This document discusses amino acids and their classification. It notes that there are 20 standard amino acids that make up proteins. Amino acids are classified as non-polar, polar, acidic, basic or aromatic based on the characteristics of their side chains. The document also discusses the general structure of amino acids, including that they contain an amino group, a carboxyl group, and a variable side chain. It further summarizes the structures and functions of peptides and proteins.

1. Amino Acids

2. Contents
• Amino Acids
– General Characters
– Structure and Classification
– Acid Base Characters of Amino Acids
• Peptides
• Proteins
– Structure and configuration
– Chemical bond involve in protein structure
– Classification
• Protein Sequencing

3. Amino Acid
General Structure
• All amino acids are α-amino acid.
• All proteinic amino acids have same structure except proline

4. Polar
Non-Polar
Ala
Ile
Val
Gly
Met Phe
Pro Trp
Leu
Acidic Neutral Basic
Asp
Glu
Tyr
Cys
Ser
Asn
Gln
Thr
Arg
Lys
His
Classification of
Amino Acid

5. Classification on the bases of polarity
1. Non-polar amino acid with
Glycine, Alanine, Valine, Methionine, Leucine, Isoleucine, Proline,
Phenylalanine, Tryptophan.
2. Polar Amino Acids
I. Negatively charge amino acid
Aspartic acid, Glutamic Acid
II. Positively charge amino acid
Lysine, Arginine, Histidine.
III. Neutral amino acid
Serine, Threonine, Asparagine, Glutamine, Cysteine, Tyrosine
Polarity of amino acid
Tyr>Ser>Asp>Glu>Asn>Gln>Arg
Non-polarity of amino acid
Phy>Ala>Val>Gly>Leu>Cys

6. 1. Which amino acid is hydrophobic?
2. Which amino acid is hydrophilic?
3. Which of the amino acids residues are most likely to be found in the
interior of the water soluble protein?

7. Classification of amino acids
• Neutral amino acids
1. Glycine-Gly-G
 Amino acid with smallest side chain
 Most abundant in collagen
 No chiral carbon (No optical activity)
 Sweet in taste
 Neurotransmitter inhibitor
2. Alanine-Ala-A
 Amino acid with methyl group
 Most abundant amino acid in protein
3. Valine-Val-V
 Branched at β-carbon
 Amino Acid with two chiral carbon

8. 4. Leucine-Leu-L
 Branched at γ-carbon
5. Isoleucine-Ile-I
 Amino acid with 2 chiral carbon
6. Serine-Ser-S
 Help in the synthesis of muscle protein
 Phosphorylation in cell signaling
7. Threonine-Thr-T
 Branched at β-carbon
 Amino Acid with two chiral carbon
8. Proline-Pro-P
 A cyclic imino acid
 Present in α-helix and β-turn

9. • Acidic amino acids
9. Aspartic acid-Asp-D
 Amino acid with β-carbonyl group
 Frequently present on N-terminus of α-helix
10. Glutamic Acid-Glu-E
• Amide form of acidic amino acids
11. Asparagine-Asn-N
12. Glutamine-Gln-Q
• Sulphur containing amino acids
13. Cysteine-Cys-C
 Amino acid with thiol group
 Involve in disulphide bond
14. Methionine-Met-M
 First amino acid in protein

10. • Basic amino acids
15. Histidine-His-H
 Amino acid with imidazole ring
 Having buffering capacity
 Help in Immune response
16. Lysine-Lys-K and 17. Arginine-Arg-R
 Rich in histone protein
 Lysine has butyl-ammonium side chain
• Aromatic ring acidic amino acids
18. Phenylalanine-Phe-F
 Maximum absorption at 280nm
 Naturally present in breast milk
 Related with phenylketonuria
19. Tyrosine-Tyr-Y
 Maximum absorption at 280nm
 Phosphorylation in cell signaling
20. Tryptophan-Trp-W
 Least present in protein, indole ring amino acid

11. General Characters of amino acids
• There are more than 500 amino acids present in the nature.
• Only 20+2 participate in the formation proteins.
• Amino acids have N-terminus, C-terminus and R-group in their structure.
• Average mass of an amino acid residue is ~ 110 Da.
• Selenocystine is 21st amino acid, analog of cysteine, having antioxidant
acitivity.
• Pyrolysisne is not present in human.
• Amino acids are made visible on the chromatogram by the treatment with
ninhydrin.
• Non-polar amino acid are found mostly in the core of protein.
Classification on the bases availability in the human body
1. Essential amino acids
Leucine, Isoleucine, Lysine, Threonine, Methionine, Phenylalanine, Valine,
Tryptophan, Histidine (conditionally essential)
2. Non-essential amino acids
Glycine, Alanine, Valine, Arginine, Serine, Asparagine, Glutamine,
Cysteine, Tyrosine, Aspartic acid, Glutamic Acid.

12. Acid base characters of amino acids
 pK can be defined as the pH at which the acid is 50% dissociated.
If- pK=pH+1………….. Acid is 91% dissociated.
pK=pH+2………….. Acid is 99% dissociated.
pK=pH-1………….. Acid is 9% dissociated.
pK=pH-2………….. Acid is 1% dissociated.
 pI (isoelectric point) is the pH at which net charge of amino acid is zero.
(total number of positive charge equal to the total number of negative
charge).
Calculation of 𝑝𝐼 =
𝑝𝐾1+𝑝𝐾2
2
For Acidic amino acids:
Calculation of 𝑝𝐼 =
𝑝𝐾1+𝑝𝐾𝑅
2
For basic amino acids
Calculation of 𝑝𝐼 =
𝑝𝐾2+𝑝𝐾𝑅
2
𝑝𝐾1 = −𝐶𝑂𝑂𝐻
𝑝𝐾2 = −𝑁𝐻3
+
𝑝𝐾𝑅 = 𝑅 − 𝑔𝑟𝑜𝑢𝑝

13. Nature of amino acid at different pI
If pI < 7 then the amino acid is acidic
pI ~ 7 then the amino acid is neutral
pI > 7 then the amino acid is basic
 If the pH of the solution is equal to the pI then net charge of amino acid
or protein is zero.
 If the pH of the solution is lower to the pI then net charge of amino acid
or protein is positive.
 If the pH of the solution is higher to the pI then net charge of amino
acid or protein is negative.
Important point:
• Aspartate has the smallest pI value
• Arginine has the largest pI value
• Amino acids tend to be least soluble in water at their isoelectric point.
Net charge: +1 0 -1
𝑝𝐾1 = 2.34 𝑝𝐾2 = 9.69

14. Peptides
• α-carboxyl group of one or first amino acid react with α-amino group of
other or second amino acid, a dipeptide is formed with release of water
molecule.
• A peptide bond is a covalent bond b/w carbonyl carbon and an imino
nitrogen also k/n as amide bond.
• The peptide bond in peptide and protein has been found to possess a
partial double bond, polar, planar and mostly trans
• The average molecular weight of amino acid residue in the peptide has
been taken 110.
Molecular weight of the peptide= (no. of aa residues X average residue
weight)- 18X number of water molecules removed

15. Some oligo-peptides
i. Aspartame (APM): is a methyl ester of the aspartic
acid/phenylalanine dipeptide. It is used as artificial sweetener, 200 time
more sweet that sugar.
ii. Glutathione: it is tripeptide, made-up of Glu-Cys-Gly. γ-carbonyl group
of Glu is involved in the peptide bond formation. It control oxidative
damage of RBC.
iii. Gramicidin: A circular deca-peptide. A bacterial synthesized antibiotic.
iv. Vasopressin and oxytocin: made-up of nine amino acids with di-sulphide
bonds, secreted by pituitary gland. Oxytocin natural hormone that causes
the uterus to contract and used to induce labor or strengthen labor
contractions during childbirth, and to control bleeding after childbirth.
Vasopressin help in the retention of water from urine by kidney and also
involve in higher of blood pressure.
v. Methionine enkephalin: penta-peptide, inhibit sense of pain.
vi. Angiotensin II: octapeptide, stimulate the release of aldosterone from the
adrenal gland.
vii. Substance P: decapeptide, k/n as neurotransmitter.