ecclesiastes 3:1

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©2000 Timothy G. Standish Ecclesiastes 3:1 1 To every thing there is a season, and a time to every purpose under the heaven:

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Ecclesiastes 3:1 1 To every thing there is a season, and a time to every purpose under the heaven:. Transcription: Concentrating on Prokaryotes. Timothy G. Standish, Ph. D. All Genes Can’t be Expressed At The Same Time. - PowerPoint PPT Presentation

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Page 1: Ecclesiastes 3:1

©2000 Timothy G. Standish

Ecclesiastes 3:1

1 To every thing there is a season, and a time to every purpose under the heaven:

Page 2: Ecclesiastes 3:1

©2000 Timothy G. Standish

Transcription:Transcription:Concentrating on ProkaryotesConcentrating on Prokaryotes

Timothy G. Standish, Ph. D.

Page 3: Ecclesiastes 3:1

©2000 Timothy G. Standish

All Genes Can’t be Expressed All Genes Can’t be Expressed At The Same TimeAt The Same Time

Some gene products are needed by all cells all the time. These constitutive genes are expressed by all cells.

Other genes are only needed by certain cells or at specific times, expression of these inducible genes is tightly controlled in most cells.

For example, pancreatic cells make insulin by expressing the insulin gene. If neurons expressed insulin, problems would result.

Page 4: Ecclesiastes 3:1

©2000 Timothy G. Standish

Logical Expression Control PointsLogical Expression Control Points DNA packaging Transcription RNA processing mRNA Export mRNA masking/unmasking and/or

modification mRNA degradation Translation Protein modification Protein transport Protein degradation

Increasing costIncreasing cost

The logical place to control

expression is before the

gene is transcribed

The logical place to control

expression is before the

gene is transcribed

Page 5: Ecclesiastes 3:1

mRNA

Transcription

IntroductionIntroduction

The Central Dogma The Central Dogma of Molecular Biologyof Molecular Biology

Cell

Polypeptide(protein)

TranslationRibosome

Reverse transcription DNA

Page 6: Ecclesiastes 3:1

©2000 Timothy G. Standish

Stages of TranscriptionStages of Transcription Transcription can be logically divided

into four distinct stages:1. Template recognition2. Initiation3. Elongation4. Termination Each stage may participate in

regulation, but template recognition and termination appear to be major players

Page 7: Ecclesiastes 3:1

©2000 Timothy G. Standish

General Model For TranscriptionGeneral Model For Transcription

RNA Polymerase

Core Enzyme

Holoenzyme

Page 8: Ecclesiastes 3:1

©2000 Timothy G. Standish

General Model For TranscriptionGeneral Model For Transcription

Page 9: Ecclesiastes 3:1

©2000 Timothy G. Standish

General Model For TranscriptionGeneral Model For Transcription

Page 10: Ecclesiastes 3:1

©2000 Timothy G. Standish

General Model For TranscriptionGeneral Model For Transcription

Page 11: Ecclesiastes 3:1

©2000 Timothy G. Standish

NusA

General Model For TranscriptionGeneral Model For Transcription

Top-Isomerase

IGyrase

Page 12: Ecclesiastes 3:1

©2000 Timothy G. Standish

NusA

General Model For TranscriptionGeneral Model For Transcription

Top-Isomerase

IGyrase

Ribosome

Ribosome

Exo-nuclease

Page 13: Ecclesiastes 3:1

©2000 Timothy G. Standish

Ribosome

Ribosome

NusA

General Model For TranscriptionGeneral Model For Transcription

Exo-nuclease

Page 14: Ecclesiastes 3:1

©2000 Timothy G. Standish

Ribosome

NusA

General Model For TranscriptionGeneral Model For Transcription

Exo-nuclease

Page 15: Ecclesiastes 3:1

©2000 Timothy G. Standish

Ribosome

NusA

General Model For TranscriptionGeneral Model For Transcription

Exo-nuclease

Page 16: Ecclesiastes 3:1

©2000 Timothy G. Standish

NusA

General Model For TranscriptionGeneral Model For Transcription

Exo-nuclease

Page 17: Ecclesiastes 3:1

©2000 Timothy G. Standish

NusA

General Model For TranscriptionGeneral Model For Transcription

Exo-nuclease

Page 18: Ecclesiastes 3:1

©2000 Timothy G. Standish

NusA

General Model For TranscriptionGeneral Model For Transcription

Exo-nuclease

Page 19: Ecclesiastes 3:1

©2000 Timothy G. Standish

NusA

General Model For TranscriptionGeneral Model For Transcription

Page 20: Ecclesiastes 3:1

©2000 Timothy G. Standish

RNA PolymeraseRNA Polymerase RNA Polymerase is a spectacular

enzyme; it performs the following functions:

1. Recognition of the promoter region2. Melting of DNA (Helicase +

Topisomerase)3. RNA Priming (Primase)4. RNA Polymerization5. Recognition of terminator sequence

Page 21: Ecclesiastes 3:1

©2000 Timothy G. Standish

Prokaryotic Transcription InitiationProkaryotic Transcription Initiation The subunit of prokaryotic RNA

polymerase is necessary for promoter recognition and binding of RNA polymerase to the promotor

Different subunits allow recognition of different types of promoters; thus the type of genes transcribed can be modulated by altering the types of subunits which attach to RNA polymerase

Page 22: Ecclesiastes 3:1

©2000 Timothy G. Standish

Prokaryotic Transcription InitiationProkaryotic Transcription Initiation

Constitutive GeneHeat Shock GeneP1 P2

Different promoters

RNAPol.

Page 23: Ecclesiastes 3:1

©2000 Timothy G. Standish

Prokaryotic Transcription InitiationProkaryotic Transcription Initiation

Constitutive GeneHeat Shock Gene P2P1

Different promoters

RNAPol.

Page 24: Ecclesiastes 3:1

©2000 Timothy G. Standish

Transcription TerminationTranscription TerminationThere are two types of termination: Rho dependent requires a protein called

Rho, that binds to and slides along the RNA transcript. The terminator sequence slows down the elongation complex, Rho catches up and knocks it off the DNA

Rho independent termination depends on both slowing down the elongation complex with a hairpin and a U-rich region that destabilizes the elongation complex

Page 25: Ecclesiastes 3:1

©2000 Timothy G. Standish

RNAPol.

5’RNA

RNA Pol.

5’RNA

TerminationTerminationRho IndependentRho Independent

Terminator

Page 26: Ecclesiastes 3:1

©2000 Timothy G. Standish

RNAPol.

5’RNA RNA

Pol.

5’RNA

TerminationTerminationRho IndependentRho Independent

Terminator

Page 27: Ecclesiastes 3:1

©2000 Timothy G. Standish

RNAPol.

5’RNA

TerminationTerminationRho DependentRho Dependent

Terminator

RNA Pol.

5’RNA The terminator

sequence slows RNA polymerase

Page 28: Ecclesiastes 3:1

©2000 Timothy G. Standish

RNAPol.

5’RNA

TerminationTerminationRho DependentRho Dependent

Terminator

Help, Rhohit me!

RNA Pol.

5’RNA

Rho catches up with RNA polymerase

Page 29: Ecclesiastes 3:1

©2000 Timothy G. Standish

RNAPol.

5’RNA

TerminationTerminationRho DependentRho Dependent

Terminator

RNA Pol.

5’RNA

The elongation complex disintegrates

Page 30: Ecclesiastes 3:1

©2000 Timothy G. Standish

Page 31: Ecclesiastes 3:1

©2000 Timothy G. Standish

TranscriptionTranscription

5’

3’

3’

5’

Template (antisense) strand

Coding (sense) strand

Page 32: Ecclesiastes 3:1

©2000 Timothy G. Standish

TranscriptionTranscription

5’

3’

3’

5’

Template (antisense) strand

Coding (sense) strand

5’

RNA

RNAPol.

Page 33: Ecclesiastes 3:1

©2000 Timothy G. Standish

TranscriptionTranscription

5’

3’

3’

5’

5’

RNAPol.

Template (antisense) strand

Coding (sense) strand

Page 34: Ecclesiastes 3:1

©2000 Timothy G. Standish

Products of TranscriptionProducts of Transcription Transcription produces three major RNA products:

1 Ribosomal RNA (rRNA) - Several rRNAs are vital constituents of ribosomes

2 Transfer RNA (tRNA) - The molecule that physically couples nucleic acid codons with specific amino acids

3 Messenger RNA (mRNA) - The nucleic acid messenger that carries encoded information from genes on DNA to the protein manufacturing ribosomes

Page 35: Ecclesiastes 3:1

©2000 Timothy G. Standish

Transfer RNA (tRNA)Transfer RNA (tRNA) Acts as the adapter molecule between the genetic code

on mRNA and the protein “language” 75-85 bases long A specific amino acid is covalently linked at the 3’ end Elsewhere on the molecule is an anticodon

complimentary to the specific amino acid codon on mRNA that codes for the amino acid carried by the tRNA

Contain a number of modified bases

Page 36: Ecclesiastes 3:1

©2000 Timothy G. Standish

A “Simple” GeneA “Simple” Gene

Protein Coding Region

Terminator Sequence

Promoter/Control Region

Transcription Start Site 3’ Untranslated Region

5’ Untranslated Region

3’5’

RNA Transcript

Page 37: Ecclesiastes 3:1

©2000 Timothy G. Standish

Transcription InitiationTranscription InitiationProteins called transcription factors bind

to the promoter region of a gene If the appropriate transcription factors

are present, RNA polymerase binds to form an initiation complex

RNA polymerase melts the DNA at the transcription start site

Polymerization of RNA begins

Page 38: Ecclesiastes 3:1

©2000 Timothy G. Standish

RNA Pol.

InitiationInitiation

T. F.

RNA Pol.

5’RNA

Promoter

T. F.

T. F.

Page 39: Ecclesiastes 3:1

©2000 Timothy G. Standish

3’

5’

5’

3’

Transcription And Translation Transcription And Translation In ProkaryotesIn Prokaryotes

Ribosome

Ribosome5’

mRNA

RNAPol.

Page 40: Ecclesiastes 3:1

©2000 Timothy G. Standish

Heat Shock Response Heat Shock Response ElementsElements

Sudden changes in the temperature of cells cause stress in response to which heat shock genes are expressed

At least some heat shock genes are thought to be chaperones that help proteins fold correctly

Heat shock genes have Heat Shock Elements (HSEs) in their control regions

Heat Shock Transcription Factors (HSTFs) bind the HSEs up regulating expression of heat shock gene products

Page 41: Ecclesiastes 3:1

©2000 Timothy G. Standish

Page 42: Ecclesiastes 3:1

©2000 Timothy G. Standish

DNA

Cytoplasm

Nucleus

G AAAAAA

Export

Degradation etc.G AAAAAA

Control of Gene ExpressionControl of Gene Expression

G AAAAAA

RNAProcessing

mRNA

RNA

Transcription

Nuclear pores

Ribosom

e

Translation

Packaging

Modification

Transportation

Degradation

Page 43: Ecclesiastes 3:1

©2000 Timothy G. Standish

5’ 3’

RNA Transcript

A “Simple” GeneA “Simple” Gene

Protein Coding Region

Terminator Sequence

Promoter/Control Region

3’ Untranslated RegionTranscription Start Site 5’ Untranslated Region

Page 44: Ecclesiastes 3:1

©2000 Timothy G. Standish

RNA Pol.

InitiationInitiation

Promoter

RNA Pol.T. F.

T. F.

T. F.

5’RNA

Page 45: Ecclesiastes 3:1

©2000 Timothy G. Standish

3’

5’

5’

3’

Transcription And Translation Transcription And Translation In ProkaryotesIn Prokaryotes

Ribosome

Ribosome5’

mRNA

RNAPol.