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Chapter-3

Amino acids, peptides, and proteins


Part-1 Amino acids

Amino acids are precursors of proteins

There are only 20 standard amino acids or primary amino acids or common amino acids

Functions of proteins
Biological catalyst
Transport

Structural support
Immune response Biological regulation

Functions of Proteins

Biological catalyst

Transport

Structural support

Functions of Proteins

Immune response

Biological regulation

Is it mathematically possible to make thousands of proteins from only 20 amino acids?


A Protein made up of only 8 amino acids has a mathematical possibilities of making 2.56 x 1010 different sequences Most proteins are made up of 200-500 amino acids

General structure of an amino acid

Stereoisomerism in -Amino acids

Almost all amino acids found in proteins exist in L-isomeric form


Exceptions!! Certain bacterial peptides contain Disomers of amino acids

Zwitterion predominates at neutral pH

Classification of amino acids


1: 2: 3: Non-polar Amino acids Polar uncharged amino acids Aromatic amino acids

4:
5:

Positively charged amino acids


Negatively charged amino acids

Non-polar amino acids


1: 2: 3: 4: 5: 6: 7: Glycine Alanine Valine Leucine Isoleucine Methionine Proline

Uncharged polar amino acids


1: Serine
2: Thereonine 3: Cysteine

4: Asparagine
5: Glutamine

Oxidation of two cysteine molecules form disulfide bond

Oxidation

Reduction

Reversible reaction

Two types of disulfide bonds

Intra-molecular disulfide bond

Insulin molecule

Inter-molecular disulfide bond

Aromatic amino acids


1: Phenylalanine 2: Tyrosine

3: Tryptophan

UV light absorption by aromatic amino acids

Lambert-Beer law

280 nm

Aromatic amino acids

Basic components of a spectrophotometer

Overlapping property

Is it Non-polar?

Is it soluble?

Structure and solubility

Which is more soluble?

Positively charged amino acids


1: Lysine

2:
3:

Arginine
Histidine

Negatively charged amino acids


1: Aspartate
2: Glutamate

Non-standard amino acids


4-Hydroxyproline N-Methyllysine 5-Hydroxylysine

Ornithine
Citrulline

Non-standard amino acids

Non-standard amino acids

Amino acid abbreviations and symbols

For convenience, the names of all the standard amino acids are designated by either three letter abbreviations or by one letter symbol

For most amino acids, the first three letters of their names represent the abbreviations

Exceptions !! Ile - Isoleucine Trp - Tryptophan Asn - Asparagine Gln - Glutamine

Amino acids can act as acids and bases


Amino acid as an acid (proton donor)

Amino acids can act as acids and bases


Amino acid as base (proton acceptor)

The dual acid base property of amino acids make them Amphoteric electrolytes
Amphoteric electrolytes are also given the name Ampholytes

Amino acid acts as diprotic acid

+1

-1

pH changes charge on amino acids

Titration curve of glycine

Amino acids with non-ionizable R groups have titration curve similar to that of glycine and also have similar pK1 and pK2values pK1refer to pKa of COOH groups and ranges from 1.8-2.4
pK2 refer to pKa of NH3+ groups and ranges from 8.8-11.0

Isoelectric point (pI)


pI is the pH at which a molecule carries NO net charge

pI of amino acids with non-ionizable R groups such as glycine and alanine is the average of pK1 and pK2 pI of glycine 1/2 (2.34 + 9.60) = 5.97

Titration curve of glutamate

pI of negatively charged amino acids is the average of pK1 and pKR


1/2 (2.19 + 4.25) = 3.22

Titration curve of histidine

pI of positively charged amino acids is the average of pK2 and pKR


1/2 (9.17 + 6.0) = 7.59

At what pH will histidine develop a positive charge?