(Bio Mathematical Lab of Sikander Aqeel)
CHAPTER [3] PROTEINS
Proteins
(7/9/2016)
Polar and A-polar Proteins of the Amino acid R Group:
It is important to have an appreciation for the relative hydrophobicity of the amino acids side chain in order to understand the role played by the different
Amino acids in protein structure and function, the more hydrophobic Leucine, Isoleucine, Valine, Tyrosine, (uncharged) and Proline,
In globular proteins the side chain R group from the more hydrophobic amino acid are folded into the interior of the protein molecule, away from the water salvation, Exception to the above rule may occur in small regions of the total protein molecule and are usually associate with a function of the protein such as providing a hydrophobic binding site for substrate or ligand molecules to the protein, Amino acids with intermediate polarity include the smaller alkyl amino acids, Asparagine, asparagines, threonine, serine, and methionine, these amino acids side chains are found both in the interior and on the solvent protein interface significant proportions, In contrast the amino acids containing charged R group at pH 7 [Lysine, arginine, histidine (charged), Glutamate and aspartate] are most always found on surface in globular protein, where the charge is stabilized by the water solvent, the rare positioning of a charged side chain into the interior of globular protein is usually correlated with an essential structure or functional role for the buried charged side chain group within the non-polar interior of the protein,
AMINO ACIDS ARE POLYMORIZED INTO PEPTIDE AND PROTEIN
The polymerized of the 20 amino acids into polypeptide chain within cell is catalyzed by enzymes and requires RNA and ribosome’s to occur chemically, the polymerized of amino acids into protein is a dehydration reaction,
The chemical rational of the reaction the a-carboxyl group of an amino acid chain R by the covalently joined to the a-NH2 group with side chain R2 by the elimination of molecule of water to form a type of amide bond known as the peptide bond,
C3H4N1O2 + C4H4N1O2 = R2 = regular + peptide
|-H2O
C7H6N2O3 + C5H4N1O2 = R3 = Di-peptide
|-H2O
C12H8N2O4 = R4 - ...Ra = Tri-peptide
The di-peptide (two amino acids residues joined by single peptide bond) can then form a second peptide bond through its terminal carboxylic acid group to the –a amino of third amino acid (R3) generating a Tri-peptide Repetition of this stepwise amino acids sequence (R1 – R2 – R3 – R4 …Ra)
The specific amino acids sequence of a natural polypeptide is determined form the genetic information,
C3H4N1O2 + C4H4N1O2 = 87 + 99 = 186
C7H6N2O3 + C5H4N1O2 = 167.5 + 111 = 278.5
C12H8N2O4 = 246
SOME EXAMPLES OF BIOLOGICALLY ACTIVE PROTEIN,
1 = Amino acids sequence = H-Tyr-Gly-Gly-Phe-Met-OH
2 = Name = Methionine encephalin
3 = Function = Opiate like peptide found in brain, that inhibits sense of pain,
SEQUENCE
Sequence = H-Tyr-Gly-Gly-Phe-Met-OH, 1.25 + 183.75 + 76.25 + 76.25 + 167.75 + 151.75 Met + 17.25 = 674.25
Methionine encephalin = 674.25
A. Tri-peptide
For example,
= a2 + b2 = c2
= a2 (Methionine) + b2 (C12H8N2O4) = c2
= a2 (674.25) + b2 (246) = c2
= a2 (454613.0625) + b2 (60516) = c2
= a + b = 515129.0625 = c2
= a + b = 515129.0625 / 45.25 (COOH) = 11384.06
= a + b = 11384
B. Water
= a2 / b2 = c2
= a2 (11384) / b2 (H2O) = c2
= a2 (11384) / b2 (18.25) = c2
= a2 (129595456) / b2 (333.0625) = c2
= a / b = 389102.51 = c2
= a / b = 389103 / 623.78 = 623.78
= a / b = 623.78 / 2.5 (H2= A//T DNA) = 249.512
= a / b = 249.512 – 97.5 (H2PO4 = 97.5) + = 152.012
= a / b = 151.75 = Methionine
The Methionine or Opiate like peptide found in brain, that inhibits sense of pain,
H2PO4 = 97.5 + 54.25 (2H2O + OH = 54.25) = 151.75
= 151.75 = Methionine is a amino acid which found in Casein wool, and other protein for use disease of liver,
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