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Bio 305: Genetics > Lecture 15 > Flashcards

Lecture 15 Flashcards

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1
Q

What is the default state of genes in eukaryotes and prokaryotes? On/Off

A

Prok: genes are on unless turned off by repressor proteins
Euk: genes are off unless turned on by transcription factors

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2
Q

What are the pre-transcriptional level regulatory mechanisms?

A
  1. Multiple copies of genes for things needed a lot (evolutionary response)
  2. DNA rearrangment: splicing DNA to create or alter genes to generate antibody diversity
  3. Chromatin structure: coiling, histone acetylation, methylation
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3
Q

What role does the promoter have in regulatory mechanisms during initiation of transcription?

A
  • Matching promoter strength to the degree you need the protein. The closer the match = the more likely RNA pol will bind (evolutionary response)
  • Sigma factors control which promoter sequences will be used (regulatory)
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4
Q

What role do DNA binding proteins have in regulatory mechanisms during initiation of transcription? Which proteins cause negative or positive regulation?

A
  • DNA binding proteins are present in euk and prok
  • The type of DBP determines whether regulation is positive or negative
  • Transcription factors = positive
  • Activators = positive
  • Repressors = negative
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5
Q

What is the difference between positive and negative regulation?

A

Positive: the presence of a bound protein is required for transcription
Negative: the absence of a bound repressor allows transcription to begin.

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6
Q

What are effector molecules?

A

Effector molecules tie binding to environmental cue. They influence the DNA-binding activities of activators and repressors. Some activator or repressor proteins must bind to their allosteric effectors before they can bind DNA. Others can bind DNA only in the absence of their allosteric effectors. Effector molecules bind to regulatory proteins and change its shape.

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7
Q

What occurs if an effector molecule causes binding of activator? repressor?

A

Activator: Activation, high transcription
Repressor: Repression, low transcription

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8
Q

What occurs if an effector molecule causes release of activator? repressor?

A

Activator: De-activation, low transcription
Repressor: Induction, high transcription

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9
Q

Where do activators and repressors bind in prok?

A

DNA segments next to the promoter

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10
Q

What is the role of an activator in prok vs euk?

A

Prok: Serve to recruit RNA pol to the promoter
Euk: Bind to the enhancer to increase transcription by recruiting TF’s. DNA must bend to position the activator proteins near promoter

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11
Q

What is the role of repressors in prok?

A

Binds at operator or silencer near the promoter. It interferes with the binding of RNA pol and TF’s

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12
Q

What are the post-transcriptional regulatory mechanisms?

A

Capping, tailing, differential splicing, transport from nucleus can be delayed, degradation of mRNA

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13
Q

What are the translational regulatory mechanisms?

A

Efficiency of ribosome binding, miroRNAs may affect elongation

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14
Q

What are the post-translational regulatory mechanisms?

A

Cleavage, glycosylation, phosphorylation, folding&assembly, transport, degradation

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15
Q

What is an operon?

A

Multiple genes transcribed from one promoter. The genes usually have a common purpose

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16
Q

What is the advantage of operons?

A

Coordinated regulation by protein binding at a single site

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17
Q

What is the purpose of the trp operon?

A

A set of 5 genes needed to MAKE tryptophan. Transcription is off when tryptophan is plentiful.

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18
Q

Describe how the trp operon works when tryptophan is present and absent.

A

Trp present: Trp is the corepressor that binds to the repressor protein to activate it. The active repressor binds to the promoter and blocks transcription.

Trp absent: The repressor is inactive because trp is not bound to it, transcription occurs

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19
Q

What is the purpose of the lac operon?

A

A set of 3 genes needed to USE lactose.

20
Q

What are the 3 structural genes and their function?

A

Lac Y: lac permease (lets lactose into cell)
Lact Z: beta galactosidase (breaks down lactose into glucose and galactose)
Lac A: transacetylase (function unknown)

21
Q

What are the two regulatory proteins involved in the lac operon?

A

LacI: repressor protein that binds the operator or lactose, active when glucose present
CAP: catabolite activator protein, responds to level of glucose present, cAMP-CAP complex binds to promoter

22
Q

Describe how the lac operon works when lactose is present and absent.

A

Lactose present: Allo-lactose binds to LacI repressor protein causing LacI to fall off the DNA so transcription can proceed

Lactose absent: LacI binds to the operator site blocking RNA pol from binding so no transcription occurs

23
Q

What is the inducer molecule for the lac operon?

A

Allo-lactose

24
Q

What was the result of Jacob & Monod’s genetic data for operator (LacI binding) site?

A

WT is inducible with IPTG (non-metabolizable lactose analog)
Z+ is dominant to Z-
O^c is constitutive
Operator is cis-acting

25
Q

What is cis vs trans acting?

A

Trans: gene product can regulate all structural lac operon genes, whether residing on the same DNA molecule OR on different ones. WT genes can complement on chromosome or F’

Cis: Operator mutations reveal that the operator site is cis-acting, it regulates the expression of an adjacent transcription unit on the SAME DNA molecule. Mutant only impacts genes on the same DNA molecule.

26
Q

What was the result of Jacob & Monod’s genetic data for repressor (LacI structure) site?

A

I+ is inducible
I- is constitutive
I+ is dominant to I-
I+ is trans-acting

27
Q

What are constitutive mutations?

A

Mutations that cause the lac operon structural genes to be expressed regardless of whether inducer was present

28
Q

What was the result of Jacob & Monod’s genetic data for the allostery of repressor?

A

I+ is inducible
I^s is always bound to operator therefore it’s always causing repression
I^s is dominant to I+

29
Q

Which lac operon mutations are constitutive?

A

O^c and I-

30
Q

What are super-repressor mutations?

A

Cause repression even in the presence of the inducer.

Example: I^s, has non-functional allosteric site

31
Q

Order the three alleles of the lacI gene in descending order of dominance according to their ability to influence the operator gene.

A

I^s > I- > I+

32
Q

Which mutations are cis-acting? trans-acting?

A

Trans: I-, I^s, I+, Z+
Cis: O^c

33
Q

What is the role of CAP in the lac operon?

A

Catabolite activator protein that responds to level of glucose present. If glucose level is low then level of cAMP increases. cAMP binds to CAP to form complex. Complex then binds to DNA to cause transcription of structural genes.

34
Q

When are the lac enzymes made?

A

When glucose is low and lactose is high

35
Q

Where does CAP bind?

A

DNA segment distinct from lac operator and promoter

36
Q

How does CAP binding function to increase transcription?

A

CAP bends DNA to help RNA pol bind to the DNA

37
Q

What is the function of the ara operon?

A

A set of genes needed to USE the sugar arabinose.

38
Q

Describe how the ara operon works when arabinose is present and absent.

A

Arabinose present: AraC protein binds to the araI region.
The CAP–cAMP complex binds to a site adjacent to araI. This binding stimulates the transcription of the araB, araA, and araD genes.

Arabinose absent: AraC protein binds to both the araI and the araO regions, forming a DNA loop. This binding prevents transcription of the ara operon.

39
Q

What is the regulatory protein for the ara operon?

A

AraC. It is a repressor in absence of arabinose. It is an activator in the presence of arabinose.

40
Q

What is trp attentuation?

A

Occurs after transcription initiation, mRNA production is decreased when tryptophan is plentiful

41
Q

What occurs when [trp] is high in WT cells? low?

A

high [trp] = no transcription

low [trp] = transcription

42
Q

What occurs when [trp] is high in TrpR mutants? low?

A

high [trp] = high transcription

low [trp] = higher transcription

43
Q

What are two important characteristics of the trp leader mRNA?

A
  1. contains two adjacent trp codons

2. can form different stem loop structures

44
Q

What occurs if tryptophan is present once translation begins?

A

The ribosome moves quickly through regions 1 and 2 which allows 3 and 4 to form a stem loop in the mRNA ahead. This stem loop interferes with RNA pol elongation terminating transcription.

45
Q

What occurs if tryptophan is absent once translation begins?

A

The ribosome stalls in region 1 at two adjacent trp codons. This allows 2 and 3 to form a stem loop in the mRAN ahead. This stem loop has no effect on RNA pol elongation allowing full mRNA to be made.

Bio 305: Genetics (17 decks)

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