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CANCER CURE via DNA
By Anthony J Luksas
iUniverse, Inc.Copyright © 2013 Anthony J Luksas PhD
All right reserved.
Chapter OneDNA, RNA and Protein
IT IS ESSENTIAL TO understand DNA, RNA and Proteins to proceed in understanding of the contents of this book. DNA is the seat of inheritance of all that we are minus the soul. One cannot explain the soul by DNA. Also, as we get into the details of DNA, RNA and Proteins, we determine the results that they produce, but there is no explainable reason why these organic molecules do what they do. That is to say, once the different atoms of carbon, oxygen, hydrogen, phosphorus and nitrogen are put together into monomers, then these monomers into polymers to make DNA, RNA and Protein (proteins contain in addition sulfur as part of some amino acids the building blocks of protein).
The laws of nature dictate the DNA, RNA and Proteins will function without exception in performing the function that was intended. Do not ask why and how, only that they do what they do. It is also interesting to know that carbon plays a major role in biochemistry that includes DNA, RNA and Proteins. Carbon is the backbone and the predominant atom in all of biochemistry – the study of molecules that are found in living systems on earth. How these molecules are made in the cell be it bacterial or human is the study of biochemistry and cell physiology and related courses, and will not be discussed in this book. We will proceed from the point where these molecules have been produced.
There are only 20 different amino acids, figure 1 and 2, therefore many of the triplets code for some of the amino acids more than once. There are three triplets that do not code for amino acids, but are used to terminate a polypeptide chain.
All DNA in all species on this earth consist of the 4 mononucleotides. The ration of each varies in species, but only these nucleotides are present.
Deoxyribonuleic acid (DNA) contains 2 purine bases – adenine (A), guanidine (G) and 2 pyrimidine bases – thyamine (T) and cytosine (C). Ribonuclaic acid [RNA] contains 2 purine bases – adenine [A] and guanidine [G], and 2 pyrimidine bases – cytosine and uridine [U], Figure 3.
The bases are attached to the No. 1 carbon of deoxyribose, the phosphoric acid is attached to the No. 5 carbon.
When the DNA polymer is formed the phosphoric acid is chemically bonded to the No. 3 carbon of the next mononucleotide (composed of nitrogenous base, five carbon sugar and phosphoric acid), and so forth. Now, if a gene (definition of a gene: segment of DNA that directs the production of a complete protein) directs the production of a complete protein of 100 amino acids, that gene is composed of at least 300 nucleotides. It has been determined experimentally that it takes 3 nucleotides to determine an amino acid. Therefore, 4 to the 3power = 64, and theoretically can determine 64 different amino acids, Figure 4.
Microorganisms that do not separate the DNA from cytoplasm by a membrane are called prokaryotes (prokaryotes are bacteria). In prokaryotic cells like bacteria, the DNA is a single chromosome exceeding 2 x 10 to the ninth in molecular weight. That chromosome is composed of 5-6 million nucleotides and, if 3 nucleotides determine an amino acid, therefore there are 3 million triplets, and if 100 amino acids compose a complete protein, therefore one gene approximately. There are, in single bacteria, approximately 30,000 genes. A virus as a comparison has approximately up to 200 genes depending on the virus; as we said above, in prokaryotic cells there is an apparent division between the cell components and the chromosomes. There is an attachment of the DNA on the chromosome in the inside of the prokaryotic cell membranes, but no separation by a membrane of DNA from cytoplasm. Eukaryotic cells contain, depending on the species, several to many chromosomes. The chromosomes consist of two double stranded DNA molecules. The DNA in eukaryotic cells is very complex and packed into chromosomes. The eukaryotic germ cells consist of one double stranded DNA.
In eukaryotic cells, there is a clear division between the chromosomes and the rest of cell components. The chromosomes are in an area separated by a membrane and that is called the nucleus. The rest of the cell area is called the cytoplasm.
Mitochondria have its own DNA. It is the cell's energy mill. It is the current belief that there existed a symbiotic relationship between prokaryotes and eukaryotes, until the prokaryote became part of the eukaryote as mitochondria. Mitochondrial DNAis single stranded like bacteria, and it divides like bacteria. The same appears to be also with chloroplasts of plants.
Ribonucleic acid (RNA) is composed of adenine (A), granine (G), cytosine (C) and uracil (U) bases, each attached to ribose, also attached to ribose are phosphoric acid. Poly RNA is created by one ribose unit with attached base at position one on the ribose and phosphoric acid attached at position five which reacts with another ribose on position three and so forth. During the process of transcription, DNA makes RNA. After transcription – messenger RNA (mRNA), as this RNA is known. There are other types of RNA made by DNA also, but mRNA is needed to translate (or make) protein. The other RNA's are ribosomal RNA (gamma RNA) and transfer RNA (t RNA).
During the process of transcription, DNA makes RNA. After transcription mRNA attaches to a ribosome in the cytoplasma, and is used to make protein.
In 1953, Watson and Crick deduced the double helical structure of DNA. The dogma that evolved from that and other developments after were the following:
1. Replication – the coupling of DNA to form identical DNA molecules
2. Transcription – the process by which DNA is transcribed (made) into RNA. The RNA then attaches to ribosome.
3. Translation – the process by which genetic message is decoded and converted into the 20-letter alphabet of protein structure.
To go into details as to the "process" of replication, transcription and translation is a mute point. There are many advanced courses given at the universities, but that knowledge is not essential to the understanding of this book.
The knowledge of how each process works, and the processes of making and transporting these molecules are unknown – it just happens. We know that these processes take place by looking at the results. Why do these formed molecules do what they do, and how do they do what they do is a mystery. Some people of higher learning try to explain not why but how by using thermodynamics and organic and inorganic chemistry of simple molecules, but in my opinion, to no avail.
Next area of understanding that will help to follow the developments in this book is what is the structure of proteins, composition of proteins, how they are made and what is their function. First, RNA makes essentially all proteins. There are some proteins that will be discussed later that are made directly by DNA – repressor proteins; but RNA makes the various proteins in the cell other than repressor proteins.
Proteins are composed of amino acids that are made by enzymes, which are proteins. Some enzymes require other molecules or elements to function. There are 20 different amino acids, as figure 1 and 2 indicates.. Amino acids can be described as a carbon atom to which are attached a hydrogen, amine (NH2), carboxyl (COOH) and an R group. The R group is what makes the amino acids different from each other. There are 20 amino acids; all proteins consist of these 20 amino acids. There are 15 neutral amino acids, 2 acidic amino acids and 3 basic amino acids. Some of these amino acids may be modified by enzymatic action like prolein into hydroxi prolein. If this modification was not made or partially made, collagen would not have a three dimensional structure, and would not function as the glue of biological systems, The blood vessels would start bleeding, organs would start to fall apart. This process is known as Scurvy. At a certain point in this process, the biological unit like man would die.
Good collagen is made by hydroxilation of proline. The enzyme (protein) requires vitamin C to function; since without vitamin C, the enzyme does not function. Many enzymes require co-factors. These co-factors are the various vitamins and some elements. Amino acids are made into proteins by the carboxyl group of one amino acid reacting with amine group of another amino acid and so forth. The bond formed between two amino acids is called a peptide bond.
Once a specific mRNA is produced from a DNA gene, it travels to a ribosome where it is translated into protein. How long the protein chain is, composition of amino acids, and position of these amino acids within the protein chain determines the function of the protein chain. As an example of the specificity of amino acids and the position of that amino acid is sickle cell anemia. Sickle cell hemoglobin is different from normal hemoglobin by only one amino acid. Hemoglobin has an alpha chain and a beta chain. The alpha chain, no change, but in the beta chain at position six-glutamine acid is replaced by valine. There are many examples.
It is interesting to note that the following is an additional piece of info to strongly suspect that mitochondrial is of bacterial origin. The mitochondria produces its own RNA and ribosomes and the synthesis of protein is characteristically like the protein synthesis apparatus similar to bacteria. This and the DNA of mitochondria strongly support the hypothesis that mitochondria are from symbiotic or parasitic bacteria resulting during evolution of eukaryotic cells.
Proteins that are produced by different RNA's on ribosomes, become enzymes, structural protein, immune protein etc. These proteins produce all the components of the cell by producing the various biochemical – lipids, lipoproteins, vitamins, carbohydrates etc.
Chapter TwoBACTERIAL, PLANT, ANIMAL AND HUMAN VIRUSES
THROUGHOUT THE FOLLOWING CHAPTERS we will explore the DNA and RNA viruses as the cause of Cancer. Bacteria do not develop so called "Cancers", but the results that bacteriophages (bacterial viruses) impart to the bacteria can be considered as Cancer. The bacteriophages confer on the bacteria that allow them to either survive in inanimate environment or living environment by producing toxins that causes the living environment to die and degrade into components that the bacteria can live on.
Therefore, bacterial plasmids and bacteriophages play a key role in the bacteria as causing either pathogenicity, or, toxin production that allows the bacteria to survive in a hostile living environment.
In cases studied, pathogens or toxin producing microbes were shown to possess a large segment of DNA – (35-170) kilobases. This includes a number of virulent genes that are not present in non-pathogens.
In enteropathogenic E.coli, there is extra DNA. How is this determined? The DNA is analyzed by hydrolyzing to gene level the DNA, and subjecting the genes to electrophoreses, not unlike DNA analysis in forensics.
In the enteropathogenic E.coli there are extra genes that do not exist in regular E.coli. Up to 10% of the bacteria in the human intestinal track are regular E.coli. Similar possibilities exist in Shigella, tetanus , B.anthraces, C.diptheria, S. pyrogenes, C.botulinum, enterohemorehagic E.coli and many others. The bacteria have to acquire a specific gene or genes to become pathogenic.
Also, extra chromosomal genes encoding other virulence factors are common among gram-negative pathogens ranging from plant pathogens to human like human Helicobacter pylori. Therefore, pathogenicity is due to acquisition of plasmids, lysogenic phages and transposons; and not to some form of adoption by the pathogens.
The following scale depicts viral infections:
Pathogens HIV Cancer Diseases
Instant effect and related may take May take
and fast viruses 20-30 years sometime or
growth to develop years to have
can be fast an effect on
growth after nerve cells,
that or slow muscle cells
Depending on the plasmid or bacteriophage in bacterial situation, the end result is better for the bacteria, and can be bad for higher organisms like plants, animals and man, but in human cells when viral infections take place and most of the cells infected are destroyed, but, some survived by the virus becoming a prophage. Since plants, animals and man genetically are very complicated, and if interactions do take place in higher organisms it is similar to bacterial infections with bacteriophages, then there are interactions that we do not know anything about, until or unless they manifest themselves in a form of a disease, and we have the capacity to identify it as a disease.
Not much is known about the cancers in plants. The crown gall tumor is caused by Agrobacterium tumefaciens. This organism is closely related to Rhizobium which depending on species fixes nitrogen in symbiotic association with leguminous plants. The leguminous plants that fix nitrogen when in symbiotic association with Rhizobium are alfalfa, clover, peas, beans, peanuts, soybeans and vetch. The association forms nodules on the roots of the plant. The bacteria and the plants can grow separately, but the bacteria will disappear from the soil if no leguminous plants are growing for a long time. The bacteria fix nitrogen only in association with the plant. There does not appear to be any genetic material transferred from the bacteria to the plant or from plant to bacteria.
It is intracellular symbionts that infects root cells that are tetraploid (cells that have four sets of chromosomes), normal diploid cells are usually destroyed by the infection. The single cell swells and the bacteria multiply and form the root modules.
If a species of Rhizobium cannot infect or if infected cell does not fix nitrogen, then by transferring the DNA from infection and nitrogen fixing by DNA mediated transformation, the non infected or non nitrogen fixing species can become infective and nitrogen fixing. Rhizobium is also attacked by bacteriophages that lyse the cells.
It is possible, but at this writing not known, if Rhizobium lysogenic state exist and that if the proper phage infects and creates the lysogenic state that is the state of the Rhizobium [in a lysogenic state] fixes nitrogen.
Agrobacterium tumefaciens causes a tumor like growth in plants called crown gall tumor. In this situation only the crown gall tumor starts, destroying the bacteria does not stop the development of the tumor. Recent experiments strongly suggest that the bacterial DNA becomes associated or integrated into the DNA of the plant cell that causes the tumor. A plasmid called Ti (tumor-inducing) is transferred from the Agrobacterium tumefaciens to the plant cell. It is then stable in the tumor tissue. It has been also shown that all oncogenic strains of Agrobacterium contain Ti plasmid. If the strains containing Ti plasma are cured of Ti plasmid, the cured strains do not induce tumors. But, if the Ti Plasmid is reintroduced into the bacteria by DNA transformation or conjugation, the resulting strain infects, transfers the Ti plasmid to plant cells and tumor develops. This is basic knowledge found in any microbiology book.
Viruses are known to induce tumors in animals. It has been determined that in fowl, sarcomas and avian leucosis are caused by infecting viruses. Rabbit papillomas is also caused by viruses. Two different leukemia's in mice are caused by viruses. All of these cancers can be induced by filterable agents. Investigation by Raus of sarcoma in fowl, and that disease bares his name – Raus sarcoma.
Here also there is absorption and penetration of the cell not unlike in bacteria. There are receptor sites for viruses that infect mammalian cells. Little is known about the molecular reaction in the absorption process.
Excerpted from CANCER CURE via DNA by Anthony J Luksas Copyright © 2013 by Anthony J Luksas PhD. Excerpted by permission of iUniverse, Inc.. All rights reserved. No part of this excerpt may be reproduced or reprinted without permission in writing from the publisher.
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