(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
ALPHA-GLOBULIN (9/13/2016)
1 = buffered = pH 8.6
2 = Alpha-globulin = 73853 molecular weight
= a2 / b2 = c2
= a2 (Alpha-globulin) / b2 (buffered pH) = c2
= a2 (73853) / b2 (8.6) = c2
= a / b = (5454265609) / b (73.96) = c2
= a / b = 73746154.79 = c2
= a / b = 73746154.79 / 8587.5 = 8587.6
= a / b = 8587.6 / 2.5 (H2= A//T DNA) = 3435.04
= a / b = 3435.04 / 3.75 (H3= C///G DNA) = 916.01
= a / b = 916 / 2 {(-) (+)} = 458
= a / b = 458 amino acids are coded for by 1690 nucleotides on chromosome 4 (4q11–q13)
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 = Alpha-globulin = 73853 molecular weight
= a2 / b2 = c2
= a2 (Alpha-globulin) / b2 (chromosomes) = c2
= a2 (73853) / b2 (46.25) = c2
= a / b = (5454265609) / b (2139.0625) = c2
= a / b = 2549839.29 = c2
= a / b = 2549839.29 / 1596.82 = 1596.82
= a / b = 1596.82 / 2.5 (H2= A//T DNA) = 638.728
= a / b = 638.728 / 3.75 (H3= C///G DNA) = 170.32
= a / b = 170.32 * 2.6890 {(-) (+)} = 458
= a / b = 458 amino acids are coded for by 1690 nucleotides on chromosome 4 (4q11–q13)
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-GLOBULIN (9/13/2016)
FOR EXAMPLE 25 % ALPHA-GLOBULIN
2 = alpha-globulin = 73853 = molar mass
3 = membrane = 100 % (normal)
Percentage
alpha-globulin = 73853 / 100 % = 738.53
= 738.53 * 25 % = 18463.25
= 18463.25 m/m = 25 % alpha-globulin
25 % alpha-globulin = 18463.25 = molar mass
= a2 + b2 = c2
= a2 (membrane) + b2 (25 % alpha-globulin) = c2
= a2 (100) + b2 (18463.25) = c2
= a + b = (10000) + b (340891600.5625) = c2
= a + b = 340901600.5625 = c2
= a + b = 340901600.5625 / 18463.52 = 18463.52
= a + b = 18463.52 / 2.5 (H2= A//T DNA) = 7385.408
= a + b = 7385.408 / 3.75 (H3= C///G DNA) = 1969.44
= a + b = 1969.44 / ~58 {kDa in size} = 33.95
= a + b = 34 / 25 % {membrane} = 1.36
= a + b = 1.36 = domain 1.5 of 8.5,
CHROMOSOMES WITH BIO-CHEMISTRY
1 = chromosomes = 46.25
3 = alpha-globulin = 73853 = molar mass
4 = membrane = 100 % (normal)
25 % alpha-globulin = 18463.25 = molar mass
= a2 / b2 = c2
= a2 (25 % alpha-globulin) / b2 (chromosomes) = c2
= a2 (18463.25) / b2 (46.25) = c2
= a / b = (340891600.5625) / b (2139.0625) = c2
= a / b = 159364.95 = c2
= a / b = 159364.95 / 399.20 = 399.21
= a / b = 399.21 / 2.5 (H2= A//T DNA) = 159.684
= a / b = 159.684 / 3.75 (H3= C///G DNA) = 42.5824
= a / b = 42.5824 / 7.4 (pH blood plasma) = 5.75
= a / b = 5.75 * 50 {ratio} = 287.5
= a / b = 287.5 / 16.95A = 16.96A
= a / b = 17A less height of helix
= alpha-globulin = 17A / 10 mononucleotide = 1.7
= = 1.7A less distance between two base pair,
So 50 percent alpha-globulin cannot activated macrophages against cancer cells,
Macrophages
Macrophages that encourage inflammation are called M1 macrophages, whereas those that decrease inflammation and encourage tissue repair are called M2 macrophages, This difference is reflected in their metabolism; M1 macrophages have the unique ability to metabolize arginine to the "killer" molecule nitric oxide, whereas rodent M2 macrophages have the unique ability to metabolize arginine to the "repair" molecule ornithine.
Human macrophages are about 21 micrometres (0.00083 in) in diameter and are produced by the differentiation of monocytes in tissues.
COLORS BY WAVELENGTH
= a / b = 287.5 / 16.95A = 16.96A
Then 287.5 / 2A = 143.75
Now 143.75 = 17A
Now 143.75 = 17A
Therefore wave length = 143.75 (nm) = too light yellow color
Then 25 % alpha-globulin = too light yellow color
Decrease inflammation and encourage tissue repair = M2 = 100 % yellow color
Macrophages that encourage inflammation are called = M1 = 25 % too light yellow color and inflammation has on the top for new changes,
Alpha-globulin
Vitamin D-binding protein belongs to the albumin gene family, together with human serum albumin and alpha-fetoprotein. It is a multifunctional protein found in plasma, ascetic fluid, and cerebrospinal fluid and on the surface of many cell types. It binds to vitamin D and its plasma metabolites and transports them to target tissues, As Gc protein-derived macrophage activating factor it is a Macrophage Activating Factor (MAF) that has been tested for use as a cancer treatment that would activate macrophages against cancer cells,
Human GC is a glycosylated alpha-globulin, ~58 kDa in size. Its 458 amino acids are coded for by 1690 nucleotides on chromosome 4 (4q11–q13). The primary structure contains 28 cysteine residues forming multiple disulfide bonds. GC contains 3 domains. Domain 1 is composed of 10 alpha helices, domain 2 of 9, and domain 3 of 4.
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