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Analyzing the structure of protein synthesis and transcription.

INTRODUCTION

Proteins are organic compounds which always contain carbon, hydrogen, oxygen and nitrogen and they often contain sulphur and phosphorus as well. Each molecule of protein is made up of many amino acids linked together by strong peptide bonds into one or more polypeptide chains. Proteins are the most complex biological molecules. They are made up of C, H, O, N, and a little S (carbon, hydrogen, oxygen, nitrogen, and a little sulfur)accomplish all life functions. Proteins are polymers of amino acid monomers. Amino Acids are joined by peptide bonds. Proteins are responsible for all life activities in a cell. This means they are responsible for muscle contraction. Muscles are made up of two major protein filaments. A thick filament composed of myosin and a thin filament composed of actin. Muscle contractions occur when these two filaments slide over one another in a series of repetitive events. An organic molecule is a molecule that is normally in or produced by a living system. These molecules typically consist of carbon atoms in rings or long chains that allow other atoms such as hydrogen, oxygen and nitrogen to attach. The organic compounds are grouped into four major categories known as carbohydrates, lipids, proteins and nucleic acids. There are twenty different types of amino acids found in proteins which can be arranged in any order in chains lasting 2000 units long enabling their variety. A protein is a specific number of amino acids assembled in a specific order.

Protein synthesis consists of two main categories: transcription, which is the process of copying RNA information to DNA, and translation, which is the process of turning RNA information to DNA. Transcription is the process of copying DNA information to RNA. It begins at the initiation site when the polymerase separates the two DNA strands and exposes the template strand for base pairing with RNA nucleotides. The RNA polymerase works its way down from the initiation site, prying apart the two strands of DNA and elongating the mRNA in the 5" A 3" direction. The entire stretch of DNA that is transcribed is called a transcription unit. The RNA polymerase continues to elongate the RNA molecule until it reaches the termination site, a specific sequence of nucleotides along the DNA that signals the end of the transcription unit. The mRNA, a transcript of the gene, is released, and the polymerase subsequently dissociates from the DNA. Translation is the process of turning RNA information to DNA. First, a small ribosomal subunit binds to a molecule of mRNA. The positioning of the mRNA is signaled by a ribosome recognition sequence of the mRNA. This tRNA carries the amino acid methionine (Met). Then the large ribosomal subunit joins the initiation complex. The initiator tRNA is in the P site.

2. Structure of Protein Molecules:

2.1 Protein Primary Structures:

The primary structure of a protein is the type and sequence of the amino acids used in the polypeptide. It is connected by peptide bonds, and the sequence determines the structure and shape of the whole protein. A peptide bond is when the carbon in the carboxyl group of one amino acid connects to nitrogen in the amino group of another amino acid. This happens through dehydration synthesis, a process when a molecule loses water. Once all the amino acids join together or connect by peptides bonds, they form a sequence of amino acids also known as a polypeptide chain that become the primary structure of a protein.

2.2 Protein Secondary Structures:

The secondary structure of a polypeptide is the way a small part, fairly near in the polypeptide sequence, curls up into an alpha helix or beta pleated sheets, or sometimes even no structured shape at all. The atoms attract each other across the space so that there are more links between atoms, causing the chain to curl. This creates a kinked chain. This is the alpha helix. A beta pleated sheet is a form of shape where the bonds create a kinked shape, and attract across the space. This causes the structure to become more like a folded piece of paper, as the chains cannot curl round to meet the attractive atoms because there are other forces pulling it the other way. This is a much looser structure than the alpha helix. The secondary structure is still two dimensional. . There are two major categories of proteins with secondary structure - Alpha-helix and Beta-plated sheets.

The alpha helix ([alpha]-helix) is a common modified in the secondary structure of proteins and it is a right hand coiled or spiral conformation (helix) in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid located three or four residues earlier along the protein sequence. This secondary structure is also sometimes called a classic Pauling-Corey-Branson a-helix. In an alpha-helix, the protein chain is coiled like a loosely-coiled spring. The "alpha" means that if you look down the length of the spring, the coiling is happening in a clockwise direction. The name [3.6.sub.13]-helix is also used for this type of helix, denoting the average number of residues per helical turn, with 13 atoms being involved in the ring formed by the hydrogen bond. Among types of local structure in proteins, the a-helix is the most regular and the most predictable from sequence, as well as the most prevalent.

The [beta]-sheet (also [beta]-pleated sheet) is a common motif of regular secondary structure in proteins. Beta sheets consist of beta strands (also [beta]-strand) connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet. A P-strand is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformation. The supramolecular association of [beta]-sheets has been implicated in formation of the protein aggregates and fibrils observed in many human diseases, notably the amyloidosis such as Alzheimer's disease.

2.3 Protein Tertiary Structures:

The tertiary structure is that which causes the secondary structure itself to fold around, creating an even more complex structure. It creates a three dimensional shape, as it folds around in many directions following the various pulls of atoms. Various types of bonds are used in these links: hydrogen bonds between R groups, disulphide bonds between two cysteines molecules, as in the primary structure, ionic bonds between R groups containing amine and carboxyl groups, and hydrophobic reactions between R groups which are non-polar all contribute to holding the tertiary structure of a protein.

2.4 Protein Quaternary Structure:

The quaternary protein structure involves the clustering of several individual peptide or protein chains into a final specific shape. A variety of bonding interactions including hydrogen bonding, salt bridges, and disulfide bonds hold the various chains into a particular geometry. There are two major categories of proteins with quaternary structure - fibrous and globular. As the fibrous proteins is the keratins in wool and hair are composed of coiled alpha helical protein chains with other various coils analogous to those found in a rope. Other keratins are found in skin, fur, hair, wool, claws, nails, hooves, horns, scales, beaks, feathers, actin and myosin in muscle tissues and fibrinogen needed for blood clots. Globular proteins may have a combination of the above types of structures and are mostly clumped into a shape of a ball.

3. Related Works:

3.1 RNA Vs DNA:

RNA is the step between DNA and protein synthesis. With a few differences, RNA is chemically similar to DNA. RNA contains ribose as its sugar and has a nitrogenous base of uracil rather than thymine. DNA contains deoxyribose as its sugar. Each nucleotide along a DNA strand has deoxyribose as its sugar and A, G, C, or T as its base, while each nucleotide along an RNA strand has ribose as its sugar and A, G, C or U as its base. RNA molecules are always single stranded.

Two major stages must occur in order to get from DNA to protein, transcription and translation. RNA helps in this process. Transcription is the synthesis of RNA. The information is transcribed from one molecule to the other. The RNA molecule that results is called messenger RNA (mRNA). Messenger RNA carries a genetic message from the DNA to the protein-synthesizing part of the cell. .

Translation occurs under the direction of mRNA. The "language" changes in this stage and the cell must translate the base sequence of an mRNA molecule into the amino acid sequence of a polypeptide. During translation, the genetic message (mRNA) is read as a sequence of base triplets, three-letter code words. These triplets, also called codons, specify the amino acid to be added at the corresponding position along a growing polypeptide chain. The end result is called the primary transcript. There are a few more important types of RNA. Transfer RNA (tRNA) serves as an adaptor molecule in protein synthesis, and translates mRNA codons into amino acids. Also, there is ribosomal RNA (rRNA), which plays important roles in the ribosomes. Two other types of RNA are small nuclear RNA (snRNA) and SRP RNA.

3.2 Genetic Engineering:

The DNA code mostly contains instructions for protein synthesis. The code is read in groups of three nucleotides and each triplet of nucleotides codes for one of the twenty amino acids which link together in a polypeptide chain to form a protein. The code is universal, so the same code applies in nearly all living organisms. Some triplets have special functions and direct protein synthesis to start or stop. Protein synthesis occurs in ribosomes where a copy of the gene coding for a protein (mRNA) is translated to produce a protein. Some proteins may be consisting of several polypeptide chains and the genes required to do this are collectively called a transcription unit. Genes code for proteins bacterium also contain small circular loops of DNA called plasmids which are not essential to the bacterium but can be useful in certain environmental conditions such as resistance to antibiotics. Because bacterium is prokaryotic and do not have a nucleus plasmids are easy to obtain in pure form and can be introduced into other cells. Plasmids are also capable of independent self-replication, which makes them useful in multiplying useful DNA. Bacteria also produce restriction enzymes, which can cut DNA at specific base sequences. Different restriction enzymes cut different base sequences and some make staggered cuts which leaves unpaired DNA ("sticky ends") and other cut leaving no unpaired DNA ("blunt ends"). Techniques used in genetically engineering cotton for insect resistance in inserting the Bt gene into the cotton plant is determining the Bt protein's amino acid sequence. Using the principles of the genetic code it is possible to construct a complementary DNA sequence called and oligonucleotide using an automated DNA synthesizer. This oligonucleotide can then be used as a DNA probe to isolate the DNA from the Bacillus thuringiensis.

3.3 Beta Globin Locus:

Understanding the control of the developmentally regulated switch of gene expression within the beta-globin locus is a mainly used in today research. Globin gene transcription switches from embryonic to fetal to adult forms in humans and embryonic to adult in chickens during development. The expression of the genes on the beta-globin locus is controlled by a series of both general and tissue-restricted transcription factors. In addition, recent models of globin switching have focused on competition and cooperation between enhancers, promoters, and the locus control region. Analyze both the human and chicken [pounds sterling]]-globin locus. To identify the similarities and differences of the locus among the two species and present different methods involved in activation. The [pounds sterling]]-Globin Gene is one of two genes that make up a multigene family. Members of a multigene family not only share DNA-sequence homology, but also have gene products that are functionally associated. The globin genes of vertebrates' expression are both developmentally and temporally regulated. The two regions that make up the globin gene family include the alpha-globin and beta-globin genes. These two genes are necessary for the formation of an effective hemoglobin molecule. This complete molecule then functions to carry oxygen in the blood. Hemoglobin synthesis requires the synchronized production of both heme and globin. While heme is the prosthetic group that can reversibly bind to oxygen, globin is the protein that encloses and safeguards the heme molecule. The [pounds sterling]- and [pounds sterling]]-globin loci, in all vertebrate species, are assembled with multiple genes encoding distinct globin protein isotypes.

3.4 DNA Fingerprinting:

DNA Fingerprinting is also referred to as DNA profiling and DNA typing. It was first developed as an identification technique in England in 1985. The original use was to expose the presence of any genetic diseases. About three years later it became used to identify criminals through the analysis of genetic material and to settle paternity disputes. The DNA fingerprinting process is called gel electrophoresis. It is a process that can sort pieces of DNA according to its size. The process is done by taking samples of DNA from the crime scene and comparing it with samples from the accused. Samples are taken from biological materials like blood, semen, hair, and saliva. In the testing process the DNA samples are first entered into the wells in a gel like substance called Agarose. The gel is placed between two electrodes, one negatively charged and the other positively charged. The wells in the Agarose are inserted on the negative side because DNA has a negative charge. Molecules of DNA then travel in lanes toward the positive side. Small molecules will travel farther than the bigger ones, because they have an easier time moving through the gel. So the molecules will then be assorted according to their size. Next, the gel is X-rayed to see the parallel bands (showed by black bars on the film) in each lane. The separated molecules of DNA form a pattern of parallel bands that show the structure of the DNA. The pattern should never change for one person. In a court of law, the results of a DNA fingerprinting examination can be used to convict or acquit an accused person. If the accused's DNA matches the one at the crime scene then that person could be convicted. Critics believe that a DNA fingerprint may not yet be reliable enough to use in the court system.

3.5 Microsatellites in DNA:

The DNA contains satellite DNA. There are three types of satellites. These are randomly repeated pieces of DNA. The second is mini satellite DNA. These are randomly repeated pieces of DNA at least 10 base pairs. The third is micro satellite DNA. These are tandem arrays of mono- to tetra nucleotides in DNA.

The 3 billion nucleotide bases only 10% of them. The findings consist of bacteria enhancements to human restrictions. The results are based on microsatellite DNA. This technique of finding these satellites can offer geneticists a new world to explore. These satellites are ever changing and helpful in detection of some diseases. To obtain DNA and run the polymerase chain reaction one must first obtain DNA. To do this one will swab the inside of the cheek for cells. This is then placed in a test tube of 10 microliters of DNA is needed. Then the six microliters of water must be added to the test tube. To set incubate the tube at 65[degrees]C for 30 minutes and vortex the tube for 15 seconds. Then the 1.5 micro litters of each primer are added to the test-tube of the DNA. There are 3 primer sets so six primer must be added. The temperature is then raised to 98[degrees]C. It must be incubated for 15 minutes. The 25 microliters redimix is now added and the polymerase chain reaction takes place. The sample is denatured at 94[degrees]C for 20 minutes. This allows the DNA strand to separate.

3.6 Gene Therapy for Alzheimer's Disease:

Gene therapy has become an upwelling in therapeutics and has introduced promising prospects for the prevention and cure of incurable or difficult to cure diseases. With the advent of concern for the growing cases of dementia globally, it has become important to constitute therapeutic methods for Alzheimer's disease. Initially analysis was done on the Duplication of amyloid precursor protein and it was found to be the cause of early onset dementia. It focused on diagnostic techniques and comparative results. A second research was analyzed based on the use of the Nerve Growth Factor to treat cholinergic neuron loss in AD Patients and this was found to not cure the disease but rather slow down the process. Another research presented here investigates the Acat1 Knockdown gene therapy that decreases amyloid - beta plaques. The hyper-phosphorylated 'tau' and synapse dysfunction in the brain with minor emphasis on the Crtc1 gene. To analyzed a WNT 7A signaling and how it promotes dendritic spinal growth and synaptic strength. The Human Genome Project is a worldwide research effort with the goal of analyzing the structure of human DNA and determining the location of the estimated 100,000 human genes. The DNA of a set of model organisms will be studied to provide the information necessary for understanding the functioning of the human genome. The information gathered by the human genome project is expected to be the source book for biomedical science in the twenty-first century and will be of great value to the field of medicine. The scientific products of the human genome project will include a resource of genomic maps and DNA sequence information that will provide detailed information about the structure, organization, and characteristics of human DNA, information that constitutes the basic set of inherited "instructions" for the development and function of a human being.

4. Genetic Testing and Social Implications:

Applied genetics are most impacts on society are as a result of genetic tests. In general, genetic tests seek to detect some feature of a person's genetic constitution. This feature can be a disease causing mutation or a marker DNA sequence used to detect presence of another gene. Obviously these procedures used for testing the status of DNA, RNA or chromosomes are included in genetic tests. What is more it is possible to include some protein based tests and classical medical examinations when they aim to detect inheritance of a trait. Prenatal tests that are applied on fetuses during pregnancy. Neonatal screening just after birth and career screening of marrying couples. Testing for serious late-onset disease before the symptoms occur. Testing to assess the probability of developing complex disease. When a positive or a negative result is obtained, we should be confident in that result with a confidence approaching 100%. To achieve such a high accuracy is not as easy as it may at first appear to be. Meiotic recombination that always occur take place during gamete generation may separate a disease-associated gene and a marker DNA sequence which is used to detect mutated genes. False positive or negative results could be obtained. In addition, genetic tests look for the most common mutations that cause the disease. For example, a test would detect CFTR? F508 (Cystic Fibrosis Trans membrane Receptor) mutation, however it is not possible to detect infinite number of other mutations. Therefore, a genetic test can give such results so that the physician is convinced that his patient is normal while he is affected by an undetectable mutation. New tests are continuously being developed. Therefore, a genetic test can give such results so that the physician is convinced that his patient is normal while he is affected by an undetectable mutation.

Conclusion:

In this study analyzed the process of transferring information from a gene to a protein and the process of transcription is copying DNA information to RNA. It begins at the initiation site when the polymerase separates the two DNA strands and exposes the template strand for base pairing with RNA nucleotides. Protein Molecules Structures are described as primary, secondary, tertiary, quaternary protein structure. In primary protein structure use the type and sequence of the amino acids used in the polypeptide. The secondary protein structure a polypeptide is the small part and polypeptide sequence, curls up into an alpha helix or beta pleated sheets. Tertiary structure creating an even more complex structure in three dimensional shapes. The quaternary protein structure uses the clustering of several individual protein chains into a final specific shape. To compare the DNA and RNA and types of RNA are small nuclear RNA (snRNA) and SRP RNA used in protein synthesis. In genetic engineering the copy of the gene coding for a protein is translated to produce a protein. The beta-globin locus is controlled by a series of both general and tissue-restricted transcription factors. Microsatellites DNA findings the bacteria enhancements to human restrictions. Gene therapy used for Alzheimer's disease. Genetic tests are used to detect the genetic constitution and a disease causing mutation or a marker DNA sequence used to detect presence of another gene. New Genetic Testing and Social Implications are continuously being developed. For this analysis the drawback to produce the accurate DNA fingerprint result is not very accurate because only a segment of DNA is used and not the complete strand and also the cost are high.

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(1) Dr. M. Thangamani and (2) B. Kalaiselvi

(1) Assistant Professor, Mahendra Engineering College for women, Tamiinadu, India.

(2) AssistantProfessor, Kongu Engineering College, Tamiinadu, India.

Received 28 January 2017; Accepted 12 May 2017; Available online 18 May 2017

Address For Correspondence:

Dr. M. Thangamani, Assistant Professor, Mahendra Engineering College for women, Tamilnadu, India.

E-mail: manithangamani2@gmail.com

Caption: Fig. 1: Protein Primary Structure

Caption: Fig. 2: Alpha Helix Protein Structure

Caption: Fig. 3: Structure of Beta-Pleated Sheets

Caption: Fig. 4: Protein Tertiary Structure

Caption: Fig. 5: Protein Quaternary Structure
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Author:Thangamani, M.; Kalaiselvi, B.
Publication:Advances in Natural and Applied Sciences
Article Type:Report
Date:May 1, 2017
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