2: DNA Polymerase, RNA Polymerases, Transcription
- Page ID
- 7752
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)Compare and contrast bacterial DNA polymerases and RNA polymerases
Note: ss=single strand ds=double strand P=phosphate
Overview:
DNA polymerases synthesize complementary DNA using a DNA template/guide
___________________DNA
E.g., ssDNA template base sequence: A T A G G C
Complementary DNA sequence T A T C C G DNA
synthesized by DNA polymerase
RNA polymerases synthesize complementary RNA sequences using DNA as a template/guide
___________________DNA
E.g., ssDNA template base sequence: A T A G G C
Complementary RNA sequence U A U C C G RNA
synthesized by RNA polymerase
Synthesis of DNA and RNA require input of energy, both ATP and charged precursors (see below)
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DNA Polymerase RNA Polymerase
Template/guide ss DNA ssDNA
Synthesize complementary DNA complementary RNA
Charged precursors deoxyadenosine tri-P= dATP adenosine tri-P= ATP
deoxythymidine tri-P=dTTP uridine tri-P=UTP
deoxycytodine tri-P= dCTP cytodine tri-P=CTP
deoxyguanosine tri-P=dGTP guanosine tri-P=GTP
primer required? Yes No
proofreading/editing? Yes* No
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*DNA polymerase proofreading/editting
Polymerases have a ”normal” or “intrinsic” mistake rate of approximately
10 -4 – 10 -5 nucleotides (this means the polymerases introduce the incorrect nucleotide every 10,000 to 100, 000 nucleotides). DNA polymerases have the ability to “proofread and edit” their mistakes. If they introduce the wrong nucleotide, they can remove or “excise” the wrong nucleotide and try again to make a correct match. This reduces the mistake rate of DNA polymerases to approximately 10-9 – 10 -10 (or only one incorrect nucleotide every 1,000,000,000 – 10,000,000,000 nucleotides). RNA polymerase cannot proofread or edit their work so RNA polymerase make many mistakes (one reason many RNA viruses, for example HIV, mutate so rapidly…..more later)
Transcription Prokaryotic repeated section
Review flow of information in cell
DNA--------> RNA ---------> Protein
replication transcription translation
I. Genetic Code: one to one relationship between specific codon (specific 3 base sequence) and an amino acid
II. Transcription: use of DNA as template/guide to synthesize complementary RNA. DNA info is rewritten in RNA sequence.
A. First step in gene expression
B. Products of transcription
1. messenger RNA=mRNA: will be translated into specific amino acid sequence of a protein
2. transfer RNA=tRNA: actual “translator” molecule, recognizes both a specific codon and specific amino acid
3. ribosomal RNA=rRNA: combined with ribosomal proteins, will form the ribosome, the “workbench” at which mRNA is translated into a specific amino acid sequence/polypeptide/protein
III. Promoters and RNA polymerases
A. Promoters: specific DNA sequences which signal the “start” points for gene transcription. Sigma factor/subunit of RNA polymerase binds to promoters to initiate transcription
B. RNA polymerases: enzyme complex which recognizes DNA promoters, binds to promoter and synthesizes complementary RNA copy using DNA as template/guide
E. coli RNA Polymerase: 2 subunits, sigma subunit and core
a. sigma subunit/factor= “brains” of RNA polymerase. Travels along DNA until it reaches a promoter, binds promoter
b. core subunit: binds to sigma attached at promoter. “Workhorse” of RNA polymerase, carries out actual RNA synthesis. Requires activated precursors and template strand, DOES NOT REQUIRE PRIMER (compare to DNA Polymerase). Synthesizes RNA in 5’ -to->3’ , similar to DNA polymerase. No proofreading ability therefore will make more mistakes than DNA Polymerase
c. sigma subunit will drop off after the first few ribonucleotides have been linked together, core continues alone. Note: core would start transcription randomly of DNA without direction of sigma subunit. Polycistronic mRNA (prok. only)
IV. Termination of transcription
terminators: DNA sequences which signal transcription stop signals. RNA polymerase releases DNA when transcription terminator sequence encountered