II- Classification according to polarity of side chain (R):

1. II- Classification according to polarity of side chain (R): A- 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 . B- 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)

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

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

4. 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.

5. 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 glycogen and glucose formation.

6. Ketogenic amino acids Leucine Lysine

7. NB: 20 amino acids enter in protein structure. There are other amino acids in the body, but not enter in protein. e.g. ornithine, citrulline are amino acids with other functions in the body. They enter in formation of urea in the liver.

8. 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 essentialhydroxy 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

9. Chemical properties of amino acids: • 1- Reactions due to COOH group: • Salt formation with alkalis, ester formation with alcohols, amide formation with amines and decarboxylation • 2- Reactions due to NH2 group: deamination and reaction with ninhydrin reagent. • Ninhydrin reagent reacts with amino group of amino acid yielding blue colored product. The intensity of blue color indicates quantity of amino acids present. • Ninhydrine can react with imino acids as proline but gives yellow color.

10. 3- Reactions due to side chain (R): 1- Millon reaction:for tyrosine gives red colored mass 2- Rosenheim reaction: for tryptophan (indole ring) and gives violet ring. 3- Pauly reaction: for imidazole ring of histidine: gives yellow to reddish product 4- Sakagushi test: for guanido group of arginine and gives red color. 5- Lead sulfate test (sulfur test): for sulfur containing amino acids as cysteine give brown color.

11. 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

13. 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. NB: All amino acids in protein have the L-configuration. L-form D-form

15. 2-Amphoteric properties of amino acids: that is they have both basic and acidic groups and so can act as a base or acid. There is an internal transfer of a hydrogen ion from the -COOH group to the -NH2 group to leave an ion with both a negative charge and a positive charge. This is called a zwitter ion Neutral amino acids (monobasic, monocarboxylic) can exist in aqueous solution as “ Zwitterion” i.e. contain both positive and negative charge. Zwitterion is electrically neutral and can’t migrate into electric field.

16. Isoelectric point (IEP, PI) = is the pH at which the zwitterion is formed (equal No. of positive and negative charge are present at the same molecule). For glycine, for example, the isoelectric point is pH 6.07; for alanine, 6.11; and for serine, 5.68. Q: How can we obtain PI of amino acid in aqueous solution? See next slide. 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.

17. Isoelectric Point: What happens if you have many ionizable groups in a single molecule, as is the case with a polypeptide or protein? Consider a protein. At a pH of 2, all these groups would be protonated, and the overall charge of the protein would be positive. (Remember, when carboxylic acid side chains are protonated, their net charge is 0.) As the pH is increased, the most acidic groups will start to deprotonate and the net charge will become less positive. At high pH, all the ionizable groups will become deprotonated in the strong base, and the overall charge of the protein will be negative. At some pH, then, the net charge will be 0. This pH is called the isoelectric point (pI).

20. The pI value can affect the solubility of a molecule at a given pH. Such molecules have minimum solubility in water or salt solutions at the pH that corresponds to their pI and often precipitate out of solution. Biological amphoteric molecules such as proteins contain both acidic and basic functional groups. Amino acids that make up proteins may be positive, negative, neutral, or polar in nature, and together give a protein its overall charge. At a pH below their pI, proteins carry a net positive charge; above their pI they carry a net negative charge. Proteins can, thus, be separated according to their isoelectric point (overall charge) on a using a technique called isoelectric focusing, which uses a pH gradient to separate proteins.