Question

This topic's discussion focuses on the basic processes of how cells are able to do what they do--the central dogma of life. In order for cells to function effectively, they need to make proteins, which, as we learned way back in Topic 2 (Ch. 4) are responsible for doing all of the work inside of (and for) the cell (enzymes) and provide the necessary structure for cells to function (cytoskeleton, some signaling molecules, binding proteins, receptors, transporters, etc.). Each cell has all of the information the organism needs to make these proteins (in the form of genes on chromosomes--the DNA), although it only makes the proteins that it needs when it needs them. The processes of reading the DNA to make the RNA and reading the RNA to make the proteins are together known as the central dogma (and sometimes DNA replication is included since it is also required for living organisms to make new cells). Your discussion postings this week should focus on some aspect of the central dogma and provide more detail for your fellow classmates. For example, one of the parts and how it is controlled, where it occurs, what can go wrong, or how they're connected. Along with the responses, this discussion should give you a much better understanding of how life actually works! Do not use other solutions. I need originality responses as well as IN TEXT CITATIONS AND A WORKS CITED REFERENCE. Please use 2 outside references.Thank you

Answer 1

Central dogma includes processes like replication, transcription and translation.

Replication of DNA is accomplished by the polymerisation of deoxyribonucleotides into new DNA strands, each synthesized on the template of one of the strands of a pre-existing DNA duplex. Nuclear DNA is replicated during the S phase of the cell cylce. In the daughter cell, one strand is derived from the mother cell; while the other strand is newly synthesized, the process called semi-conservative replication.

Details: Replication can be semiconservative, bidirectional or semidiscontinuous.

The DNA replication starts with the recognition of the site of origin of replication called replication fork. DNA replication needs participation of more than 20 enzymes and proteins called DNA replicase system or replisomes. Unwinding of DNa is brought about by Rep protein, DNA helicase II, and helix-destabilising / single stranded binding protein (SSBprotein). The protein A or DnaA binds at specific sites of origin and opens the duplex. The toisomerase enzymes (also called nicking-closing enzymes / DNA swivelases and DNA gyrase) nick the strands of the DNA and catalyse the uncoiling and supercoiling of the duplex. The polymerisation of the new strand by DNA polymerases takes place from 5' to 3' direction. Thus the template is read in 3' to 5' direction.

How does a cell know that there is a problem with replication?

dsDNA is intrinsically more stable than ssDNA, although the latter can be stabilized and protected by single-strand DNA binding proteins. Researchers have recently discovered that, in eukaryotes, the replication protein A (RPA) is a form of red flag in the cell: when RPA is coating long strands of ssDNA, this signals a checkpoint. This concept underscores an important feature: presence of ssDNA signals that "something is wrong" and this also holds true for other phases of the cell cycle. In other words, whether ssDNA is created during replication, or outside of S phase, it will always trigger the checkpoint to correct the errors. Scientists don't know the entire answer, but they have learned that RPA-coated ssDNA attracts a specific protein with a complicated name: the ataxia telangiectasia mutated and Rad3 related kinase, also known as ATR (Cimprich & Cortez 2008). ATR associates with RPA and activates its intrinsic kinase activity. This starts activity that temporarily halts S phase progression. Therefore, ATR is also known as the S phase "checkpoint kinase." ."[Ref: Sapna-Das Bradoo DNA replication and checkpoint control in S phase, 2010, Nature education].

Next process is the transcription of DNA into RNA. It is the synthesis of an RNA molecule on a template DNA strand by the polymerization of ribonucleotides. The RNA molecule initially synthesized is called a primary transcript which undergoes various post-transcriptional modifications to change into the final active form. There are 3 stages of transcription: Initiation, elongation and termination.

Initiation: Eukaryotic RNA polymerases bind to the promoters of specific genesfollowed by a local unwinding of DNA duplex, formation of a transcription bubble around the transcription initiation site. A dinucleotide RNA transcript is formed by hydrogen bonding of two ribonucleotides to the first two nucleotides in the template DNA in the transcription site.RNA plymerase I trnacribes DNA into rRNA. RNA polymerase II transcribes many mRNA genes in all cells.

A promoter occuring at the upstream from its transcription initaiton site in the form of GC box consisting of highly conserved base sequences like GGGCGG or some of its complements, OR TATA box consisting of base seauence like TATATAA. Another less conserved promoter sequence is CCAAT box. The more upstream GC box and CCAAT boxes offer inital binding sites for transcriptional factors and polymerase II while TATA box fixes the specific initaion site of the relevant gene.

Elongation: As the polymerase is translocated progressively along the coding strand in the 3' to 5' direction, the transcription bubble also moves ahead in the same direction to expose the progressively downstream bases of the transcription region. After this, the DNA strands rewind behind the polymerase to reinstate the original DNA duplex with the 5'-ppptail of the RNA transcript dangling out from it. Adding new ribonucleotide to the 3'-OH terminus of the already laid RNA transcript, it is getting elongated. A gene is thus transcribed simultaneously by many RNA polymerase molecules into as many moleucles of RNA transcripts.

Termination: This can be recognised by a termination protein, rho factor. When it attaches to the DNA, plymerase can not move further and the enzyme dissociates from DNA, thus consequently the newly formed mRNA is released. In the case Rho independent termination, mRNa produced will form intrachain base pairin to make a hairpin structure. This obstructs further movement of polymerase , thus enzyme and mRNA are released. [Ref: Cliffnotes, University of Nottingham]

Translation is the final process in the central dogma. It is the synthesis of peptides under the direction of specific genetic codes of mRNA. Ribosomes and tRNAs participate in translating the message of the genetic code into the aminoacid sequence of the nascent peptide. Amino acids are polymerized sequentially into a peptide starting from its N-termuinal end and following the 5' to 3' sequnece in the coding mRNA.

How it is controlled?

The regulatory mechanism is primarily targeted on the control of ribosome recruitment on the initiation codon, but can also involve modulation of the elongation or termination of protein synthesis. Cap-dependent translational control occurs mainly during the initiation step, involving eukaryotic initiation factors (eIFs) and accessory proteins.. [Ref: Nahum Sonenberg, Regulation of translational initiation in Eukaryotes, Mechanisms and Biological Targets, 2013]

Textbook Ref: 1. Textbook of Biochemistry by Vasudevan and Sreekumari
2. Textbook of Biochemistry by Debjyothi Das