A novel approach to predicting aminoacids and proteins by relation Even-Odd (First part)

A novel approach to predicting aminoacids and proteins by relation Even-Odd

(First part)

Lutvo Kurić

Independent Researcher

Bosnia and Herzegovina

72290 Novi Travnik

Kalinska 7

Tel. 061 763 917

lutvokuric@yahoo.com

Abstract

The subject of this thesis is a digital approach to the investigation of the biochemical basis of genetic processes. The digital mechanism of nucleic acid and protein bio-syntheses, the evolution of biomacromolecules and, especially, the biochemical evolution of genetic language, have been analyzed by the application of cybernetic methods, information theory and system theory, respectively.

Experimental research of existence or not existence of aminocide code performs in science for a longer period, but that phenomenon is still not completely explained. Scientists, firstable investigate possibility that genetic code has a stereochemical origin (D. Grafstein, Anderson, Jukas, Yoshiyki Kuchino, Yamao, Cribbs, etc.) While that, they do not pay enough attention o. program cybernetic and information lawfulness in genetic processes. And, that it is necessary to explore that aspect of those problems points the discoveries, which we discovered in that researches of schedule of periodic in biochemical process. Detailed analysis of periodic schedule of genetic code tells us that periodicity is accomplished by sequencing of molecule is based on a mathematically law.

. This paper is to report that we discovered new methods for development of the new technologies in genetics. It is about the most advanced digital technology which is based on program, cybernetics and informational systems and laws. The results in practical application of the new technology could be useful in bioinformatics, genetics, bio-chemistry, medicine and other natural sciences.

Methods

Digital image where Amino Acids Code Matrix is represented is in the form of numbers. That image can be created with the help of the new scientific methods. At the first stage of our research we replaced Amino Acids from the Amino Acid Code Matrix with numbers of the atoms in those Amino Acids. By this way we got digital image of Amino Acids Code matrix. Then we mathematically analyzed those digital images of this Code Matrix. After we making such analysis, we discovered existence of digital codes in this Matrix, which interconnect all Amino Acids and other sequences in genetics. Given below is a brief introduction about the way we discovered those Amino Acids digital codes and how those codes interconnect all Amino Acids of this Matrix.

Results of research

Results of our research show that the processes of sequencing the molecules are conditioned and arranged not only with chemical and biochemical, but also with program, cybernetic and informational lawfulness too. At the first stage of our research we replaced nucleotides from the Amino Acid Code Matrix with numbers of the atoms in those nucleotides.

The prediction algorithms

During the research of secrets of genetic processes functioning we found out that sequences in those processes are interconnected by various digital codes. One of those codes is a relation: odd-even and digital codes 19 and 7. In this text we will give experimental proof that this digital code does exist and it connects amino acids in proteins. We will prove that the process of sequencing amino acids is conditioned and determined not only by biochemical, but by programme, cybernetic, and informational laws.

Data Structure

In group of triplets from X to Y there are two codes which interconnect all those triplets. Those are codes A and B.

Formula of codes A and B

{[SA(R1,2,3,n) x B] - [SB(R1,2,3,n) x A] + (AB)} = A²B;

SA, SB = Groups of triplets UCAG

Number of atoms in triplets UCAG

R1,2,3,n = Natural numbers from X to Y;

Solution:

A = 7; B = 19;

At the first stage of our research we replaced nucleotides from the Amino Acid Code Matrix with numbers of the atoms in those nucleotides.

U = 12 atoms; C = 13 atoms; A = 15 atoms; G = 16 atoms

Digital Genetic Code

Number of atoms in triplets Table 1

36

37

38

39

40

41

42

43

44

45

46

47

48

UUU

UCU

UCC

CCC

UCA

GCU

GCC

AGU

GGU

GGC

GAA

GGA

GGG

CUU

CCU

UUA

UGU

UCG

CCG

GAU

GCA

GCG

AAG

GAG

UUC

CUC

AUU

ACU

UGC

AAU

AAC

AGC

AAA

AGA

AGG

UAU

GUU

CCA

AUA

ACA

GAC

CGG

CAU

ACC

CGC

GUA

ACG

UUG

GUC

UAA

CAA

GUG

CUA

CAC

AUG

CAG

AUC

CUG

UAG

CGA

If we replace triplets with number of atoms in those triplets in tables of genetic code, we will get digital Tables of genetic code.

Number of atoms in triplets Table 2

	A1	A2	A3	A4	A5	A6	A7	A8	Sum
B1	36	37	37	37	38	38	38	39	300
B2	39	39	39	40	40	40	40	40	317
B3	40	40	40	40	41	41	41	41	324
B4	41	41	41	41	41	42	42	42	331
B5	42	42	42	43	43	43	43	43	341
B6	43	43	43	43	44	44	44	44	348
B7	44	44	44	44	44	45	45	45	355
B8	45	46	46	46	47	47	47	48	372
	330	332	332	334	338	340	340	342

An even Genetic Code Matrix

Number of atoms in triplets

36		38	38		38				42		42		42	44
40		40	40		40				44		44		44	44
40		40	40		40				44		44		44	44
40		42	42		42				46		46		46	48
î		ê	ê		í				î		ê		ê	í
	636											708

An odd Genetic Code Matrix

Number of atoms in triplets

37		37	37		39				43		43		43	43
39		39	39		41				43		43		43	43
41		41	41		41				43		45		45	45
41		41	41		41				45		47		47	47
î		ê	ê		í				î		ê		ê	í
	636											708

In those examples, the mathematical balance in distribution of atoms is achieved

An even and odd genetic code matrix

Even code matrix

Number of atoms in triplets

36		38	38		38				37		37		37	39
40		40	40		40				39		39		39	41
40		40	40		40				41		41		41	41
40		42	42		42				41		41		41	41
î		ê	ê		í				î		ê		ê	í
	636											636

Odd code matrix

Number of atoms in triplets

43		43	43		43				42		42		42	44
43		43	43		43				44		44		44	44
43		45	45		45				44		44		44	44
45		47	47		47				46		46		46	48
î		ê	ê		í				î		ê		ê	í
	708											708

Those tables tells us that there is exact mathematical balance in arrangement of nucleotides in genetic matrix code.

Number of atoms in triplets of nucleotides in digital even Tables of genetic code is 1344. First triplet has 36 atoms, second 38, third 38, etc. Those tables contain 32 triplets. Genetic gravitation can be found when we calculate number of atoms in groups with 7 and 19 triplets.

Mathematical gravitation in genetic processes

A result of our research tells us that there are forces of mathematical gravitation in genetic processes. Those forces of gravitation attract nucleotides, and that's how triplets of corresponding nucleotides are created. Also, they attract amino acids to peptide chains and that's how proteins and other organic compounds are created. Further we'll mention some concrete mathematical evidences of existence of force of mathematical gravitation in genetic processes. We discovered gravitation in those processes with the use of following formula:

Formula for mathematical gravitation in genetic processes

We can calculate mathematical gravitation in genetic processes with the help of codes 19 and 7:

(X1,2,3,n + X2,3,4,,n + X3,4,5,n…, + X4,5,6,n) = (7x19x7);

At(ucag) =(36+37+37+37+38+38+38+39,39,39,39,40,40,40,40,40+40+40+40+40+41+ +41+41+41+41+41+41+41++41+42+42+42+42+42+42+43+43+43+43+43+43+43+43+

+43++44+44+44+44+44+44+44+44+44+45+45+45+45+46+46+46+47+47+47+48)=2688;

At(ucag) = Number of atoms UCAG

Number of atoms in triplets of nucleotides in digital Tables of genetic code is 2688. First triplet has 36 atoms, second 37, third 37, etc. Those tables contain 64 triplets. Genetic gravitation can be found when we calculate number of atoms in groups with 7 and 19 triplets.

Measuring genetic gravitation

Mathematical gravitation in genetic processes manifests on various ways. Here are some examples:

Distance 4 in digital genetic code matrix

		An even code matrix									An odd code Matrix
36			38	38	38		150		37			37	37	39		150
38			38	38	40		154		37			37	39	39		152
38			38	40	40		156		37			39	39	39		154
38			40	40	40		158		39			39	39	39		156
40			40	40	40		160		39			39	39	41		158
40			40	40	40		160		39			39	41	41		160
x			x	x	x		0		x			x	x	X		0
x			x	x	x		0		x			x	x	X		0
44			44	44	44		176		43			43	45	45		176
44			44	44	44		176		43			45	45	45		178
44			44	44	46		178		45			45	45	45		180
44			44	46	46		180		45			45	45	47		182
44			46	46	46		182		45			45	47	47		184
46			46	46	48		186		45			47	47	47		186
1204			1214	1222	1232		4872		1203			1213	1223	1233		4872

(150+154+156+158+160+160+160+160+160+160+162+164+166+168+168+168+170+172+174+176+

+176+176+176+176+176+178+180+182+186 = 4872;

(150+152+154+156+158+160+162+164+164+164+164+164+164+166+1688+170+172+172+172+172+

+172+172+174+176+178+180+182+184+186) = 4872;

(1204+1232) = (1214+1222); (1203+1233) = (1213+1223);

(150+186) = (154+182) = (156+180); etc.

D1=150: D2=154; D4=156, etc.

Codes 19 and 7 in even code matrix

(D1+D2+D3…, + D19) + (D29+D28+D27..., + D11) = 6384 = [(19 x 7) x Y]

(D2+D2+D4…, + D20) + (D28+D27+D26…, + D10) = 6384 = [(19 x 7) x Y]

(D3+D2+D5…, + D21) + (D27+D26+D25…, + D9) = 6384 = [(19 x 7) x Y]

etc.

Codes 19 and 7 in odd code matrix

(D1+D2+D3…, + D19) + (D29+D28+D27…, + D11) = 6384 = [(19 x 7) x Y]

(D2+D2+D4…, + D20) + (D28+D27+D26…, + D10) = 6384 = [(19 x 7) x Y]

(D3+D2+D5…, + D21) + (D27+D26+D25…, + D9) = 6384 = [(19 x 7) x Y]

etc.

Distance 5 in digital genetic code matrix

		An even code Matrix										An odd code Matrix
36			38	38	38	40		190		37			37	37	39	39			189
38			38	38	40	40		194		37			37	39	39	39			191
38			38	40	40	40		196		37			39	39	39	39			193
38			40	40	40	40		198		39			39	39	39	41			197
40			40	40	40	40		200		39			39	39	41	41			199
40			40	40	40	40		200		39			39	41	41	41			201
x			x	x	x	x		0		x			x	x	x	x			0
x			x	x	x	x		0		x			x	x	x	x			0
x			x	x	x	x		0		x			x	x	x	x			0
44			44	44	44	44		220		43			43	43	45	45			219
44			44	44	44	44		220		43			43	45	45	45			221
44			44	44	44	46		222		43			45	45	45	45			223
44			44	44	46	46		224		45			45	45	45	47			227
44			44	46	46	46		226		45			45	45	47	47			229
44			46	46	46	48		230		45			45	47	47	47			231
1158			1168	1176	1184	1194		5880		1158			1166	1176	1186	1194			5880

(190+194+196+198+200+200+200+200+200+202+204+206+208+210+210+212+214+216+218+220+

+220+220+220+220+222+224+226+230) = 5880;

(189+191+193+197+199+201+203+205+205+205+205+205+207+209+211+213+215+215+215+215+

+215+217+219+221+223+227+229+231) = 5880;

(1158+1194) = (1168+1184) = (1176 x 2); (1158+1194) = (1166+1186) = (1176 x 2);

(190+230) = (194+226) = (196+224), etc. (189+231) = (191+229) = (193+227), etc.

Codes 19 and 7 in even code matrix

(D1+D2+D3…, + D19) + (D29+D28+D27..., + D11) = 7980 = [(19 x 7) x Y]

(D2+D2+D4…, + D20) + (D28+D27+D26…, + D10) = 7980 = [(19 x 7) x Y]

(D3+D2+D5…, + D21) + (D27+D26+D25…, + D9) = 7980 = [(19 x 7) x Y]

etc.

Codes 19 and 7 in odd code matrix

(D1+D2+D3…, + D19) + (D29+D28+D27…, + D11) = 7980 = [(19 x 7) x Y]

(D2+D2+D4…, + D20) + (D28+D27+D26…, + D10) = 7980 = [(19 x 7) x Y]

(D3+D2+D5…, + D21) + (D27+D26+D25…, + D9) = 7980 = [(19 x 7) x Y]

etc.

Distance 6 in digital genetic code matrix

36	38	38	38	40	40	230		37	37	37	39	39	39	228
38	38	38	40	40	40	234		37	37	39	39	39	39	230
38	38	40	40	40	40	236		37	39	39	39	39	41	234
38	40	40	40	40	40	238		39	39	39	39	41	41	238
40	40	40	40	40	40	240		39	39	39	41	41	41	240
40	40	40	40	40	40	240		39	39	41	41	41	41	242
X	x	x	X	x	x	0		x	x	x	x	x	x	0
X	x	x	X	x	x	0		x	x	x	x	x	x	0
X	x	x	X	x	x	0		x	x	x	x	x	x	0
44	44	44	44	44	44	264		43	43	43	43	45	45	262
44	44	44	44	44	44	264		43	43	43	45	45	45	264
44	44	44	44	44	46	266		43	43	45	45	45	45	266
44	44	44	44	46	46	268		43	45	45	45	45	47	270
44	44	44	46	46	46	270		45	45	45	45	47	47	274
44	44	46	46	46	48	274		45	45	45	47	47	47	276
1114	1122	1130	1138	1146	1154	6804		1113	1121	1129	1139	1147	1155	6804

Codes 19 and 7 in even code matrix

(D1+D2+D3…, + D19) + (D29+D28+D27...., + D11) = 9576 = [(19 x 7) x Y]

(D2+D2+D4…, + D20) + (D28+D27+D26…, + D10) = 9576 = [(19 x 7) x Y]

(D3+D2+D5…, + D21) + (D27+D26+D25…, + D9) = 9576 = [(19 x 7) x Y]

etc.

Codes 19 and 7 in odd code matrix

(D1+D2+D3…, + D19) + (D29+D28+D27…, + D11) = 9576 = [(19 x 7) x Y]

(D2+D2+D4…, + D20) + (D28+D27+D26…, + D10) = 9576 = [(19 x 7) x Y]

(D3+D2+D5…, + D21) + (D27+D26+D25..., + D9) = 9576 = [(19 x 7) x Y]

etc.