amino acid function. There are 10 non-polar amino acids found in protein core, and there are 10 polar amino acids. These have enzymatic roles and can be used to bind DNA, metals and other naturally occuring ligands. There are essential amino acids and non-essential amino acids. Essential amino acids are the ones that the body cannot synthesise on its own. The essential amino acids in humans are: histidine, leucine, isoleucine, lysine, methionine, valine, phenylalanine, tyrosine and tryptophan [1]. These amino acids have to be supplied to the body via digested proteins that are then absorbed in the intestine and transported in the blood to where they are needed[2]. The digestion of cellular proteins is also an important source for amino acids. Non-essential amino acids can be synthesised from compounds already existing in the body.

Amino acids have been abbreviated into a 3 letter code as well as a 1 letter code. For example, glycine has the 3 letter code 'Gly' and is assigned the letter 'G' (see single letter amino acid codes).

List of the 20 Amino acids, single letter code, three letter code, their charges, and side chain polarity:

Amino acid single letter code three letter code charge polarity
alanine A Ala neutral nonpolar
arginine R Arg +ve polar
asparagine N Asn neutral polar
aspartate D Asp -ve polar
cysteine C Cys neutral polar
glycine G Gly neutral nonpolar
glutamine Q Gln neutral polar
glutamate E Glu -ve polar
histidine H His +ve polar
isoleucine I Ile neutral nonpolar
leucine L Leu neutral nonpolar
lysine K Lys +ve polar
methionine M Met neutral nonpolar
phenylalanine F Phe neutral nonpolar
proline P Pro neutral nonpolar
serine S Ser neutral polar
threonine T Thr neutral polar
tryptophan W Trp neutral nonpolar
tyrosine Y Tyr neutral polar
valine V Val neutral nonpolar

Amino acid structure

All amino acids have a carboxyl terminus and an amino terminus, but they differ in their residual groups. Amino acids are bonded together by a covalent linkage called a peptide bond [3]. Amino acids contain both a carboxyl group (COOH) and an amino group (NH2). The core amino acid structure is:

              NH2-----C(H)(R)----COOH

where (R) is the side chain unique to each different amino acid.

Large amino acids form the rigid region of the polypeptide backbone while the small amino acids form the flexible regions of the polypeptide allowing the protein to fold into it's three dimensional shape. This is what allows the polypeptides primary sequence to fold to an alpha helix which is one strand coiled. A beta strand is two strands coiled to an antiparallel helix. The core of the polypeptide is made up of the hydrophobic amino acids like phenyalanine, tyrosine, and tryptophan [4]. These three amino acids are also aromatic and are the largest amino acids. The other hydrophobic amino acids, but are not aromatic, are: proline, valine, isoleucine, leucine and methionine.

Amino acids are referred to as chiral due to the alpha carbon being connected to four different groups. They can exist as one of two mirror images referred to as theL isomer and the D isomer with only the L form of the amino acid isomer present within proteins [5].

Amino acids in solution at neutral pH exist predominantly as dipolar ions, or zwitterions. In the dipolar form, the amino group is protonated, and the carboxyl group is deprotonated. The ionization state of an amino acid varies with pH [6].

A series of amino acids joined by peptide bonds form a polypeptide chain, and each amino acid unit in a peptide is called a residue. The formation of a dipeptide from two amino acids is accompanied by the loss of a water molecule. 

Amino acids in Translation

During the translation of mRNA amino acids bind to the ribosome as it reads the mRNA and using the information given it produces a specific amino acid sequence producing a polypeptide chain. The 30S subunit binds to the mRNA first, and the 50S subunit binds second to form the 70S initiatior complex [7].

References

  1. Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: W.H. Freeman and Company, pg650.
  2. Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: W.H. Freeman and Company, pg650.
  3. Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science. 1268. (Page 59)
  4. J.M.Berg, J.L.Tymoczko, L.Stryer,(2007) Biochemistry, 6th edition, New York: W.H.Freeman and company (page 27).
  5. Berg J. Tymoczko J. Stryer L., Biochemistry Sixth Edition (2007, WH Freeman, New York (page 27)
  6. J.M.Berg, J.L.Tymoczko, L.Stryer,(2007) Biochemistry, 6th edition, New York: W.H.Freeman and company (page 27)
  7. Berg J, Tymoczko J, Stryer L (2007) Biochemistry sixth edition, New York: W. H. Freeman and Company (page 34)

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