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a dna polymerase ** an enzyme that catalyzes the polymerization of deoxyribonucleotides into a dna strand.dna polymerases are best-known for their role in dna replication,in which the polymerase"reads"an intact dna strand as a template and uses it to synthesize the new strand.the newly-polymerized molecule ** complementary to the template strand and identical to the template's original partner strand.dna polymerases use a magnesium ion for catalytic activity.
dna polymerase can add free nucleotides to only the 3’end of the newly-forming strand.th** results in elongation of the new strand in a 5'-3' direction.no known dna polymerase ** able to begin a new chain(de novo).dna polymerase can add a nucleotide onto only a preex**ting 3'-oh group,and,therefore,needs a primer at which it can add the first nucleotide.primers cons**t of rna and dna bases with the first two bases always being rna,and are synthesized by another enzyme called primase.an enzyme known as a helicase ** required to unwind dna from a double-strand structure to a single-strand structure to facilitate replication of each strand cons**tent with the semiconservative model of dna replication.
error correction ** a property of some,but not all,dna polymerases.th** process corrects m**takes in newly-synthesized dna.when an incorrect base pair ** recognized,dna polymerase reverses its direction by one base pair of dna.the 3'->5' exonuclease activity of the enzyme allows the incorrect base pair to be exc**ed(th** activity ** known as proofreading).following base exc**ion,the polymerase can re-insert the correct base and replication can continue.
dna polymerases h**e highly-conserved structure,which means that their overall catalytic subunits vary,on a whole,very little from species to species.conserved structures usually indicate important,irreplicable functions of the cell,the maintenance of which provides evolutionary advantages.
some viruses also encode special dna polymerases,such as hepatit** b virus dna polymerase.these may selectively replicate viral dna through a variety of mechan**ms.retroviruses encode an unusual dna polymerase called reverse transcriptase,which ** an rna-dependent dna polymerase(rddp).it polymerizes dna from a template of rna.
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a polymerase(ec 2.7.7.6/7/19/48/49)** an enzyme whose central function ** associated with polymers of nucleic acids such as rna and dna.the primary function of a polymerase ** the polymerization of new dna or rna against an ex**ting dna or rna template in the processes of replication and transcription.in association with a cluster of other enzymes and proteins,they take nucleotides from solvent,and catalyse the synthes** of a polynucleotide sequence against a nucleotide template strand using base-pairing interactions.
it ** an accident of h**tory that the enzymes responsible for the catalytic production of other biopolymers are not also referred to as polymerases.
one particular polymerase,from the thermophilic bacterium,thermus aquaticus(taq)(pdb 1bgx,ec 2.7.7.7)** of vital commercial importance due to its use in the polymerase chain reaction,a widely-used technique of molecular biology.
other well-known polymerases include:
terminal deoxynucleotidyl transferase(tdt),which lends diversity to antibody he**y chains
reverse transcriptase,an enzyme used by rna retroviruses like hiv,which ** used to create a complementary strand to the preex**ting strand of viral rna before it can be integrated into the dna of the host cell.it ** also a major target for antiviral drugs.
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rna polymerase(rnap or rnapol)** an enzyme that produces rna.in cells,rnap ** needed for constructing rna chains from dna genes as templates,a process called transcription.rna polymerase enzymes are essential to life and are found in all organ**ms and many viruses.in chemical terms,rnap ** a nucleotidyl transferase that polymerizes ribonucleotides at the 3' end of an rna transcript.
control of the process of gene transcription affects patterns of gene expression and,thereby,allows a cell to adapt to a changing environment,perform specialized roles within an organ**m,and maintain basic metabolic processes necessary for survival.therefore,it ** hardly surpr**ing that the activity of rnap ** both complex and highly regulated.in escherichia coli bacteria,than 100 transcription factors h**e been identified,which modify the activity of rnap.
rnap can initiate transcription at specific dna sequences known as promoters.it then produces an rna chain,which ** complementary to the template dna strand.the process of adding nucleotides to the rna strand ** known as elongation;in eukaryotes,rnap can build chains as long as 2.4 million nucleosides(the full length of the dystrophin gene).rnap will preferentially release its rna transcript at specific dna sequences encoded at the end of genes known as terminators.
products of rnap include:
messenger rna(mrna)—template for the synthes** of proteins by ribosomes.
non-coding rna or"rna genes"—a broad class of genes that encode rna that ** not translated into protein.the most prominent examples of rna genes are transfer rna(trna)and ribosomal rna(rrna),both of which are involved in the process of translation.however,since the late 1990s,many new rna genes h**e been found,and thus rna genes may play a much significant role than previously thought.
transfer rna(trna)—transfers specific amino acids to growing polypeptide chains at the ribosomal site of protein synthes** during translation
ribosomal rna(rrna)—a component of ribosomes
micro rna—regulates gene activity
catalytic rna(ribozyme)—enzymatically active rna molecules
rnap accompl**hes de novo synthes**.it ** able to do th** because specific interactions with the initiating nucleotide hold rnap rigidly in place,facilitating chemical attack on the incoming nucleotide.such specific interactions explain why rnap prefers to start transcripts with atp(followed by gtp,utp,and then ctp).in contrast to dna polymerase,rnap includes helicase activity,therefore no separate enzyme ** needed to unwind dna.
binding and initiation
rna polymerase binding in prokaryotes involves the α subunit recognizing the upstream element(-40 to-70 base pairs)in dna,as well as the σ factor recognizing the-10 to-35 region.there are numerous σ factors that regulate gene expression.for example,σ70 ** expressed under normal conditions and allows rnap binding to house-keeping genes,while σ32 elicits rnap binding to heat-shock genes.
after binding to the dna,the rna polymerase switches from a closed complex to an open complex.th** change involves the separation of the dna strands to form an unwound section of dna of approximately 13 bp.ribonucleotides are base-paired to the template dna strand,according to watson-crick base-pairing interactions.supercoiling plays an important part in polymerase activity because of the unwinding and rewinding of dna.because regions of dna in front of rnap are unwound,there ** compensatory positive supercoils.regions behind rnap are rewound and negative supercoils are present.
elongation
transcription elongation involves the further addition of ribonucleotides and the change of the open complex to the transcriptional complex.rnap cannot start forming full length transcripts because of its strong binding to promoter.transcription at th** stage primarily results in short rna fragments of around 9 bp in a process known as abortive transcription.once the rnap starts forming longer transcripts it clears the promoter.at th** point,the-10 to-35 promoter region ** d**rupted,and the σ factor falls off rnap.th** allows the rest of the rnap complex to move forward,as the σ factor held the rnap complex in place.
the 17-bp transcriptional complex has an 8-bp dna-rna hybrid,that **,8 base-pairs involve the rna transcript bound to the dna template strand.as transcription progresses,ribonucleotides are added to the 3' end of the rna transcript and the rnap complex moves along the dna.although rnap does not seem to h**e the 3'exonuclease activity that characterizes the proofreading activity found in dna polymerase,there ** evidence of that rnap will halt at m**matched base-pairs and correct it.
the addition of ribonucleotides to the rna transcript has a very similar mechan**m to dna polymerization-it ** believed that these polymerases are evolutionarily related.aspartyl(asp)residues in the rnap will hold onto mg2+ions,which will,in turn,coordinate the phosphates of the ribonucleotides.the first mg2+will hold onto the α-phosphate of the ntp to be added.th** allows the nucleophilic attack of the 3'oh from the rna transcript,adding an additional ntp to the chain.the second mg2+will hold onto the pyrophosphate of the ntp.the overall reaction equation **:
(nmp)n+ntp->(nmp)n+1+ppi
termination
termination of rna transcription can be rho-independent or rho-dependent:
rho-independent transcription termination ** the termination of transcription without the aid of the rho protein.transcription of a palindromic region of dna causes the formation of a hairpin structure from the rna transcription looping and binding upon itself.th** hairpin structure ** often rich in g-c base-pairs,making it stable than the dna-rna hybrid itself.as a result,the 8bp dna-rna hybrid in the transcription complex shifts to a 4bp hybrid.these last 4 base-pairs are weak a-u base-pairs,and the entire rna transcript will fall off