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Chemical principles: Amino acid structure

Introduction

 

Amino acids are the organic compounds which are considered to be the “building blocks of proteins”. They have the same basic structure and a variable group orientated around a central carbon atom called the α-carbon. A carbon atom can form four covalent bonds. These are to a hydrogen atom, a carboxylic acid (–COOH) and an amine (–NH2 group), and the variable "R" group (or side chain) which gives each type of amino acid its unique properties. The diagram below shows three ways that amino acids are commonly drawn. In the dash and wedge diagram (2) the wedge comes forward out of the page and the dash goes backward out of the page to indicate the 3D shape.

 

Amino acid structure

All proteogenic amino acids follow the structure presented above, except for one. The amino acid proline forms a covalent bond between the amino group and the R group. This makes the structure of proline unusually rigid which can result in a number of effects on protein structure. For example proline can disrupt secondary structure components including helices and sheets. Repeating proline patterns in a polypeptide can also give rise to left handed helices. The rigidity of proline also helps to stabilise folded proteins, and as a result the proteins of thermophilic bacteria often have a high proprtion of proline residues.

 

 



 

There are 22 standard amino acids, of which humans use the 20 encoded by the universal genetic code. The other two, found in some prokaryotic cells, are signalled by special mRNA sequences. Non-standard amino acids are not directly encoded in the mRNA but have the amino acid structure described above so are part of the same chemical group. These can be synthesised in a laboratory, or arise from post-translational modification or as intermediate molecules in biosynthetic pathways (for example in producing amino acids). Amino acids frequently have more than one carbon. These are identified using letters from the Greek alphabet, counting from the α-carbon towards the end of the side chain (for example, β-, γ-, δ-, and ε-carbons), the last being the ω-carbon.

 

Classification

 

Amongst the many ways of classifying proteinogenic amino acids, some the most important ones are based on the charge proprieties of the side chain:

 

a)      Polar or non-polar structure:

  • Non-polar: glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophan, methionine;
  • Polar: serine, threonine, tyrosine, cysteine, glutamine and asparagin.

 

b)      Acid/ base present:

  • Acidic : glutamic acid and aspartic acid;
  • Basic:  histidine, lysine, and arginine;

 

The term “zwitterion” comes from a German word which means “hybrid”, and it is used to describe compounds with both a negative and positive charge, each on different atoms. Carboxylic acids (-COOH) donate a proton if they are in a moderately weak base solution, and amines (-NH2) gain a proton if they are in a moderately weak acid solution. Because amino acids have both –COOH and -NH2 groups,  a proton is donated from the carboxyl group and accepted by the amino group. This creates a zwitterion as shown in the diagram below. Because they are also ionic compounds, they are highly soluble in water.

 



 

If the pH of the solution in which the amino acid is dissolved changes from physiological, the zwitterion will also change into a negatively or positively charged compound. Therefore, if the amino acid is dissolved into a strong acid, the COO- will gain a proton, and if it’s dissolved into a strong base, the NH3+ will donate a proton. The diagram below shows association and dissociation of protons to these groups at different pHs.

 



Stereochemistry

 

It is important to understand the 3D structure of the amino acids, to be able to determine their stereochemical proprieties. Except for glycine (where the side chain is a H atom), all the natural amino acids are chiral molecules. Chiral molecules are mirror images which cannot superimpose, in the same way that however your rotate your left hand it can never exactly match your right.

 

In nature chirality most commonly occur around a carbon atom, where four different groups are bound around it. This is shown form amino acids in the diagram below. The two mirror images are called enantiomers of each other or optical isomers. They are refered to as right or left-handed or the D- or L- form. All the proteins in the human body are made up of L-isomers of amino acids; the D-isomers are very rare.

 



Useful videos

 

References

 

  • Garrett, R. and Grisham, C. (2010) Biochemistry 4th Edition.  Belmont, CA, Brooks/Cole, Cengage Learning.
  • Berg, J., Tymoczko, J. and Stryer, L. (2002). Biochemistry. 5th Edition. New York, W.H. Freeman Publishing.
  • Bettelheim, F., Brown, W., Campbell, M., and Farrell, S. (2010). Introduction to general, organic, and biochemistry. 9th Edition. Belmont, CA, Brooks/Cole.

 

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