1. Amino Acids and Proteins

2. Structure of amino acids
The hydrolysis of most proteins produces about twenty different amino acids.
The acids have an amino group bonded to the  carbon:-
an -amino acid

3. Amino acid classification
The 20 amino acids are further classified:
neutral - one amino and one carboxyl group
acidic - one amino and two carboxyl groups
basic - two amino and one carboxyl group

4. Neutral amino acids Name Symbol Structure
Alanine Ala or A CH3CH(NH2)CO2H
Asparagine Asn or N H2NCOCH2CH(NH2)CO2H
Cysteine Cys or C HSCH2CH(NH2)CO2H
Glutamine Gln or Q H2NCOCH2CH2CH(NH2)CO2H
Glycine Gly or G CH2(NH2)CO2H
Isoleucine Ile or I CH3CH2CH(CH3)CH(NH2)CO2H
Leucine Leu or L (CH3)2CHCH2CH(NH2)CO2H
Methionine Met or M CH3SCH2CH2CH(NH2)CO2H
Phenylalanine Phe or F C6H5CH2CH(NH2)CO2H
Proline Pro or P

5. Neutral amino acids Name Symbol Structure
Serine Ser or S HOCH2CH(NH2)CO2H
Threonine Thr or T HOCH(CH3)CH(NH2)CO2H
Tryptophane Try or W
Tyrosine Tyr or Y
Valine Val or V (CH3)2CHCH(NH2)CO2H

6. Acidic amino acid Name Symbol Structure
Aspartic acid Asp or D HO2CCH2CH(NH2)CO2H
Glutamic acid Glu or E HO2CCH2CH2CH(NH2)CO2H

7. Basic amino acids Name Symbol Structure
Arginine Arg or R HN=C-H(CH2)3CH(NH2)CO2H
NH2
Histidine His or H
Lysine Lys or K H2N(CH2)4CH(NH2)CO2H

8. Essential amino acids
Humans can synthesize only 10 of these amino acids. The remaining amino acids must be obtained from dietary sources and are so called essential amino acids.
These are: Isoleucine, Leucine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine, Arginine, Histidine, and Lysine.

9. Stereochemistry of -Amino Acids
Most naturally occurring amino acids have the same configuration about the  carbon:
L-(-)-glyceraldehyde
L-(-)-serine
natural amino acids

10. Acid-base Properties of Amino Acids

11. Physical Properties high melting points with decomposition
very water soluble
insoluble in non-polar organic solvents such as ether

12. Isoelectric Points
- the pH of a dilute aqueous solution of the amino acid at which the amino acid is exactly neutral.
The isoelectric point of neutral amino acids lies between pH = 4.8 and For the basic amino acids, it is in the range 7.8 to The range is 2.7 to 3.2 for acidic amino acids.

13. Isoelectric Points
At a pH above the isoelectric point, amino acids form anions; at a lower pH, protonation occurs and cations form. An amino acid is the least soluble at its isoelectric point.

14. Electrophoresis
Electrophoresis uses isoelectric point differences to separate amino acids and proteins.
The amino acid is spotted on a strip of paper (or gel) on a center line.
The strip is moistened with a buffer solution of a given pH.
Electrodes are attached to the ends of the slip and a potential applied.
Depending on the amino acid’s charge, it will migrate either to the positive or negative electrode. The rate and direction of migration depends on the buffer pH and the isoelectric point of the amino acid.

15. Synthesis of amino acids - the Hell-Volhard-Zelinsky reaction
alanine

16. Synthesis of amino acids - the Strecker synthesis
NH3 adds first to give an imine then CN- attacks

17. The Peptide Bond
The principal chain contains the amide bonds; the substituents, R, make up the side chains. The individual amino acids which make up the peptide are often referred to as amino acid residues.
In some proteins, two or more polypeptide chains are joined together by disulfide bridges.

18. Nomenclature
Starting from the free amine end of the peptide, the names of the amino acids are joined together with each amino acid being considered as a substituent of the following amino acid. The name ends with the name of the final amino acid:
phenylalanylleucylthreonine
Phe-Leu-Thr

19. Aspartame an artificial sweetener sold under the trade name Nutrasweet+ H
N-CH-C-NH-CH-C-OCH 3 3 CH CH -C H 2 2 6 5 - CO 2
aspartylphenylalanine methyl ester
Asp-Phe-OCH3
the ester ending is indicated by -OCH3 in the abridged notation.

20. Angiotensin II
Angiotensin II is a blood pressure regulating hormone. It contains 8 amino acid residues. It is possible to arrange these in 40,320 different ways only one of which corresponds to the hormone!
Its structure is actually: Asp-Arg-Val-Tyr-Ile-His-Pro-Phe.

21. Sequential Degradation of Peptides
Step 1: breaking disulfide linkages and purification of products
Many polypeptides consist of two or more chains which are joined together by disulfide bridges. These bridges must be broken and the fragment products separated. This is done by an oxidation:
chain A chain B chain A chain B

22. Purification
The various methods used to separate polypeptides depend on size, solubility in a given solvent, charge or ability to become bonded to a support material (chromatography).
dialysis - filtration through a semi-permeable membrane
ion exchange chromatography
electrophoresis
chromatography

23. Step 2. What amino acids are present?
The polypeptide is completely hydrolyzed (HCl 6M, 110C, 24hr) to give a mixture of the free amino acids:

24. Amino Acid Analysis
The mixture is separated using an automated system.
The apparatus includes an ion exchange column with a negatively charged support (usually carboxylate or sulfonate). The amino acid mixture, in weakly acidic solution, is added to the column.
According to structure, the amino acids are more or less protonated and so will be retained more or less strongly on the column. The pH of the eluant is gradually increased which results in deprotonation and the subsequent elution of the amino acids.
Elution begins with the strongest acid and ends with the weakest.

25. Amino Acid Analysis
The eluant then passes into an analyzer which holds a special indicator, ninhydrin. The amino acid eluant forms a violet-purple color by reaction with the ninhydrin and the color’s intensity is proportional to the quantity of acid present.

26. Step 3. The sequential analysis of amino acids starting at the free amino end
There are a number of methods used to determine the N-terminal amino acid of a peptide. They are all based on the fact that it is the only amino acid with a free amino group.

27. Sanger Degradation

28. Edman Degradation
Phenyl isothiocyanate, C6H5N=C=S, is a reagent which permits the progressive removal and identification of the N-terminal amino acid. The rest of the chain is not affected by the reaction therefore progressive removal is possible.

29. Edman Degradation

30. Specific Cleavage of Peptides
A number of enzymes catalyze the hydrolysis of peptide bonds at specific points in an amino acid sequence. These enzymes are called proteases, peptidases or proteolytic enzymes.
Trypsin is an example. It catalyzes the hydrolysis of polypeptides at the acyl group of arginine or lysine residues.
Chymotrypsin cleaves at the acyl side of the aryl substituted acids phenylalanine, tyrosine and tryptophan.

31. C-terminal residue
The enzyme carboxypeptidase cleaves the C-terminal amide bond in a peptide. The peptide is incubated with the enzyme until the first amino acid is detected.

32. A peptide!
Treatment of a peptide with 2,4-dinitrofluorobenzene followed by hydrolysis gives N-dinitrophenylvaline. Leucine is the free acid.
The peptide contains one of each of the following amino acid residues Leu, Ser, Phe, Pro, Tyr, Lys, Gly and Val.
Partial hydrolysis gives four peptides which contain the indicated amino acids:
peptide A:- Leu, Ser, Phe peptide B:- Ser, Pro, Tyr, Lys
peptide C:- Tyr, Lys, Gly peptide D:- Lys, Val, Gly