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The Role Of Dna And Rna In Determining Protein Structure

1. Introduction - The Role Of Dna And Rna In Determining Protein Structure

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The study is going to discuss DNA, the process of synthesis of protein, and the role of DNA and RNA in determining protein structure. Therefore the study is going to discuss the structure of nucleotides, DNA and the importance of nucleotide base pairs, and the results in the double helix. The study will also discuss the gene sequences of DNA that code for polypeptides and the nucleotide sequences, which code for the amino acid sequence in the polypeptide. The study also involves the comparison between the structure of DNA and RNA. The transcription process, including the role of messenger RNA and Enzymes, will also be highlighted in the study to understand the process of protein synthesis. The study will also describe the process of translation, including the role of m-RNA and t-RNA. Genetic Control of Protein Production in Prokaryotic as per the Lac Operon and the effects of mutation on amino acid sequences of polypeptide and explanation of the results will also be discussed in the study.

1.1Structure of Nucleotides 

Nucleotide refers to the structural unit of the “Nucleic acid” as well as DNA. The nucleotides are made up when nucleotides are attached to the phosphate group. The structure of nucleotides is composed of three important things such as the “5-carbon sugar, nitrogenous base, and the phosphate group”. The nitrogenous base is believed as the “central information-carrying part”. The sugar differs in the nucleotides of the DNA and the RNA. The sugar of the DNA is known as Deoxyribose sugar. Therefore, the sugar of the RNA is known as the Ribose sugar. The last part of the nucleotide is the phosphate group, which is attached to the 5-carbon sugar and formed the “sugar-phosphate backbone”. Nucleotides can be divided into two subgroups such as purine and pyrimidine (Spiegel et al. 2020). The DNA and the RNA have a similar purine base such as adenine and guanine. Therefore, the pyrimidine base is changed in DNA that is Cytosine and Thymine. In addition, the pyrimidine base of the RNA is CYtosine and Uracil. 

1.2 The structure of DNA and the importance of Nucleotide Base pair and results in The Double Helix 

The double-helical structure of the DNA is made up of nucleotides. The double-helical structure is formed as the result of the hydrogen bond between the base of the two-strand of the DNA helix. Therefore the study suggests that the sugar and the phosphate group lined on the periphery of the helical structure and the nitrogen base lay on the middle section of the double helix (Hofer  et al. 2019).

The importance of Nucleotide Base pair and results in The Double Helix are

  • It is important of the formation of the Double Helix structure of the DNA
  • It is also significant for the replication of the DNA 
  • It applies a significant role in the protein formation and the process of the central dogma.
  • Another important role of the base pair is associated with the formulation of the “semiconservative replication process”.

1.3 Gene sequences of DNA that code for polypeptides

The DNA is associated with the three types of codons. These codons help in the expression of the genes. These codes also help in the analysis of the gene sequencing and the protein sequencing of the amino acid in the genes. The expression of these condons also helps in the expression of the genetic sequences of the upcoming proteins (Hoitsma et al. 2019). 

1.4 The nucleotide sequences which code for the amino acid sequence in the polypeptide 

AUG, GUG, AGC ate the codeones that help in the coding of the amino acids. The coding of the amino acids also helps in the determination of the amino acid sequences of the polypeptide chains (Ruiz-Torres et al. 2021). 

1.5 DNA replication is Semi-Conservative according to the role of DNA polymerase

DNA replication is a semiconservative process and the reason behind this concept is that

  • The name comes from the fact that the whole process produces one new copy of the DNA and the other one is the original strand of the parental DNA. 
  • After the separation of the DNA double strands Two different strands produce two new DNA strands one of the strands is continuous and the other one is broken in nature which becomes continuous after the effect of the “Ligase enzyme”(Peter et al. 2021).

Due to the development of the two new strands and one strand is new and the other strand is containing the parental strand this is known as “Semi-Conservative process”.

Role of DNA Polymerase 

The primary and the main role of the “Dna polymerase” is to replicate the genome order. This helps to carry the “Genetic Information” from one generation to the other generation. DNA polymerase alpha helps to synthesize the Primers in DNA replication. 

 1.6 Comparison between the structure of DNA and RNA

  • DNA and RNA have the different 5 carbon sugars. The DNA contains the deoxyribose sugar whereas the RNA has the only ribose sugar.
  • DNA consists of the double helical strand whereas RNA consists of the single helical strand (Lin et al. 2021).
  • DNA follows the Chargaff rules whereas the RNA does not follow the rule.
  • The base proteins of the DNA are adenine, thymine, GUanine and the CYtosine whereas in the RNA thymine is not present but the cytosine is p[resent as the nitrogen base.
  • DNA acts as the functional unit of heredity that passes the information from one gene to another. Whereas the RNA helps in the synthesis of the protein in the cell

2.1 Transcription process, including the role of messenger RNA and Enzymes

“Transcription” is the beginning of the protein synthesis process after the “replication”. In this process, the DNA sequence is converted into RNA, which is translated into the protein after this step. The unwinding of the DNA double helix is done before the beginning of this step. There are three steps in this process and the steps are

Transcription Initiation

In the initiation of this process the enzyme “RNA polymerase” binds with the DNA at t5he region of “Promoter” (Cramer, 2019). This promoter region helps to bind the RNA polymerase in the particular region of the DNA. In the prokaryotic cells, the promoter region is located between the downstream region “10 and -35.”

Elongation of process

The “Elongation” of the RNA strands is done by the “Addition of nucleotides”. The development of the RNA polymerase occurred according to the “template strand”. The development through the DNA template is done from the 3’ to 5’ direction (Lambert et al. 2018). The addition of the nucleotide is done to the 3’ end of the RNA by the enzyme RNA polymerase. RNA strands have “Uracil (U)” in the replacement with “Thymine (T)”.

Termination of Transcription

RNA polymerase transcribes the whole RNA strand until it reaches the Stop signal. The ending of the RNA synthesis is known as “Termination”. There are two major types of the termination process is involved in this process. The “Rho-dependent” termination process is dependent on the “Rho factor” which helped a lot to separate the DNA template from the newly synthesized RNA strand. The other termination process is “Rho-independent termination (Bushweller, 2019)”. The newly transcribed RNA strands detached from the DNA template from the “CG nucleotide rich sequence.”

The role of messenger RNA

  • mRNA can “Carry the protein synthesis sequence” from DNA.
  • The “three-base codon” of mRNA helps to bind the tRNA with it
  • After the attachment of tRNA and mRNA amino acid addition becomes starts.

Different enzymes in Transcription

  • “RNA polymerase” helps to bind the nucleotides to elongate the RNA strands.
  • “RNA polymerase I” is responsible for the [production of the rRNA (Bushweller, 2019).
  • “Rna Polymerase III” is responsible for the synthesis of the tRNA.

2.2 Description of the process Translation, including the role of m-RNA and t-RNA in This process

“Translation” is the last step of the “Central Dogma”. In this translation process, the enzymes decode the mRNA to synthesize the polypeptide chain from that mRNA. In the mRNA three nucleotides together create a codon which helps in the addition of the amino acids which is the backbone of the polypeptide chain (Kirkland et al. 2020). There are “61 codons are present” are present in an mRNA which is responsible for the synthesis of the polypeptide chain. There are three main steps are involved in this step and the steps are

Initiation

This is the first step of the translation process where the two subunits of “ribosomes” connect to the mRNA. After that tRNA attach to the mRNA with their “Receptor” region.

Elongation

This is the second step of the Translation Process. At the 5’end of the tRNA the amino acids got attached and the addition of the tRNAs on the mRNA helps to add the new amino acids at their terminal length as per the sequence of the Codons (Holtet al. 2019).

Termination

 The last step of protein synthesis is termination. The protein synthesis ends with the main three termination codons. “UAA, UAG, and UGA” are the termination codon that helps to detach the amino acid chain from the ending of the tRNA, and after the post-translational modification; this amino acid chain acts as protein (Florin, 2018).

2.3 Genetic Control of Protein Production In Prokaryotic as per the Lac Operon

“Lac operon” is one type of an operon, which is a combination of different genes with a promoter. The genes of the operon are associated with the synthesis of the protein.

Structure of lac Operon

The lac operon is made up of three structural genes “LacZ, LacY, and LacA”. All of these three genes are mainly transcribed as the mRNA, which is controlled by a “Promoter”.

Functions of the genes and control on Protein Synthesis

  • “LacZ” gene is responsible for the synthesis of the enzyme “Beta-galactosidase” which helps to cleave the disaccharide Lactose into “Glucose and Galactose”.
  • “LacY” is responsible for the synthesis of the “Beta-galactosidase permease”, which acts as a “transmembrane symporter (Browning et al. 2019).”
  • “LacA” is one type of “trans-acetylase”.

“The promoter” region is responsible for the RNA polymerase addition. The enzyme is responsible for transcription.

The “Operator” is the negative regulatory site bound with the “Lac Repressor” protein. This operator region is associated with the overlap situation with the promoter. During the binding period of the Lac Repressor “RNA polymerase” is not able to bind with the promoter as a result the transcription starts.

TheCAP Binding site” is positively “Regulatory site.” which is attached with the “Catabolite activator Protein”. During the binding period of this CAP protein, the structure helps in the promotion of Transcription (Browninget al. 2019). 

2.4 Effects of mutation on amino acid sequences of polypeptide and explanation of the results

Mutation represents the changes in the nucleotide sequences in the DNA as a result the amino acid chain becomes disturbed as a result the protein shows an abnormality in its function. There are mainly three types of Mutation that can be occurred in the DNA (Baugh et al. 2018). These three mutations are

  1. Base substitutions
  • Transition
  • Transversion
  • Silent
  • Missense
  1. Deletions
  2. Insertions

Effects of this mutation on amino acid sequences

The mutation in the DNA structure creates the mutation in the amino acid structure also. This alters the whole protein structure. Mutation in the amino acid sequence creates a “loss of function” in the protein. It also "decreases the workability of the protein." Overall, the mutation in the amino acid sequences creates an abnormality in the protein, which creates which is responsible for the different kinds of diseases in the human body (Sahaet al. 2020). “Alzheimer's disease and Parkinson's disease” are examples of the mutation in the protein. Overall, the negative effects of the mutation can be observed if it occurs in the protein.

3. Conclusion

 The whole topic is based on the concept of “Central Dogma”. From the DNA replication to the Translation, every step is included under this model. Every step is subdivided into three parts: “Initiation, Elongation, and Termination”. A huge amount of enzymes and factors are associated with these functions. This is the reason this essay is able to discuss the role of the enzymes associated with any step and the effect of that enzyme on that particular molecular activity. The last portion of the essay is focused on the synthesis of protein and the effect of Mutation on the protein synthesis which is associated with the different mutational; diseases.

Reference

Baugh, E.H., Ke, H., Levine, A.J., Bonneau, R.A. and Chan, C.S., 2018. Why are there hotspot mutations in the TP53 gene in human cancers?. Cell Death & Differentiation25(1), pp.154-160.

Browning, D.F., Godfrey, R.E., Richards, K.L., Robinson, C. and Busby, S.J., 2019. The exploitation of the Escherichia coli lac operon promoter for controlled recombinant protein production. Biochemical Society Transactions47(2), pp.755-763.

Bushweller, J.H., 2019. Targeting transcription factors in cancer—from undruggable to reality. Nature Reviews Cancer19(11), pp.611-624.

Cramer, P., 2019. Organization and regulation of gene transcription. Nature573(7772), pp.45-54.

Florin, S., 2018. Realia in translation. In Translation as social action (pp. 122-128). Routledge.

Holt, C.E., Martin, K.C. and Schuman, E.M., 2019. Local translation in neurons: visualization and function. Nature structural & molecular biology26(7), pp.557-566.

Kirkland, J.L. and Tchkonia, T., 2020. Senolytic drugs: from discovery to translation. Journal of internal medicine288(5), pp.518-536.

Lambert, S.A., Jolma, A., Campitelli, L.F., Das, P.K., Yin, Y., Albu, M., Chen, X., Taipale, J., Hughes, T.R. and Weirauch, M.T., 2018. The human transcription factors. Cell172(4), pp.650-665.

Saha, P., Banerjee, A.K., Tripathi, P.P., Srivastava, A.K. and Ray, U., 2020. A virus that has gone viral: amino acid mutation in S protein of Indian isolate of Coronavirus COVID-19 might impact receptor binding, and thus, infectivity. Bioscience reports40(5).

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