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Molecular Biology (BYMB1) > Week 3 (Control Of Gene Expresion) > Flashcards

Week 3 (Control Of Gene Expresion) Flashcards

1
Q

Can the environment regulate gene expression?

A
  • environmental factors can control gene expression (induction or repression)
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2
Q

What modulates gene expression?

A
  • activators

- represses

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3
Q

Describe two examples of negative regulation

A

The repressor binds to the promoter region of the gene and the repressor protein prevents transcription by competing with RNA polymerase

-Removal of the ligand (repressor becomes inactive because of the conformational change) switches the gene on by removing the repressor protein
Or
-Addition of the ligand switches the gene on by Removing repressor protein (ligand causes conformational changes in repressor) so RNA polymerase can bind to the gene

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4
Q

Describe positive regulation

A

The bound activator protein promotes transcription by helping RNA polymerase bind to the weak promoter

  • Addition of the ligand switches causes conformational changes that prevent the activator protein from recognising the sequence so the gene off as the activator is removed
  • Removal of the ligand causes conformational changes in the activator protein which switches the gene off as the activator protein is removed
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5
Q

Define Operon

A

A group of genes/ segment of DNA that functions as a single transcription unit.
(A group of genes that are transcribed together as a single mRNA molecule)
It is comprised of an operator sequence (within the promoter region), a promoter and two or more structural genes that are transcribed into one polycistronic mRNA

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6
Q

What happens when tryptophan is present in a growth medium?

A

The operon is switched off

  1. The repressor is bound with the tryptophan
  2. This allows the repressor to bind to the operator sequence in the promoter
  3. The repressor competes with RNA polymerase
  4. Genes for tryptophan producing enzymes are not transcribed
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7
Q

What is the uptake of lactose mediated by?

What is lactose hydrolysed into?

A

Lactose permease

lactose is hydrolysed by beta-galactosidase to make glucose and galactose

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8
Q

Describe the organisation of the Lac operon

A

Promoter + operator + 3 structural genes (permease, beta galactosidase, transacetylase that help cells utilise lactose as it’s carbon source)

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9
Q

Why does gene expression need to be controlled?

A
  • Because it is unnecessary for genes to be expressed all the time and
  • transcription is a process that demands a lot of energy, if all genes were expressed all the time, it would use a colossal amount of energy
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10
Q

What is the term transcription regulators used classify?

A

Activator and repressor proteins that modulate gene expression

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11
Q

What is the main mechanism of action of both activators and repressors?

A

Ligand binding that causes conformational change in the repressor/ activator

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12
Q

The trp operon is a repressible system. What does it consist of?

A
  • A promoter
  • An operator
  • 5 structural genes that code for enzymes that make tryptophan
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13
Q

What happens when tryptophan is not present in a growth medium?

A

Operon is switched on

  1. No tryptophan to bind with repressor
  2. Repressor cannot bind with the promoter/ no competition with RNA polymerase
  3. Genes for tryptophan synthesis will be transcribed
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14
Q

What is the LAC operon regulated by?

A

Lac repressor
CAP promoter

Allolactose ( isomer of Lacoste) that induces the lac operon

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15
Q

Explain the regulation of the Lac operon: when there is no lactose

A
  1. The separate promoter and inhibitor continuously express the lac respires or protein
  2. lac repressor protein binds to the lac operator sequence and inhibits transcription by preventing RNA polymerase from binding
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16
Q

Explain the regulation of the Lac operon: when allolactose is present

A
  1. Allolactose binds to the repressor causing a conformational change
  2. Repressor no longer able to recognise the operator sequence so RNA polymerase can so transciption of the 3 lactose genes (operon) can occur
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17
Q

Explain the consequences of the preferential use of specific carbon sources?

A

E.Coli prefers glucose over lactose

  • sufficient glucose= no expression of the lac operon
  • glucose depletion = expression of lac operon only when lactose is present
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18
Q

What is cyclic AMP (cAMP)?

A

A secondary messenger (ligand)

Hydrolysis of ATP by adenylyl cyclase and cleavage by cyclic AMP phosphodiesterase to produce AMP

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19
Q

What happens to cyclic [AMP] in relation to [glucose]

A

Glucose present= Low [cAMP]

Glucose absent = High [cAMP]. Stress signal for the mobilisation of alternative carbon sources

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20
Q

What happens when glucose runs out?

What allows the cyclic AMP receptor protein (catabolise activator protein) to bind to DNA?

A

When glucose runs out [cAMP] increases

  1. cAMP binds to the CRP (Cyclic AMP receptor protein= CAP) and causes conformational changes (acting as an activator)
  2. It helps RNA polymerase transcribe genes
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21
Q

When will the lac related genes be transcribed?

A

When glucose is absent and lactose is present

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22
Q

Lac operon: explain why the operon is off when both glucose and lactose present

A

cAMP levels are low so no activator bound (no transcription of the operon)

23
Q

Lac operon: explain why the operon is off when only glucose and not lactose is present

A

Lactose repressor is bound
AND
Low levels cAMP

24
Q

Lac operon: explain why the operon is off when both glucose and lactose absent

A

-cAMP levels increase (glucose is absent) and bind to activator on the promoter region
BUT
-No lactose so repressor is also bound

25
Q

Lac operon: explain why the operon is On when there is no glucose but there is lactose present

A
  • High levelss of cAMP that bind to the activator which recruits RNA polymerase so genes can be transcribed
  • lactose binds to repressor, causes conformational changes that remove it from the operator sequence
26
Q

Why is the control of gene expression in eukaryotes more complicated?

A

Combination of multiple repressors and activators that can be integrated to regulated expression

27
Q

Do eukaryotes have operons?

A

They are very rare as genes tend to be individually transcribedand regulated

28
Q

What are the 4 transcription factors that control the Eve (evenly skipped) gene expression

A
  • biocid
  • Giant
  • Hunchback
  • Kruppel

There is a spatially distinct localisation of the 4 transcription factors

29
Q

Which 2 Transcription factors activate Eve transcription?

A

Bicoid and Hunchback

30
Q

Which 2 transcription factors suppress Eve transcription

A

Kruppel and Giant

31
Q

What does the combination of multiple repressors and activators in drosophila allow?

A

Haspatially define expression of Eve

32
Q

The different cell types of a multicellular organisms contain the same DNA. How do they become different from one another?

A

They express different sets genes (RNA and protein molecules)

33
Q

Name some of the steps in which gene expression can be regulated in the pathway from DNA to RNA to protein

A
  1. Transcriptional control: controlling when and how often a given gene is transcribed
  2. RNA processing control: controlling the splicing and processing of RNA transcripts
    3.RNA transport and localisation control: selected which completed mRNAs are exported from the nucleus to the cytosol and determining where in the cytosol they are localised
  3. Translational control: selecting which mRNAs in the cytoplasm are translated by ribosomes
    5: mRNA degradation control: selectively destabilising certain mRNA molecules in the cytoplasm
    6 protein activity control: selectively activating/ inactivating, degrading , or localising specific protein molecules after they have been made
34
Q

What is the function of transcription regulators?

A

Proteins that recognise specific DNA sequences called cis-regulatory sequences

35
Q

What are cis regulatory sequence?

A

Specific DNA sequences that are on the same chromosome as the genes they control

36
Q

How often would you expect an exact 6 nucleotide sequence to occur?

A

6

Once every 4 = 4096

37
Q

What is the benefit of operons?

A

Allows the expression of multiple genes to be coordinated

38
Q

What is the repressor and cis regulatory sequence in relation to the control of tryptophan expression?

How are these components controlled?

A

Transcription regulator= tryptophan repressor
Cis regulatory sequence = tryptophan operon

The repressor can bind to DNA only if it has also bound several molecules of tryptophan

When the concentration of tryptophan drops the repressor no longer binds to DNA and the tryptophan operon is transcribed

39
Q

Why is the gene that encodes the tryptophan repressor protein always being transcribed (at a low level?

A

Allows the bacterium to respond rapidly to the rise or fall in tryptophan

40
Q

How do activator proteins provide assistance to RNA polymerase?

A

They bind to the cis regulatory sequence and are positioned, with respect to the promoter so that favourable interactions occur

41
Q

What are activators and repressors a class of?

A

Transcription regulation proteins

42
Q

Can the activity of a single promoter be controlled by several different transcription regulators?

A

Yes

E.g. the Lac operon in E.Coli is controlled by both the Lac repressor and the CAP activator

43
Q

The control region of the Lac operon needs to integrate two different signals so that the operon is highly expressed only when two conditions are met? What are they?

A
  1. Lactose must be present

2. Glucose must be absent

44
Q

What has to bind to CAP before it can bind to DNA?

A

Cyclic AMP

45
Q

Where are cis regulatory sequences located?

A

Usually very near to the start point of transcription but some can be located 100s or 1000s of from the genes they control

46
Q

Does DNA looping occur more often in bacteria or in eukaryotes?

A

DNA looping rarely occurs in bacteria however it occurs in nearly every eukaryotic gene

47
Q

How many transcription factors does (eukaryotic) RNA Polymerase II need?
How many transcription factors does the bacterial RNA polymerase need?

A

5 general TFs are needed by RNA polymerase II

The bacterial TF only needs 1 (a sigma subunit)

48
Q

What is the difference between transcription factors and transcription regulators?

A

Transcription factors assemble on the promoters of all genes transcribed by RNA polymerase II

Transcription regulators are devoted to turning individual genes on and off

49
Q

How do transcription activators promote transcription?

A

They trigger changes to the chromatin structure of the promoters, making the underlying DNA more accessible

This is achieved through histone replacement and modification, nucleosome remodelling and removal

50
Q

Transcription activators can act at different steps

A
  1. Promoting binding of additional regulators
  2. Assembling RNA polymerase at promoters
  3. Releasing the already assembled RNA polymerases from promoters
  4. Released RNA molecules that become stalled
51
Q

What does the Eve gene is Drosophila control?

A

The development of the Drosophila embryo

52
Q

What does the uneven distribution of transcription regulators cause?

A

It causes the Eve gene to be expressed in 7 precisely positioned stripes

53
Q

What is the regulatory region of the Eve gene contains the cis regulatory sequence responsible for?

A

Specifying a particular stripe of Eve expression along the embryo

54
Q

Can a single transcription regulator contribute to the control of many genes?

A

Yes

Molecular Biology (BYMB1) (14 decks)

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