B- Classification according to polarity of side chain (R): 1- Polar amino acids: in which R contains polar hydrophilic group so can forms hydrogen bond with H2O. In those amino acids, R may contain: 1- OH group : as in serine, threonine and tyrosine 2- SH group : as in cysteine 3- amide group: as in glutamine and aspargine 4- NH2 group or nitrogen act as a base (basic amino acids ): as lysine, arginine and histidine 5- COOH group (acidic amino acids): as aspartic and glutamic . - They tend to orient to the outside of water soluble (globular) proteins • tend to orient to the inside of lipid soluble (membrane) proteins

2- Non polar amino acids: R is alkyl hydrophobic group which can’t enter in hydrogen bond formation. 9 amino acids are non polar ( glycine, alanine, valine, leucine, isoleucine, phenyl alanine, tryptophan, proline and methionine). - They tend to orient to the inside of water soluble (globular) proteins • tend to orient to the outside of lipid soluble (membrane) proteins

(Those + basic and acidic amino acids) 9 amino acids are non polar

http://www.youtube.com/watch?feature=player_detailpage&v=WKBAuKsTkZs

III- Nutritional classification: 1- Essential amino acids: These amino acids can’t be formed in the body and so, it is essential to be taken in diet. Their deficiency affects growth, health and protein synthesis. 2- Semiessential amino acids: These are formed in the body but not in sufficient amount for body requirements especially in children. Summary of essential and semiessential amino acids: Villa HM = Ten Thousands Pound V= valine i= isoleucine l= lysine l= leucine A = arginine* H= histidine* M= methionine T= tryptophan Th= threonine P= phenyl alanine *= arginine and histidine are semiessential 3- Non essential amino acids: These are the rest of amino acids that are formed in the body in amount enough for adults and children. They are the remaining 10 amino acids.

IV- Metabolic classification: according to metabolic or degradation products of amino acids they may be: 1- Ketogenic amino acids: which give ketone bodies . Lysine and Leucine are the only pure ketogenic amino acids. 2- Mixed ketogenic and glucogenic amino acids: which give both ketonbodies and glucose.These are: isoleucine, phenyl alanine, tyrosine and tryptophan. 3- Glucogenic amino acids: Which give glucose. They include the rest of amino acids. These amino acids by catabolism yields products that enter in glucose formation.

Leucine Lysine Ketogenic amino acids

Modified amino acids Some amino acids are formed by modification of one of the 20 amino acids after synthesis of proteins Hydroxyproline and hydroxylysine Proline and lysine are hydroxylated enzymatically after translation to form hydroxyproline and hydroxylysine which are important in collagen structure (see later in collagen biosynthesis).

2. Phospho-amino acids a. Ser, Thr and Tyr hydroxyl groups can be phosphorylated b. important in activation and inhibition of enzymatic activity

3. Cysteine can form cystine with disulfide bonds

Non protein amino acids These amino acids don’t enter in protein structure, but have other functions in the body. Examples: ornithine, citrulline They enter in formation of urea in the liver.

Non protein amino acids (continued) β-alanine: is another example of non protein amino acids. it is a constituent of the vitamin pantothenic acid (one of the vitamin B complex)

1- Leucine amino acid is: a) non polar, non essential and ketogenic b) non polar, essential and ketogenic c) non polar essential and glucogenic d) polar, essential and ketogenic 2-  Which of the following is an essential hydroxy amino acid : a) cysteine b) threonine c) tryptophan d) serine 3- Which of the following statements concerning the peptide shown below is correct: Gly-Cys-Glu-Ser-Asp-Arg-Cys The peptide contains glutamine The peptide contains a side chain with a secondary amino group (imino group) The peptide contains a majority of amino acids which are positively charged at physiologic pH (7.4) The peptide is able to form internal disulfide bond

Physical properties of amino acids: 1- Optical activity: Optical activity is the ability of a chiral (asymmetric) molecule to rotate the plane of plane-polairzed light. Chiral molecule is the molecule that has asymmetric carbon atom which is attached to four different groups. So, all amino acids (except glycine) are optically active because they have four different groups attached to α-carbon Optically active molecules means also they have two isomers (enantiomers) that are mirror image to each other

amino acids enantiomers are either (D- or L-) amino acids enantiomers are either (D- or L-). They are named D or L according to arrangement of the groups COOH, R, NH2 and H. around the chiral α carbon atom. Sighting with the hydrogen atom away from the viewer, if these groups are arranged clockwise around the carbon atom, then it is the D-form. If counter-clockwise, it is the L-form. L-form D-form

All amino acids in protein have the L-configuration (except glycine which is optically inactive).

2-Amphoteric (acid-base) properties of amino acids in aqueous solutions: Amino acids have both basic and acidic groups and so can act as a base or acid so called amphoteric.

At low pH (acidic pH e.g. 2) amino acid will act as a base and accept proton from acidic medium and will carry positive charge. Both COOH and NH2 are protonated. (-NH3+ & -COOH) At high pH (alkaline pH) amino acid will act as an acid and will lose its H of COOH and will carry negative charge. Both COOH and NH2 are deprotonated (-NH2 & -COO-). At neutral pH, the amino acid will carry both positive and negative charges (zwitterion is formed). amines are protonated(-NH3+) and carboxylates are deprotonated (-COO-). This pH is called isoelectric point.

Isoelectric point (IEP, pI) = Isoelectric point (IEP, pI) of amino acid is the pH at which the zwitterion is formed (equal No. of positive and negative charge are present at the same molecule and the net charge will be zero. Zwitter ion can’t move in electric field. Q: How can we obtain pI of amino acid in aqueous solution?

NB: Zwitterions have minimum solubility at their IEP (PI) and some amino acids can be isolated by precipitation from water by adjusting the pH to the required isoelectric point.