Lecture #9

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Transcription is __ to __ on a template that is __ to __

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Prokaryotic & Eukaryotic Transcription

183 Terms

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Transcription is __ to __ on a template that is __ to __

5’ to 3’, 3’ to 5’

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coding strand (nontemplate strand)

the DNA strand that has the same sequence as the mRNA and is related by the genetic code to the protein sequence that it represents

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RNA Polymerase

An enzyme that synthesizes RNA using a DNA template (formally described as a DNA-dependent RNA polymerase)

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RNA sequence is complementary to ________ strand and ________ to coding strand.

template, coding

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Promoter

a region of DNA where RNA polymerase binds to initiate transcription

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Startpoint

The position on DNA corresponding to the first base incorporated into RNA

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Terminator

A sequence of DNA that causes RNA polymerase to terminate transcription

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Transcription Unit

The sequence between sites of initiation and terminations by RNA polymerase; it may include more than one gene

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Promoter and terminators define the

unit

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Upstream

sequences in the opposite direction from expression

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Downstream

sequences proceeding farther in the direction of expression within the transcription unit

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primary transcript

the original unmodified RNA product corresponding to a transcription unit

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Transcription occurs by base pairing in a

“bubble” of unpaired DNA

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RNA polymerase separates the two strands of DNA in a transient “bubble” and uses

one strand as a template to direct synthesis of a complementary sequence of RNA

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The bubble is 12 to 14 bp, and the RNA-DNA hybrid within the bubble is

8 to 9 bp

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RNA synthesis occurs in the

transcription bubble

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17

RNA polymerase surrounds

the bubble

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18

Transcription has ____ stages

three

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19

RNA polymerase binds to

a promoter site on DNA to form a closed complex

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RNA polymerase initiates

transcription (initiation) after opening the DNA duplex to form a transcription bubble (the open complex)

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RNA polymerase catalyzes

transcription

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During elongation

the transcription bubble moves along DNA and the RNA chain is extended in the 5’ to 3’ direction by adding nucleotides to the 3’ end.

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Transcription stops (termination) and the DNA duplex reforms when

RNA polymerase dissociates at a terminator site

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Bacterial RNA Polymerase consists of

multiple subunits

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25

Holoenzyme

The RNA polymerase form that is competent to initiate transcription. It consists of the five subunits of the core enzyme and sigma factor.

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RNA polymerase has _ types of subunit

4

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Catalysis derives from the

B and B’ subunits

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CTD (C-terminal domain)

The domain of RNA polymerase that is involved in stimulating transcription by contact with regulatory proteins

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RNA Polymerase holoenzyme consists of

the core enzyme and sigma factor

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30

Bacterial RNA polymerase can be divided into

the a2BB’w core enzyme that catalyzes transcription and the sigma subunit that is required only for initiation

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31

Sigma factor changes the DNA-bidning properties of RNA polymerase so that

its affinity for general DNA is reduced and its affinity for promoter is increased

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Sigma factor controls

specificity

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33

The rate at which RNA polymerase binds to promoters can be too fast to be accounted for by

simple diffusion

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34

RNA polymerase binds to

random sites on DNA and exchanges them with other sequences until a promoter is found.

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35

Proposed mechanisms for how RNA polymerase finds a promoter

  • sliding

  • intrasegment transfer “hopping”

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36

The holoenzyme goes through

transitions in the process of recognizing and escaping from promoters

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Ternary complex

The complex in initiation of transcription that consists of RNA polymerase and DNA as well as a dinucleotide that represents the first two bases in the RNA product

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There may be a cycle of ______ __________ before the enzyme moves to the next phase

abortive initiations

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Sigma factor is usually released from RNS polymerase when the

nascent RNA chain reaches ~10 bases in length

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40

Sigma factor controls

binding to DNA by recognizing specific sequences in promoters

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conserved sequence

sequences in which many examples of a particular nucleic acid or protein are compared and the same individual bases or amino acids are always found at particular locations

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A promoter is defined by the presence of short _________ _________ at specific locations

consensus sequences

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43

The promoter consensus sequences usually consist of

a purine at the startpoint, a hexamer with a sequence close to TATAAT centered at ~ -10 (-10 element or TATA box), and another hexamer with a sequence similar to TTGACA at ~ -35 (-35 element)

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44

Individual promoters usually differ from the consensus at

one or more positions

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Promoter efficiency can be affected by

additional elements as well; it can be increased of decreased by mutation

  • UP element

  • Down mutations

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46

UP element

A sequence in bacteria adjacent to the promoter, upstream of the -35 element, that enhances transcription

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47

DNA elements and RNA polymerase modules contributing to promoter recognition by

sigma factor

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Down mutations to decrease promoter efficiency usually

decrease conformance to the consensus sequences, whereas up mutations have the opposite effect

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Up mutations

have the opposite effect of down mutations, increases conformance to the consensus sequences

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50

Mutations in the -35 sequence can affect

initial binding of RNA polymerase

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Mutations in the -10 sequence can affect

binding or the melting reaction that converts a closed to an open complex

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52

Footprinting

a technique for identifying the site on DNA bound by some protein by virtue of the protection of bonds in this region against attack by nucleases

  • a high resolution method for characterizing RNA polymerase-Promoter and DNA-Protien interactions in general

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A protein protects a series of bonds against nuclease attack

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54

The consensus sequences at -35 and -10 provide

most of the contact points for RNA polymerase in the promoter.

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The point of contact lie primarily on

one face of the DNA

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56

RNA polymerase contacts

one face of DNA

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57

Interactions between sigma factors and Core RNA polymerase change during

promoter escape

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A domain in sigma occupies

the RNA exit channel and must be displaced to accommodate RNA synthesis

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Abortive initiations usually occur

before the enzyme forms a true elongation complex

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Sigma factor is usually released from RNA polymerase by

the time the nascent RNA chain reaches ~10 nt in length

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A model for enzyme movement is suggested by the

crystal structure

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DNA moves through a channel in RNA polymerase and

makes a sharp turn at the active site

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Changes in conformations of certain flexible modules within the enzyme control

the entry of nucleotides to the active site

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DNA is forced to make a turn at the active site by

a wall of protein

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66

Bacterial RNA polymerase terminates at

discrete sites

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There are two classes of terminators

  • intrinsic terminators

  • rho-dependent terminators

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intrinsic terminators

those recognized solely by RNA polymerase itself without the requirement for any cellular factors

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rho-dependent terminators

requires a cellular protein called rho

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The DNA sequences required for termination are located

upstream of the terminator sequence

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Intrinsic termination requires

recognition of a terminator sequence in DNA that codes for a hairpin structure in the RNA product

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The signals for termination lie mostly within sequences

already transcribed by RNA polymerase

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Termination relies on

scrutiny of the template and/or the RNA product that the polymerase is transcribing

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An intrinsic terminator has two features

Single-stranded U-run & G-C-rich region in stem

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Readthrough

it occurs at transcription or translation when RNA polymerase or the ribosome, respectively, ignores a termination signal because of a mutation of the template or the behavior of an accessory factor

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Antitermination

A mechanism of transcriptional control in which termination is prevented at a specific terminator site, allowing RNA polymerase to read into the genes beyond it.

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Rho factor is a protein that

binds to nascent RNA and tracks along the RNA to interact with RNA polymerase and release it from the elongation complex

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rut

an acronym for rho utilization site, the sequence of RNA that is recognized by the rho termination factor

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Rho terminates transcription

  1. RNA polymerase transcribes DNA

  2. Rho attaches to rut site on RNA

  3. Rho translocating along RNA

  4. RNA polymerase pauses at hair pin and rho catches up

  5. Rho unwinds DNA-RNA hybrid

  6. Termination: all components released

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Polarity

The effect of a mutation in one gene in influencing the expression (at transcription or translation) of subsequent genes in the same transcription unit.

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Antitermination complex

Proteins that allow RNA polymerase to transcribe through certain terminator sites

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Rho can terminate when

a nonsense mutation removes ribosomes

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Wilt Type transcription

  1. Ribosomes pack mRNA behind RNA polymerase

  2. Ribosomes impede rho attachment and/or movement

  3. Rho attaches but ribosomes impede its movement

  4. Transcription continues

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Nonsense mutant transcription

  1. Ribosomes pack mRNA behind RNA polymerase

  2. Ribosomes dissociate at mutation

  3. Rho obtains access to RNA polymerase

  4. Transcription terminates prematurely

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85

Supercoiling is

an important feature of transcription

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86

Negative supercoiling

increases the efficient of some promoters by assisting the melting reaction

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87

Transcription generates

positive supercoils ahead of the enzyme and negative supercoils behind it. and these must be removed by gyrase and topoisomerase

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Transcription changes

DNA structure

Negative supercoils → Transcribing DNA → Overwound (Positive supercoils)

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Topoisomerase relaxes

negative supercoils

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Gyrase introduces

positive supercoils

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91

Competition for sigma factors can

regulate initiation

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92

E.coli has _______ sigma factors

seven, each of which causes RNA polymerase to initiate at a set of promoters defined by specific -35 and -10 sequences

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93

Sigma factor controls

promoter recognition

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94

Holoenzyme with σ⁷⁰ recognizes one set of promoters

Substitution of sigma factor causes enzyme to recognize a different set of promoters

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95

The activities of the different sigma factors are regulated by

different mechanisms

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anti-sigma factor

a protein that binds to a sigma factor to inhibit its ability to utilize specific promoters

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97

Heat Shock response

a set of loci that is activated in response to an increase in temperature that causes proteins to denature (and other abuses to the cell)

  • all organisms have this response

  • the gene products usually include chaperones that act on denatured proteins

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98

sigma factors may be

organized into cascades

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99

A cascade of sigma factors is created

when one sigma factor is required to transcribe the gene coding for the next sigma factor

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The early genes of phage SPO1 are transcribed by

host RNA polymerase

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