Lecture 7 Transcription and Gene Regulation Flashcards

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1
Q

What is a gene?

A

The sum of all transcribed and non-transcribed regions that are necessary to properly express a gene (must consider not just the coding region, but also the regulatory region etc)

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2
Q

The transcribed region of a gene is referred to as the:

A

Transcription unit

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3
Q

What is the open reading frame (ORF) of the transcription unit?

A

The coding region (operon-derived mRNAs harbor more than one ORF)

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4
Q

Some genes encode _____ that are no translated

A

RNAs

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5
Q

Not everything that is transcrbed is necessarily coding: provide an examp

A

5’ and 3’ UTR (untranslated regions) and introns

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6
Q

Regulatory sequences are commonly located in the _________ regions of a gene but sequences with important ______ functions may reside in the transcription unit and coding region

A

Regulatory sequences are commonly located in theNON-TRANSCRIBED regions of a gene but sequences with important REGULATORY functions may reside in the transcription unit and coding region

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7
Q

Transcription occurs via _____ _______

A

RNA polymerase

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8
Q

During transcription _____ the DNA is melted; Transcription then occurs in a “______”

A

During transcription INITIATION the DNA is melted; Transcription then occurs in a “TRANSCRIPTION BUBBLE”

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9
Q

What is the nontemplate strand?

A

Coding strand = “sense” strand Identical in sequence to the mRNA 5’-3’

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10
Q

What is the template strand?

A

Non-coding strand = “antisense” strand 3’-5’

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11
Q

Principle difference between bacterial and eukaryotic gene regulation?

A
  • The ground state is ON in bacterial gene regulation (DNA is accessible at all times)
    • Gene requires repression to turn “off”
  • Whereas ground state in eukaryotes is OFF (because of nucleosomes = DNA is inaccessible)
    • Gene requires activation “on”
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12
Q

Bacterial RNA Polymerase is a multi-subunit protein complex

  • ____different gene products required for the ____ enzyme
  • Two ___ subunits which are identical and encoded by the same gene
  • ___, ____ and _____ are encoded by three additional genes
  • _____ _____ is needed for specific binding of the RNA polymerase to the promotor
A

Bacterial RNA Polymerase is a multi-subunit protein complex

  • Four different gene products required for the Core enzyme
  • Two Alpha subunits which are identical and encoded by the same gene
  • omega, beta and beta prime are encoded by three additional genes
  • sigma factor is needed for specific binding of the RNA polymerase to the promotor
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13
Q

What is Holoenzyme?

A

Core enzyme (of RNA polymerase) plus Sigma factor

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14
Q

Sigma factor has the ability to bind to the ____ ____ _____ which drastically improves the ability to bind to promotors

A

Sigma factor has the ability to bind to the Core RNA Polymerase which drastically improves the ability to bind to promotors

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15
Q

What is a promoter?

A

Region of a gene containing regulatory sequences that are close to (or contain) the transcription start site

Required for transcription initiation via RNA polymerase

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16
Q

What is positive regulation?

A

Involves an activator

  • activator bind to activator binding site
    • allows RNA polymerase to bind to promotor
17
Q

What is negative regulation?

A

Involves a Repressor

  • Bind to operator sequences (part of promoter)
  • Either prevents binding of RNA polymerase OR blocks progress of RNA polymerase
18
Q

What is the Operator Sequence?

A
  • part of promoter
  • designed to interfere with transcription (ie turns gene off)
19
Q

What is a ligand? What is it’s role in transcription?

A

Small units (metabolites/hormones/peptide hormones) that can bind to activators (via ligand-binding site/allosteric site) = change conformation of protein = Activating: Promote binding of DNA or Inhibiting: Promote release of DNA from activator-binding site

20
Q

What is an allosteric site?

A

Region of protein to which a small molecule can bind (the ligand) resulting in a conformational change of the protein that modifies the activity of the protein

The result can be inhibitory or activating

21
Q

The lac operon comprises three genes:

A

Beta-galactosidase

Permease

Transacetylase

22
Q

What are operons?

A

A group of genes that are adjacent to each other and transcribed together (under control of a single regulatory region)

23
Q

What result on mRNA does an operon have?

A

Resulting mRNA is polycistronic

24
Q

Are operons found in eukaryotes or bacteria?

A

bacteria

Very rare in eukaryotes

25
Q

An mRNA that can encode more than one polypeptide separately within the same RNA molecule is called:

A

Polycistronic

26
Q

What are operators?

Are they found in bacteria or eukarya?

A

Region of DNA that acts as a binding site for a repressor protein

  • Found in bacteria (has not been identified in eukaryotes)
27
Q

What are the three structural genes of the Lac operon? What do they do?

A
  1. lacZ: beta-galactosidase
    • cleaves lactose into galactose and glucose
    • also produces beta1,6-allolactose
  2. lacY: transports lactose into the cell
  3. lacA: transfers acetyl group to certain sugars
28
Q

What are the two regulatory genes of the Lac operon?

A
  1. lacI: lac repressor - not part of the lac operon but the lacI gene lies nearby (upstream of lac operon)
  2. CAP: catabolite activator protein
    • also known as CRP (cAMP receptor protein)
29
Q

What are the two Substrates/Effectors (ligands/inducers) of the lac operon?

A
  1. beta-1,6-allolactose: a transient byproduct of beta-galactosidase activity
    • Triggers conformational change in lac repressor
  2. cAMP: cyclic adenosine monophosphate
    • Allosteric effector for CAP/CRP - made when glucose is low
30
Q

What two conditions must be met to have the lac operon induced?

A
  1. Lactose is present in the growth medium
  2. Glucose is absent from the growth medium
31
Q

If glucose is present in the growth medium what happens?

A

Glucose is preferred sugar: Basal transcription

32
Q

What is Basal transcription?

A
  • occurs when RNA polymerase binds to DNA in the absence of activators and repressors (RNA polymerase Is neither specifically recruited to nor prevented from binding to the promotor)
33
Q

What is the general mechanism of operator function?

A
  • competition for promotor occupancy
  • operator-bound repressor blocks binding or transcription of RNA polymerase
  • Operator doesn’t have to be located between -10 and -35 elements
  • Basal level of transcription generally refers to random binding of RNA Pol to the promoter in the absence of activators and repressors
34
Q

Under what conditions of the lac operon might you see basal transcription?

A

Basal transcription can occur in a repressed state

35
Q

Lac operon overview:

If we have neither the CAP(activator) nor Lac repressor what do we see?

Can happen in ___glucose, ____lactose conditions

A

Basal transcription - RNA polymerase will bind occasionally

Can happen in _+_glucose, _+_lactose conditions

36
Q

In +glucose, -Lactose conditions what would we see?

A

No lactose in the medium = attracts binding of Lac repressor = operon is off

37
Q

What would happen in -glucose, -lactose conditions?

A

No lactose = attracts Lac repressor = Operon off

38
Q

What would we observe in -Glucose, +lactose conditions?

A

Operon ON = this is the only state where we see a fully activated operon

Presence of lactose in the absence of glucose = CAP binds and repressor is removed

39
Q
A