BIO ALGEBRA OF LIVING ORGANISMS

(Bio Mathematical Lab of Sikander Aqeel) 

CHAPTER [3] PROTEINS  

Proteins  

(8/27/2016) 

Charge and Chemical Properties of Amino acids and Proteins, 

An understanding of protein requires knowledge of the ionizable side chain groups of the common amino acids, these ionizable groups common to proteins and amino acids, the acid form of the respective ionizable groups are on the left of the sum, while the respective properties base are on the right side, characteristic of the acid form is that nitrogen-containing groups are positively charged, whereas the acid forms that contain oxygen and sulfur atoms are natural, 

Titration of a Monoamine Dicarboxylic Acid 

A more complecated example of the relationship between molecular charge and pH is the example of Glutamic acid, its ionized forms and titration curve are shown in Glutamic acid, the a-COOH pKa = 2.2, the Y-COOH pka = 4.3, and the a-NH3+ pKa = 9.7, the zwitterions form is generated after 1.5 equiv of base are sided to the low pH form, and the isoelectric pH (pI) is calculated from the average of the two pKa values that form the boundaries of the zwitterions form, 

Common Charge Properties of Amino acids and Proteins 

All **ysis of the charge form present in the other common amino acids shows that the relationship found between pH and the respective pI constant for Glutamate and Glutamate is perfectly true, This is at the solution pH less than the pI of amino acid, the amino acid is positively charged, at a pH greater than the pI, the amino acid negatively charged, The degree of positive and negative charge is a function of the distance between the pH and the pI value of the amino acids and is calculable for an amino acid by chromosomes of DNA, 

(8/26/2016)

Protein contain multiply ionizable side chain group and pI value characteristic of protein will depend on the relative concentration of the different acids and base R group, as protein containing many ionizable residue, calculation of its iso-electric pH form pKa value would be difficult, accordingly the pI value for proteins are almost always experimentally measured by determining the pH value in which the protein does not  move in an electrical field, the pI values found for some representative proteins are giving protein pI, 

As with amino acids at a pH greater than the pI, the protein will have a negative net charge, at a pH less than the pI, the protein have a positive net charge, the magnitude of the net charge of a protein will increases as a function of the distance between pH and pI, 

For example human: human plasma albumin contains on 585 amino acid residue of which there are 61-Glu, 36-Asp, 57-Lys, 24-Arg, and 16-His 

And the albumin pI = 4.9 at which pH the net charge is zero, at pH 7.5 the imidazolium group of histidine have been partially titrated and albumin has a formal negative charge of -10 at pH 8.6 additional group have been titrated to their basic form, and the formal net charge is approximately -20 at pH 11 the net approximately -60 on the acid side of the pI value, at pH 3 the approximately net charge on the albumin molecule in solution is +60           

Separation of Amino acids and Protein Based on pI Value (8/28/2016) 

The techniques of electrophoresis isoelectric focusing and ion exchange chromatography are some of the more important techniques for the study of biological molecules based on charge, 

In electrophoresis an ampholyte (protein, Peptide, Amino acid) in a solution buffered at a particular pH is placed in an electric  field, depending on the relationship of the buffer pH to the pI of the molecule, the molecule will either move toward the (-) or the anode (+), or remain stationary (pH = pI) 

An example of classical apparatus for protein electrophoresis is apparatus consist of a U-tube in which is placed a protein solution, followed by a buffer solution carefully layered over the protein solution, the migration of the protein is observed with an optical device that measures changes in the refractive index of the solution as the protein migrates toward the anode, 

This apparatus historically led to the separation and operational classification of protein in human plasma, 

For the plasma protein separation, the solution is buffered at pH 8.6, which is at a pH substantially above the pI of the important plasma protein, the proteins are negatively charged and move toward the positive      

1 = buffered = pH 8.6

2 = Plasma Albumin = 96000 molecular weight 

  = a2 / b2 = c2 

  = a2 (Plasma Albumin) / b2 (buffered pH) = c2 

  = a2 (96000) / b2 (8.6) = c2 

  = a / b = (9216000000) / b (73.96) = c2 

  = a / b = 124607896.16 = c2 

  = a / b = 124607896.16 / 11162.79 = 11162.79

  = a / b = 11162.79 / 2.5 (H2= A//T DNA) = 4465.116

  = a / b = 4465.116 / 3.75 (H3= C///G DNA) = 1190.6976 

  = a / b = 1190.6976 / 2.0353 {(-) (+)} = 585.02

  = a / b = 585 amino acids of Human Plasma Albumin 

The molecule will either move toward the (-) or the anode (+), or remain stationary (pH = pI), so Separation of Amino acids and Protein Based on pI Value 

CHROMOSOMES WITH BIO-CHEMISTRY 

1 = chromosomes = 46.25

2 = Plasma Albumin = 96000 molecular weight 

  = a2 / b2 = c2 

  = a2 (Plasma Albumin) / b2 (chromosomes) = c2 

  = a2 (96000) / b2 (46.25) = c2 

  = a / b = (9216000000) / b (2139.0625) = c2 

  = a / b = 4308429.51 = c2 

  = a / b = 4308429.51 / 2075.67 = 2075.68

  = a / b = 2075.68 / 2.5 (H2= A//T DNA) = 830.272

  = a / b = 830.272 / 3.75 (H3= C///G DNA) = 221.40 

  = a / b = 221.40 * 2.6422 {(-) (+)} = 584.98

  = a / b = 585 amino acids of Human Plasma Albumin   

The molecule will either move toward the (-) or the anode (+), or remain stationary (pH = pI), so Separation of Amino acids and Protein Based on pI Value