1. Amino Acids

2. Amino Acids
Amino acid: a compound that contains an amino group, a carboxyl group and a side-chain that is specific to each amino acid.
-Amino acid: an amino acid in which the amino group is on the carbon adjacent to the carboxyl group
The are 20 common α-amino acids used by the ribosomes to make proteins. These 20 have L chirality at the α-carbon.

3. Chemistry of Amino Acids
R side chain |
H2N— C —COOH | H
The building blocks of proteins
20 amino acids are naturally incorporated into polypeptides and are called proteinogenic or standard amino acids. These 20 are encoded by universal genetic code.
10 standard amino acids (Lys, Met, His, Leu, Ile, Thr, , Try, Phe, Val & Arg) are called "essential" for humans because they cannot be created from other compounds by the human body, and so must be taken in as food.
From these building blocks different organisms can make such widely diverse products as enzymes, hormones, antibodies, antibiotics, and a large number of other substances having distinct biological activities.
Also used as single molecules in biochemical pathways

4. Chemistry of Amino Acids
Two functional groups:
carboxylic acid group
amino group on the alpha () carbon
Have different side groups (R)
Properties dictate behavior of AAs

5. Stereochemistry of AAs
All amino acids (except glycine) are optically active (chiral)
2 forms of enantiomers/stereoisomers
d = dextrorotatory ,dextro means right
l = levorotatory, levo means left
D, L = relative to glyceraldehyde

6. Stereochemistry of AAs
Only L-isomers are constituents of proteins
Twenty kinds of side chains varying in size, shape, charge, hydrogen bonding capacity, hydrophobic character and chemical reactivity are found in proteins

10. Amino acids join together via peptide bonds
Chain of amino acids = peptide or protein
Two amino acids can react with loss of a water molecule to form a covalent bond.
Amide linkage is planar
NH and CO are anti

11. Classification of Amino Acids
Classification based on side-chain structure:
Non-polar amino acids.
Polar, uncharged amino acids.
Acidic amino acids.
Basic amino acids.
Other side chain structural classifications:
Aromatic, cyclic, hydroxyl, and thiol amino acids.

12. Classification of Amino Acids
R =

13. Classification of Amino Acids

14. Essential Amino Acids
An essential amino acid is an amino acid that cannot be synthesized itself by the organism (usually referring to humans), and therefore must be supplied in the diet.
10 amino acids are essential amino acid
They are - arg, his, ile, leu, lys, met, phe, thr, trp, val
Must obtain from the diet
An adequate diet must contain these essential amino acids. Typically, they are supplied by meat and dairy products
Essential amino acids help the body function and regulate neurotransmitters, chemicals in the brain that control mood and behavior.
A lack of essential amino acids can cause emotional or physical difficulties and lead to health disorder

15. List of Essential & Nonessential Amino Acid
Histidine
Alanine
Isoleucine
Aspartate
Leucine
Cysteine
Lysine
Glutamate
Methionine
Glutamine
Phenylalanine
Glycine
Threonine
Proline
Tryptophan
Serine
Valine
Tyrosine
Arginine
Asparagine

17. Zwitterions
Although -amino acids are commonly written in the unionized form, they are more properly written in the zwitterion (internal salt) form (Germ. Zwitter means hybrid)
Both the –NH2 and the –COOH groups in an amino acid undergo ionization in water.
At physiological pH (7.4), a zwitterion forms
Both + and – charges
Overall neutral
Amphoteric
Amino group is protonated
Carboxyl group is deprotonated
Soluble in polar solvents due to ionic character

18. Acid-Base Properties of Amino Acids
Figure : The ionic forms of the amino acids.

19. pKa Values of Amino Acids
Alpha carboxyl group: pKa = ~2
Alpha amino group: pKa = ~9
pKa Values of Amino Acids

20. The isoelectric point is the pH at which there is zero net charge
Amphoteric molecules called zwitterions contain both positive and negative charges depending on the
functional groups present in molecule
Using Glycine again:
Charges in the first ionization: +1  0
Charges in the second ionization: 0  -1
So, in the case of glycine, the pH at
which there is most of the zero net
charge form occurs half way between
the first and second ionizations.
pI = average of pKa’s = ½ (pK1 + pK2)
pIglycine = ½ ( ) = 5.97

21. Reactions of amino acids
Amino acids will undergo reactions characteristic of the amino
(amide formation) and carboxylic acid (ester formation) groups.
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 & reaction with ninhydrin
Ninhydrin reagent reacts with amino group of amino acid yielding colored product. The intensity of color indicates quantity of amino acids present.
Ninhydrin can react with imino acids as proline and hydroxy proline but gives yellow color

22. Detecting Amino Acids
Ninhydrin is the classical reagent for detecting amino acids.
Reaction requires 2-5 min at 100oC and is sensitive at the nanomole level.
Ruhemann’s Purple
570 nm
Note: The product from Pro is
Yellow and absorbs at 440 nm.

23. Peptides and Proteins 20 amino acids are commonly found in protein.
These 20 amino acids are linked together through “peptide bond forming peptides and proteins.
The chains containing less than 50 amino acids are called “peptides”, while those containing greater than 50 amino acids are called “proteins”.
Peptide bond formation: Peptide bond is the amide bond between the -carboxyl group of one amino acid and the -amino group of another
. α-carboxyl group of one amino acid (with side chain R1) forms a covalent peptide bond with α-amino group of another amino acid ( with the side chain R2) by removal of a molecule of water. The result is : Dipeptide ( i.e. Two amino acids linked by one peptide bond). By the same way, the dipeptide can then forms a second peptide bond with a third amino acid to give Tripeptide. Repetition of this process generates a polypeptide or protein of specific amino acid sequence.

24. Peptide bond
The trans conformation
of the peptide bond.

25. Peptides and Proteins
Peptide: a short polymer of amino acids joined by peptide bonds; they are classified by the number of amino acids in the chain
dipeptide: a molecule containing two amino acids joined by a peptide bond
tripeptide: a molecule containing three amino acids joined by peptide bonds
12-20 residues (Each unit/AA) – oligopeptide.
polypeptide: a macromolecule containing many amino acids
Linear polymers (no branches)
AA monomers linked head to tail through formation of peptide bonds
protein: a biological macromolecule of molecular weight 5000 g/mol or greater, consisting of one or more polypeptide chains

26. 1- Dipeptide ( two amino acids joined by one peptide bond):
Examples on Peptides:
1- Dipeptide ( two amino acids joined by one peptide bond):
Example: Aspartame which acts as sweetening agent being used in replacement of cane sugar. It is composed of aspartic acid and phenyl alanine.
2- Tripeptides ( 3 amino acids linked by two peptide bonds).
Example: GSH (Glutathione) which is formed from 3 amino acids: glutamic acid, cysteine and glycine. It helps in absorption of amino acids, protects against hemolysis of RBC by breaking H2O2 which causes cell damage.
3- Octapeptides: (8 amino acids)
Examples: Two hormones; oxytocin and vasopressin (Antidiuretic Hormone -ADH).
4- Polypeptides: More than 10 amino acids: e.g. Insulin hormone

27. Arg - Pro - Pro - Gly - Phe – Ser - Pro - Phe - Arg
 Biologically active peptides:
oxytocin, bradykinin, vasopressin
Peptides (and proteins) have their unique pI values depending on the AA compositions.
Arg - Pro - Pro - Gly - Phe – Ser - Pro - Phe - Arg
Bradykinin causes blood vessels to dilate & causes blood pressure to lower
Vasopressin
Insulin has two peptide chains (A chain has 21 AAs & B chain has 30 AAs) held together by two disulfide linkages