Friday, March 22, 2013

Biomolecules of Cell - Proteins (Amino Acids)

Before going ahead and understanding proteins - the biomolecules, it is important to first understand amino acids. Amino acids are the organic compounds mainly bonded to a hydrogen atom, a carboxyl group (COO-) and an amine group (NH2) along with a side chain (represented as R in the diagram) which is specific to every amino acid. There are about 500 amino acids known. The two broad groups into which these amino acids can be distributed are: proteinogenic amino acids and non-proteinogenic amino acids. The word ‘proteinogenic’ means ‘protein building’. Interesting to note is that of these 500 amino acids, only 23 naturally occurring amino acids come under proteinogenic amino acids i.e.; these amino acids are precursors to proteins. Of these 23, 20 proteinogenic amino acids are encoded by codons (triplet) in genetic code and are called ‘standard’ amino acids. The other three which are ‘non-standard’ amino acids are pyrrolysine, selenocysteine and N-formylmethionine. The pyrrolysine is found in methanogenic organisms and other eukaryotes. Selenocysteine is present in non-eukaryotes as well as in some eukaryotes. While N-formylmethionine, as we all know takes part in protein synthesis initiation in bacteria and also in protein synthesis that takes place in organelles (chloroplast and mitochondria).Here, in this post, we will discuss about the standard 20 amino acids.
Each amino acid has a distinctive 3-letter code and 1-letter code which is mostly use to represent them. Here is the list of 20 standard amino acids with their 3-letter code and 1-letter code.
(Gly, G)
(Ala, A)
(Val, V)
(Leu, L)
(Ile, I)
(Pro, P)
(Phe, F)
(Tyr, Y)
(Trp, W)
(Ser, S)
(Cys, C)
(Thr, T)
(Met, M)
Aspartic Acid
(Asp, D)
(Asn, N)
Glutamic Acid
(Glu, E)
(Gln, Q)
(His, H)
(Lys, K)
(Arg, R)

Characteristics of Amino Acids:
Since in all amino acids, the carboxyl and amine groups are attached to primary or α-carbon atom, these amino acids are known as α-amino acids. All amino acids except glycine exists as enantiomers (mirror images of each other that are non-superimposable) called as L or D amino acids. Remember that L and D configuration of amino acid does not refer to the optical activity of the amino acid itself. In fact, it refers to the optical activity of isomer of glyceraldehyde (from which all amino acids can be synthesized theoretically). All proteinogenic amino acids exist as L-stereoisomers (meaning left-handed isomers).
The two functional groups of amino acids as carboxyl group and amine group make them amphiprotic meaning it can act as an acid or base.  Carboxylic acid (-COOH) groups can be deprotonated to form carboxylate (COO- ) whereas amino groups (NH2) can be protonated to from positively charged ammonia (NH3+) groups. This form when the net charge on the amino acid is zero is called a zwitterion. Remember that, when the pH of any amino acid is greater than the pKa of the carboxylic group of that amino acid, the negative carboxylate ion predominates i.e.; at higher pH, the net charge on amino acid is negative. At pH values lower than the pKa of the alpha-ammonium group, the nitrogen is protonated because of positively charged alpha ammonium group meaning at low pH, the net charge on the amino acid will be negative.
Essential Amino Acids:
of the 20 standard amino acids are essential amino acids meaning that they are not synthesized or created from another compound inside the body and hence has to be taken externally in the form of food. The remaining amino acids are non-essential meaning they need not be taken from the outside.
The nine essential amino acids are arginine (essential only in growing children where they have to obtain from their diet), histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine. Is it difficult to remember these 9 amino acids? Here are three ways by which you can make it mnemonic:
1. PVT TIM HALL (like ‘private tim hall’ is someone’s name) OR
2. MAT VIL PhLY (pronounce as if ‘matw ill fly’ where, Ph is for phenylalanine, Y is for tyrosine)
2. By remembering this sentence: Any Help In Learning These Little Molecules Proves Truly Valuable.
Types of Amino Acids Depending on the Properties of Side Chain:
There are certain unique chemical properties of each amino acid due to its side chains which we will discuss here.  The amino acids can be grouped into four broad categories according to the properties of side chains.
1. Non-Polar Amino Acids or Hydrophobic Amino Acids: Ten amino acids have non-polar side chains meaning that they do not interact with water. Glycine is the simplest amino acid. alanine, valine, leucine and isoleucine have up to four carbon atoms and their side chains are hydrophobic and hence these amino acids are located in the interior of the protein where they are unable to interact with water. Proline also has a hydrophobic side chain. It is interesting to note that it is unique such that the side chain is bonded to nitrogen atom of amine as well as α-carbon thereby forming a cyclic structure. Thus, proline is an imino acid instead of amino acid. The amino acids cysteine and methionine have sulphur in their side chains. Methionine is quite hydrophobic but cysteine is less as it has sulfhydryl group (SH) group. Cysteine plays an interesting role as it can form disulphide bonds between two cysteine residues of side chains of two proteins. The two amino acids, phenylalanine and tryptophan contain hydrophobic aromatic rings.

2. Polar Amino Acids or Hydrophilic Amino Acids: Five amino acids have polar side chains but are uncharged. Serine, threonine and tyrosine have hydroxyl groups in their side chains. Aspargine and glutamine have polar amide (O=C=NH2). These proteins can interact with water to form hydrogen bonds and hence are hydrophilic and are located on the outside of the proteins.

3. Positively Charged Amino Acids/ Basic Amino Acids:  Three amino acids have side chains with charged basic or positive groups. Lysine, arginine and histidine come under this category of basic amino acids.

4. Negatively charged amino acids/Acidic amino acids: Remaining two amino acids as aspartic acid and glutamic acid have side chains which have carboxyl groups and hence are acidic in nature. These are hydrophilic and hence are located on the outer surface of the proteins.

Here, we end with the basics of amino acids. In the next post, we will see about the proteins.