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Molecular and Microbial Genetics > Gene Regulation > Flashcards

Gene Regulation Flashcards

Gene Regulation I,II,III (DOES NOT INCLUDE GLOBAL GENE REGULATION)

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1
Q

What is gene expression?

A

Taking the information in DNA (a gene) and copying
that information into mRNA (transcription) and then translating that mRNA into a protein (translation).

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2
Q

Steps of transcription?

A

(DNA->mRNA)
1. Initiation
2. Elongation
3. Termination

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3
Q

Steps of translation?

A

(mRNA->Protein)
1. Initiation
2. Elongation**
3. Termination

**The step during gene expression where the most energy is consumed.

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4
Q

Gene expression is most often regulated where?

A

The point of transcription initiation.

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5
Q

What is an operon?

A

Two or more genes lie adjacent to each other and are transcribed on the same mRNA.

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6
Q

What are ways to regulate gene expression?

A

A.) Operons
B.) The Promoter
C.) Transcriptional regulatory proteins
D.) Negative gene regulation

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7
Q

What are the two types of regulatory proteins?

A
  1. Repressor proteins
  2. Activator proteins
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8
Q

Describe repressor proteins

A

Will bind to a sequence site in DNA near a promoter called the “operator site”. When this occurs, the repressor protein blocks access to the promoter by RNA polymerase. This greatly reduces the initiation of a new round of transcription.

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9
Q

Describe activator proteins

A

Bind to a sequence site in DNA called the “activator site” upstream of the promoter sequence. When this happens, this greatly increases the initiation of a new round of transcription.

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10
Q

What type of transcriptional regulatory protein increases the initiation of a new round of transcription?

A

Activator proteins

(Repressor proteins decrease it)

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11
Q

What type of transcriptional regulatory protein decreases the initiation of a new round of transcription?

A

Repressor proteins

(Activator proteins increase it)

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12
Q

What can change (modulate) the activity of a regulatory protein?

A

An effector molecule

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13
Q

How many types of effector molecules are there? What are they?

A

There are two:
1. Co-repressor
2. Inducer

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14
Q

What was an example of a co-repressor from our notes that controlled the trp repressor protein?

A

The amino acid tryptophan

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15
Q

What was the first mechanistic model to explain how gene expression is regulated in response to something called “lactose induction”?

A

The lac operon model

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16
Q

Explain the concept of lactose (enzyme) induction.

A

Special enzymes are required to ferment lactose and these specific protein enzymes are only made when lactose is present in the growth medium, that is, they are “induced” by the presence of lactose.

What was determined by Jacob and Monod is that when no lactose is present. The lac I gene codes for the lac repressor protein. When lactose is present, lactose acts as an “inducer” molecule and binds to the lac repressor protein. Now the lac repressor protein no longer binds to the lac O operator site on DNA.

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17
Q

What are Lac- mutants?

A

Mutants that no longer ferment lactose.

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18
Q

What are “constitutive” mutants?

A

Mutants that showed no lactose induction. That is they produce the lac enzymes regardless of whether lactose is present or not in the growth medium.

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19
Q

What lac genes are “trans” acting?

A

Lac Z, lac Y, and lac I

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20
Q

What lac genes are “cis” acting?

A

Lac P and lac O

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21
Q

What is lac Z?

A

Structural trans-acting gene that codes for the enzyme Beta-galactosidase.

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22
Q

What does Beta-galactosidase do?

A

Splits the disaccharide lactose into glucose plus galactose.

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23
Q

What is lac Y?

A

Structural trans-acting gene that encodes the lac permease.

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24
Q

What does lac permease do?

A

It is required to transport lactose into the E. coli cell.

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25
Q

What does it mean for lac P to be cis acting?

A

A wild-type copy of this gene could not complement the mutant form of the gene.

26
Q

Which genes are lac - mutants with respect to the lac operon?

A

Lac Z, Y, and P

27
Q

Which genes are constitutive mutants with respect to the lac operon?

A

Lac I and O

28
Q

What is lac I?

A

A trans acting gene that codes for the lac repressor protein.

29
Q

What is the second (other) regulatory protein that controls the lac operon called?

A

CAP (catabolite activator protein)

{It is a global regulatory protein that regulates more than one gene or operon in E. coli.}

30
Q

What is widely used as a genetic tool to measure the activity of different gene promoters?

A

The lac promoter plus lac Z

31
Q

What is lac A?

A

It is a third structural gene that was found; however, the function of this gene is not known and was thus not discovered by Jacob and Monod.

32
Q

What is an example of negative gene regulation?

A

The lac operon

33
Q

What is an example of positive gene regulation?

A

The arabinose operon

34
Q

What is the arabinose operon?

A

It is a set of 3 genes encoding enzymes required to ferment the sugar arabinose.

35
Q

What acts as an inducer of transcription of the arabinose operon?

A

Arabinose. This is because, like the lac operon, the arabinose operon is induced (turned on) only when the sugar arabinose is present in the growth medium.

36
Q

The non-inducible arabinose operon mutants showed what type of phenotype? What does this mean?

A

A “super-repressed” phenotype. This means that there was no expression of the operon regardless whether arabinose was present or not.

37
Q

What type of regulatory protein controls the arabinose operon?

A

An activator protein

38
Q

What type of regulatory protein controls the lac operon?

A

A repressor protein

39
Q

How many “structural genes” does the arabinose operon contain and what are they called?

A

There are 3 of them:
1. B
2. A
3. D

40
Q

What is the promoter shared by the three structural genes found in the arabinose operon?

A

PBAD

41
Q

What codes for the ara C activator protein?

A

A gene called “ara C” which is separate from the B, A, and D structural genes.

42
Q

Where does ara C bind to? What does this do?

A

Ara C will bind to the activator site which is a sequence code (upstream of the promoter) called “ara I”. This binding of the ara C activator protein to the ara I activator site will turn on transcription of the arabinose operon.

43
Q

What are the two functional states that the ara C activator protein can exist in?

A

The P1 functional state and the P2 functional state

44
Q

When will ara C be in the P1 functional state?

A

When no arabinose is bound to it.

45
Q

When will ara C be in the P2 functional state?

A

When arabinose is bound to it.

46
Q

Describe in detail the P1 state of the ara C activator protein.

A

In the P1 state, ara C binds to ara I (in a subregion called I1). A copy of ara C also binds to an upstream operator site called O2. Then the two copies of ara C bind to each other and this causes the DNA to bend. This bending of the DNA is thought to block the ability of RNA polymerase to bind to the PBAD promoter to initiate transcription. Thus, when no inducer (arabinose) is present, ara C may actually repress transcription initiation.

47
Q

Describe in detail the P2 state of the ara C activator protein.

A

When the inducer, arabinose, is present it binds to ara C and changes the activator to the P2 functional state. In the P2 state, two copies of ara C bind to the activator site ara I. This produces a slight bend in the DNA. Meanwhile, RNA polymerase binds to the PBAD promoter adjacent to ara I. The slight bend in DNA produced when ara C binds to the activator site brings ara C into direct physical contact with RNA polymerase. This physical contact by ara C with RNA polymerase causes RNA polymerase to bind much tighter to the promoter and this in turn increases the frequency of new transcription initiation. Thus, the activator ara C “turns on” transcription of the operon by RNA polymerase.

48
Q

What is transcription attenuation?

A

Regulation at the level of transcription termination (rather than initiation of transcription). Usually a switch between “normal” termination of transcription (mRNA transcript copies all the way to the end of the structural gene in an operon) to premature transcription termination (transcription ends before reaching the structural genes).

49
Q

How was one of the 1st examples of transcription attenuation discovered?

A

From analysis of mutations in the trp operon.

50
Q

What is the TPP operon?

A

It is a 4 gene operon that is required to synthesize the co-enzyme thiamine pyrophosphate (TPP).

51
Q

What is thiamine pyrophosphate (TPP)?

A

It is an important co-enzyme for certain decarboxylase and other enzymes.

52
Q

True or false: The TPP operon is controlled via a regulatory protein (i.e. repressor protein or activator protein).

A

False.

TPP does not use a regulatory protein. It is rather controlled by a “riboswitch”.

53
Q

Where is TPP regulated and how?

A

At the level of transcriptional termination (rather than initiation of transcription). It is controlled via a riboswitch.

54
Q

What is a riboswitch?

A

Metabolite binding (sensor) regulating RNA at the 5’ end of mRNA. It is composed of a specially folded structure called an “aptamer”.

55
Q

Where is the aptamer found?

A

In the 5’ UTR region of the mRNA copy of the operon.

56
Q

What is an aptamer?

A

It is a specially folded structure in the RNA molecule that can specifically recognize and bind to a small molecule metabolite. In the case of TPP operon, this small ligand is TPP (thiamine pyrophosphate).

57
Q

What does the aptamer recognize and bind to?

A

TPP (thiamine pyrophosphate)

58
Q

How is the “anti-terminator” stem-loop formed?

A

When sequence 1 and sequence 2 (2 of the 4 sequences found between promoter and first structural gene) base pair in the mRNA strand.

59
Q

How does the terminator stem-loop lead to the termination of transcription?

A

It makes physical contact with RNA poly. and de-stabilizes the elongation complex.

60
Q

How is the “terminator” stem-loop formed?

A

When sequences 2 and 3 (2 of the 4 sequences found between the promoter and first structural gene) base pair in the mRNA strand.

Molecular and Microbial Genetics (5 decks)

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