Sikander Aqeel

BIO ALGEBRA OF LIVING ORGANISMS

Sep 5th 2016, 11:16 am

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(Bio Mathematical Lab of Sikander Aqeel)

CHAPTER [3] PROTEINS

Proteins

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,

Separation of Amino acids and Protein Based on pI Value

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,

ALPHA 1-ANTITRYPSIN DEFICIENCY (9/6/2016)

Electric pole: The peaks in order of their rate of migration, related to the order of their pI values, are the albumin the a1, a2-, and b-globulins, fibrinogen, and the y1-, y2-globulins, these peaks represent tens of hundred of individually different plasma proteins that have a similar migration rate to the anode at pH 8.6, their rate of migration under these proteins that is widely used for purpose of their identification and classification,

ANTITRYPSIN

Different **ytical methods are used to determine A1AT phenotype. As protein electrophoresis is imprecise, A1AT phenotype is **ysed by isoelectric focusing (IEF) in the pH range 4.5-5.5, where the protein migrates in a gel according to its isoelectric point or charge in a pH gradient.

Normal A1AT is termed M, as it is migrates toward the center of such an IEF gel. Other variants are less functional, and are termed A-L and N-Z, dependent on whether they run proximal or distal to the M band. The presence of deviant bands on IEF can signify the presence of alpha 1-antitrypsin deficiency. Since the number of identified mutations has exceeded the number of letters in the alphabet, subscripts have been added to most recent discoveries in this area, as in the Pittsburgh mutation described above.

• PiMM: 100% (normal)

• PiMS: 80% of normal serum level of A1AT

• PiSS: 60% of normal serum level of A1AT

• PiMZ: 60% of normal serum level of A1AT

• PiSZ: 40% of normal serum level of A1AT

• PiZZ: 10-15% (severe alpha 1-antitrypsin deficiency)

• PiZ is caused by a glutamate to lysine mutation at position 342 (366 in pre-processed form)

• PiS is caused by a glutamate to valine mutation at position 264 (288 in pre-processed form)

Other rarer forms have been described; in all there are over 80 variants.

FOR EXAMPLE 25 % ANTITRYPSIN

1 = α1-antitrypsin = C2001H3130N514O601S10

2 = α1-antitrypsin = 44324.5 = molar mass

3 = PiMM = 100 % (normal)

Percentage

α1-antitrypsin = 44324.5 / 100 % = 443.245

= 443.245 / 25 % = 11081.125

= 11081.125 m/m = 25 % α1-antitrypsin

= a2 + b2 = c2

= a2 (PiMM) + b2 (25 % α1-antitrypsin) = c2

= a2 (100) + b2 (11081.125) = c2

= a + b = (10000) + b (122791331.265625) = c2

= a + b = 122801331.265625 = c2

= a + b = 122801331.265625 / 11081.57 = 11081.58

= a + b = 11081.58 / 2.5 (H2= A//T DNA) = 4432.632

= a + b = 4432.632 / 3.75 (H3= C///G DNA) = 1182.0352

= a + b = 1182.0352 / 5.5 {pH range} = 214.91

= a + b = 215 / 100 % {PiMM normal} = 2.15

= a + b = 2.15 pH of pepsin enzyme of stomach protein,

Alpha 1-antitrypsin deficiency

Nomenclature

The protein was originally named "antitrypsin" because of its ability to covalently bind and irreversibly inactivate the enzyme trypsin in vitro. Trypsin, a type of peptidase, is a digestive enzyme active in the duodenum and elsewhere.

(Duodenum is a part of small intestine between the stomach and the Jejunum),

CHROMOSOMES WITH BIO-CHEMISTRY

1 = chromosomes = 46.25

2 = α1-antitrypsin = C2001H3130N514O601S10

3 = α1-antitrypsin = 44324.5 = molar mass

4 = PiMM = 100 % (normal)

Percentage

α1-antitrypsin = 44324.5 / 100 % = 443.245

= 443.245 / 25 % = 11081.125

= 11081.125 m/m = 25 % α1-antitrypsin

= a2 + b2 = c2

= a2 (25 % α1-antitrypsin) + b2 (chromosomes) = c2