Amino Acids, Biology tutorial

Occurrence of Amino Acids in Nature:

Fundamentally, amino acids are building blocks of proteins. Most amino acids happen naturally in conjugated form as components of proteins. Those which happen usually in proteins are known as common amino acids. These are 20 in number. Certain amino acids and derivatives, though, are not found in proteins. They however carry out useful biological roles.

Basic Structure of Amino Acids:

i) How Carbon Atoms in Amino Acids are named:

Amino acids are organic compounds composed of hydrogen, carbon, nitrogen, oxygen and, in a few cases, sulfur. Basic structure of the amino acid molecule comprises of carbon atom which is bonded to the amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom and fourth group which varies from one amino acid to another and is frequently referred to as -R group or side chain. -R group can differ widely and is liable for differences in chemical properties. Name, amino acid, comes from amino group and acid group that are the most reactive parts of molecule. Amino acids which are significant in biological world are referred to as a-amino acids as amino group is bonded to a-carbon atom, that is, one adjacent to carboxyl group.

ii) Chirality in Amino Acids:

Chiral compounds are compounds that have at least one chiral carbon atom or chiral centre. The chiral carbon or centre is carbon atom to which 4 different functional groups are covalently linked. For typical amino acid, four different functional groups comprise:

i) Carboxyl group (-COOH) or its carboxylate ion form (-COO-)

ii) Amino group (-NH2) or its ammonium ion form-NH3+)

iii) Hydrogen atom (H)

iv) A variable side chain (Also known as R group). R group provides each amino acid its identity. All amino acids with exception of glycine have chiral cetre at alpha carbon (Cα).

iii) Concept of Stereoisomerism:

Stereochemistry of biomolecules deals with three-dimensional arrangement of constituent atoms of molecule in space. Each fixed spatial arrangement of atoms in the molecule is known as molecule's configuration. The Carbon compound may have different forms (configurations) in which different atoms are set differently in space. Such forms of compound are referred to as its stereoisomers. Alpha carbon (Cα) of amino acids, because of its tetravalency, is easily bonded to 4 atoms. When all the atoms are different, carbon atom is said to be chiral or asymmetric and number of stereoisomers which can happen in such chiral compound is normally provided by 2n, where n is number of chiral carbon(s) in compound.

For instance, Glycine has only one stereoisomer as its n=0, Alanine has one chiral carbon therefore; number of its tereoisomers is 21 i.e. 2.

 In stereochemistry, stereoisomers which are mirror images of each other are known as enantiomers while pairs of stereoisomers which are not mirror images of each other are known as diastereomers.

D- and L-Configurations of Amino acids:

In 1891, Emil Fischer suggested D, L system of nomenclature for asymmetric/chiral compounds (like amino acids and sugars). System specifies absolute configuration of substituents around chiral centre with reference to glyceraldehyde, a 3-carbon sugar.

By this system, stereoisomers which have configuration similar to that of D-glyceraldehyde are designated L, and those with configuration similar to L-glycceraldehyde are designated L. This can be done by just aligning carboxyl group (COOH) of amino acid with aldehyde group (CHO) of glyceraldehydes as illustrated for Alanine and Tyrosine below:

i) Using Perspective Formulas:

303_Amino acid structure-Perspective Formulas.jpg

Amino acids that happen in proteins are generally L- isomers and only living cells generate this form. This is due to biochemical reactions are stereospecific. For instance, enzymes are specific in their actions, recognizing only one isomer and not other.

ii) Using Fischer Projection Diagrams:

1715_Amino acid structure-Fischer Diagrams.jpg

Structures of Some Amino Acids:

  • All amino acids are similar structurally
  • They all contain carboxyl, amino group, hydrogen atom and the side chain (R group) covalently linked to alpha carbon atom.
  • They vary mainly in nature of their side chains (R groups); R groups in amino acids differ in structure, size/length and electric charge.
  • Each amino acid can be remembered for the particular characteristic in side chain: Glycine, the amino acid with the simplest structure, has H as its side chain; Alanine has a methyl group (-CH3)in place of R; Valine has the isopropyl R group; Phenylalanine and tyrosine have aromatic /benzene ring in side chain;
  • At physiological pH, amino acids are ionic in nature with amino and carboxyl groups preferring ammonium (+NH3) and carboxylate (COO-) defines rather than amino (NH2) and carboxyl (COOH) states respectively. Amino acids are thus drawn showing these ionic forms.

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