Involvement of Proteins in DNA Function

Describe the following points..

Involvement of proteins in DNA function

Involvement of protein structure in RNA function

The role of the protein structure in the function of the DNA and the RNA has been discussed in the report. Protein plays an important role in the damage and repair of DNA. It has important role in the maintenance of the helical structure of DNA. The role of the various proteins in the maintenance of DNA and RNA structure and function has been discussed.

Living organisms are dependent on three large types of molecules to continue their biological functions. The large molecules are RNA, DNA and protein. The simple summary of the three macromolecules will be that DNA produces RNA and RNA produces protein. It is important to analyze the involvement of protein in the function of the DNA and RNA as it is the basic molecule necessary for all the biological functions of the body (Moore and Steitz, 2010). DNA is the macro molecule that is responsible for encoding the instructions that is required for the reproduction of the living organism. Proteins are responsible for catalyzing the biochemical reactions. It provides food and energy that is required by every living organism. The role of RNA is multifunctional but the main responsibility of RNA is to make protein. The instructions for synthesis of protein are encoded by the DNA. Thus it is important to analyze the importance of protein structure in the functioning of DNA and RNA since all the three macromolecules are interconnected to one another (Boehr, Nussinov and Wright, 2009).

Proteins are involved in the various functions of DNA. DNA is the basic macromolecule of all biological organisms. The damage and repair of the DNA structure is done by chromatin. The structure of chromatin is an important factor for the determination of the efficiency and the mechanism of DNA repair. The phosphodiester backbone of the DNA is broken as a result of its exposure to physical and chemical assaults like certain genotoxic agents or alkylating agents. The recognition of the damaged DNA is essential as they cannot participate in the process of replication and has to be removed. The lesions in the DNA are recognized by proteins, for e.g., XPA-RPA, XPC-HR23B and XPE protein complexes. The eukaryotic cells are packed with a nucleo-protein complex known as chromatin. The fundamental unit of chromatin is the nucleosome. It comprises of 146 base pairs of DNA(Ursic, 2004). They are wrapped around the octamer that is made of core histones. Histone  proteins plays a major role both structural and functional in maintenance of the transition between active and inactive states of chromatin. The histone protein forms a octamer with eight complex of protein and a nucleosome core particle at the centre. There are two copies of each of four histone proteins (H3, H$, H2A and H2B). It has been identified that there is interrelationship between the chromatin and DNA repair. The cellular proteins that are involved in the process of repair of the damage containing DNA are known as DDB (Rohs et al., 2009). There are other forms of chromatin proteins and transcription factors that which is known as the “non repair proteins”. The chromatin functions are controlled by the High mobility group (HMG) proteins that are visible in the cells of the eukaryotes. The HMG proteins serve as the structural component of the chromatin. The HMG box proteins bind with DNA and assist its various functions of bending, looping, super coiling and unwinding (Xin ,Taudte , Limbach and Zitomer , 2000)

Involvement of Protein Structure in RNA Function

A single gene can perform multiple functions as there are several proteins that bind both DNA and RNA. Such DNA-RNA proteins are known as DNA-RNA binding proteins (DRBPs). These proteins have unique functional characteristics whichstem from their unique structural features. The DBRPs regulate various cellular process of the body. They control the process of transcription, translation, licensing of the genes and micro RNA biogenesis and the maintenance of telomere (Wright and Dyson, 1999).

The DNA binding proteins are single stranded in nature. They assist in nuclear metabolism of all organisms including bacteria. The two proteins namely ssDNA and replication protein (RPA) play an essential role in the metabolism of DNA. They bind to DNA and keep it unfolded andplay a role in the assembly and disassembly of numerous protein complexes during replication of DNA (Zou et al. , 2006). The role of RPA in the process of repair of DNA has become evident. The involvement of the particular sequences of DNA by proteins is dependent on mechanisms that are generally of two types. The hydrogen bonds are formed with the help of the unique bases. It is formed in the major groove and there are the proteins that prevent the deformation of the DNA helix. The binding of the residues of arginine in the grooves is a mode which is used for the recognising the protein DNA. The main example of this binding is seen in the nucleosome core particle (Puttaraju, 2001). They help in the detection of the variations in the DNA shape with the electrostatic phenomena helps the protein to use the information that is present in the minor grooves (Lee and Chung, 2001).

Source: www.dandrealab.org

The process of repair of DNA damage has been discussed in the diagram. The FA/BRCA pathway is followed for the process of DNA damage repair. The activation of the DNA duplex by the complex interaction of the enzymes has been discussed (Fall et al., 2004).

The chaperones act as very sophisticated machine for protein that provides assessment in the unfolding and folding of the molecules of RNA. The chaperones help the molecules of RNA to reach to their usual 3 dimensional structure. It is seen that RNA has the general tendency of misfolding the proteins.The activity of chaperones is very important and highly advantageous to the highly dependent function of the RNA (Tompa, 2005).

The proteins and the RNA interact with one another to perform diverse functions. Unique tRNAs are attached to the aminoacyl t-RNA synthetases for the translation of the codes related to genes in the production of the proteins. There is interaction between the protein and the RNA when they form complex structural elements which are secondary such as loops, bulges and stem. The RNA binding sites of the proteins that are involved in the synthesis of the proteins are 1.5 times the mass of the RNA complexes. They are twice the size of the viral complexes. These comprises of two structural domains (Fu, 2014). One has interaction with the acceptor stem and the other has interaction with the anticodon part of the RNA. This has separated the recognition site of the RNA (Widlak, Pietrowska and Lanuszewska, 2005). The protein binding with the RNA maintains the structural cohesion of the protein structure.

Role of Protein in DNA and RNA Function

The expression of the genes in Eukaryotes involves a complex interaction between the transcripts which are primary that are involved in the process of maturation of the transcripts which includes slicing, transcription and termination. There are several proteins that form part of the transcriptosome that is associated with the domain of C- terminal. C- terminal is the end of the amino acid chain. During the translation of protein from mRNA it creates the c-terminus. It is the biggest subunit of RNA of the eukaryotes polymerase II. These proteins act as a bridge between the RNA and the polymerase. The role of the proteins in the processing of the RNA cannot be ignored.

One of the major roles of RNA is to facilitate the translation of the DNA molecule into the RNA molecule. This takes place with a series of biochemical reactions that enable the translation of the RNA into protein. hnRNA is the direct duplicate of the DNA. There are introns and extrons which are present in the coding and the non-coding regions of the nucleotides. Post transcriptional processing occurs in the hnRNA that involves the removal of the introns and there is addition of the adenines. They are added to the single stranded molecule of RNA. The mRNA is found to attach itself to the ribosome and allows it to initiate thesynthesis of protein. There is the location of another type of RNA in the protein in the ribosome which is known as the tRNA. The matching of the specific codon occurs by the amino acid and the process begins at the specific sites of the mRNA. There are certain chemical reactions that are transferred to the growing polypeptide by the interactions of the chemicals for the production of the protein. The ribosomes that are involved in the conversion of the mRNA into proteins are found to be large and complex (Bader et al., 2001).

Source : www.cell.com

The process of transcription and translation has been shown in the diagram. The formation of single strand of RNA from double stranded DNA has been discussed. The protein formation has been shown (Goodman, 2008).

Conclusion

The report has highlighted the involvement of structure of the protein the functions of DNA and RNA. It is evident from the report that protein plays an important role in the repair of DNA. There is involvement of chromatin in the repair of the DNA. The functions of the proteins are controlled by the HMG group of proteins. They assist in repair of the damaged DNA so that the replication of the DNA is not hampered. There are also special DNA-RNA binding proteins that are involved in the process of assembly of the protein complexes in the DNA. Protein structure has important role in the functions of RNA. Protein is synthesized by the process of translation of RNA. The synthesis of the protein is an important aspect as the macro molecules are involved in several functions. The proteins are involved in the repair of the double stranded DNA and the single stranded RNA. The folding of the protein molecules is assisted by the chaperone protein machines. They function in the mechanism of folding and unfolding of the RNA.Therefore protein structure plays a major role in the function of DNA and RNA. DNA damage and repair is done by the proteins. The RNA function is maintained by protein.

References

Xin, H., Taudte, S., Kallenbach, N. R., Limbach, M. P., and  Zitomer, R. S. (2000). DNA binding by single HMG box model proteins. Nucleic acids research,28(20), 4044-4050.

Zou, Y., Liu, Y., Wu, X., & Shell, S. M. (2006). Functions of human replication protein A (RPA): from DNA replication to DNA damage and stress responses.Journal of cellular physiology, 208(2), 267-273.

Bader, A., Schneider, M., Bister, K. and Hartl, M. (2001). TOJ3, a target of the v-Jun transcription factor, encodes a protein with transforming activity related to human microspherule protein 1 (MCRS1). Oncogene, 20(51), pp.7524-7535.

Boehr, D., Nussinov, R. and Wright, P. (2009). Erratum: The role of dynamic conformational ensembles in biomolecular recognition. Nature Chemical Biology, 5(12), pp.954-954.

Fu, X. (2014). Potential protein-encoded synthesis of DNA and RNA. Hypothesis, 12(1).

Lee, J. and Chung, J. (2001). Diverse functions of BRCA1 in the DNA damage response. ERM, 3(15).

microRNAs control the function of telomeres in cancer. (2014). RNA & DISEASE.

Moore, P. and Steitz, T. (2010). The Roles of RNA in the Synthesis of Protein. Cold Spring Harbor Perspectives in Biology, 3(11), pp.a003780-a003780.

Puttaraju, M. (2001). Messenger RNA Repair and Restoration of Protein Function by Spliceosome-Mediated RNA Trans-Splicing. Molecular Therapy, 4(2), pp.105-114.

Rohs, R., West, S., Sosinsky, A., Liu, P., Mann, R. and Honig, B. (2009). The role of DNA shape in protein–DNA recognition. Nature, 461(7268), pp.1248-1253.

Tompa, P. (2005). The interplay between structure and function in intrinsically unstructured proteins. FEBS letters, 579(15), 3346-3354.

Ursic, D. (2004). Multiple protein/protein and protein/RNA interactions suggest roles for yeast DNA/RNA helicase Sen1p in transcription, transcription-coupled DNA repair and RNA processing. Nucleic Acids Research, 32(8), pp.2441-2452.

Widlak, P., Pietrowska, M. and Lanuszewska, J. (2005). The role of chromatin proteins in DNA damage recognition and repair Mini-review. Histochemistry and Cell Biology, 125(1-2), pp.119-126.

Wright, P. and Dyson, H. (1999). Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. Journal of Molecular Biology, 293(2), pp.321-331.