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MICR 221 > Lecture 7 > Flashcards

Lecture 7 Flashcards

Week 3

1
Q

In what ways do bacteria constantly monitor their surroundings?

A

Answer: Bacteria constantly monitor their surroundings for nutrients, stressors (e.g., antibiotics), and other cells.

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2
Q

Question: Why do bacteria make proteins according to conditions?

A

Answer: Bacteria make proteins according to conditions to avoid wasteful production and optimize resource utilization.

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3
Q

Question: What are the three levels of regulation controlling protein production and function in bacteria?

A

Answer: The three levels of regulation are transcriptional regulation (mRNA production), translational regulation (mRNA translation), and post-translational regulation (protein activity).

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4
Q

Question: What is transcriptional regulation in bacteria?

A

Answer: Transcriptional regulation in bacteria involves controlling the production of mRNA, influencing the synthesis of proteins.

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5
Q

Question: What is translational regulation, and how does it impact bacterial cells?

A

Answer: Translational regulation in bacteria refers to the control of mRNA translation into proteins. It plays a role in determining the rate of protein synthesis based on cellular conditions.

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6
Q

Question: How is post-translational regulation involved in controlling cellular functions in bacteria?

A

Answer: Post-translational regulation in bacteria involves modifying protein activity after translation, fine-tuning their functions to adapt to changing conditions.

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7
Q

Question: What is the significance of certain proteins for bacteria in the context of host colonization and infection?

A

Answer: Certain proteins are crucial for bacteria to colonize hosts and cause infections, but they are not needed outside the host environment.

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8
Q

Question: Why are certain genes not transcribed outside the host?

A

Answer: Certain genes are not transcribed outside the host because the proteins encoded by these genes are specifically required for interactions within the host environment.

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9
Q

Question: What are some factors through which bacteria can sense the host environment?

A

Answer: Bacteria sense the host environment through factors such as temperature (e.g., humans: 37 °C), nutrients (e.g., heme), and interactions with the host’s immune system.

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10
Q

Question: What is the role of temperature in bacterial sensing of the host?

A

Answer: Temperature, such as the human body temperature (37 °C), is a factor sensed by bacteria to determine their location within a host.

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11
Q

Question: What are the actions taken by bacteria in response to sensing the host environment?

A

Answer: In response to sensing the host environment, bacteria make proteins to attach to host cells, evade the immune system, and potentially kill host cells.

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12
Q

Question: Provide an example of a bacterial action related to pathogenesis.

A

Answer: An example of a bacterial action related to pathogenesis is the production of proteins that allow attachment to host cells, evasion of the immune system, and potentially causing harm to host cells.

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13
Q

What does RNA polymerase do in transcription?

A

transcribes DNA, making mRNA

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14
Q

What are the roles of the promoter and terminator?

A

Promoter: where to start
Terminator: where to stop

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15
Q

What is mRNA translated by?

A

ribosome

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16
Q

Question: What is a common feature of multiple genes that share a promoter in bacteria?

A

Answer: Multiple genes that share a promoter in bacteria often form operons, where a single promoter controls the transcription of multiple genes.

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17
Q

Question: Provide an example of a well-known operon and its characteristics.

A

Answer: An example is the lac operon. Transcription of the lac operon results in the production of polycistronic mRNA, and the genes within the operon typically have related functions.

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18
Q

Question: What is the outcome of the transcription of an operon in bacteria?

A

Answer: The transcription of an operon in bacteria produces polycistronic mRNA, allowing for the coordinated expression of multiple genes with related functions.

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19
Q

Question: What are the components of the core enzyme of RNA polymerase (RNAP)?

A

Answer: The core enzyme of RNA polymerase consists of five subunits.

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20
Q

Question: How do operons help bacteria respond to stimuli?

A

Answer: Operons in bacteria help coordinate the response to stimuli by allowing the simultaneous regulation of multiple genes involved in related functions.

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21
Q

Question: What is the significance of genes in operons having related functions?

A

Answer: Genes in operons having related functions enable bacteria to efficiently coordinate their response to environmental stimuli, as these genes often work together in specific biological pathways.

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22
Q

Question: What are the three main functions of RNA polymerase during transcription?

A

Answer: RNA polymerase performs three main functions during transcription: unwinding the DNA, synthesizing RNA de novo, and rewinding the DNA.

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23
Q

Question: What are Sigma (σ) factor proteins needed for in the process of transcription initiation?

A

Answer: Sigma (σ) factor proteins are needed for RNA polymerase (RNAP) to recognize promoters.

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24
Q

Question: Describe the initial step in transcription initiation.

A

Answer: The RNAP holoenzyme binds to the promoter region.

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25
Q

Question: What are the specific sites on the promoter where RNAP binds during transcription initiation?

A

Answer: The -35 and -10 sites are the locations on the promoter where RNAP binds.

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26
Q

Question: What is formed when the RNAP holoenzyme binds to the promoter?

A

Answer: The formation of the closed complex occurs when the RNAP holoenzyme binds to the promoter.

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27
Q

Question: What happens during the open complex formation in transcription initiation?

A

Answer: RNAP unwinds DNA to form the open complex.

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28
Q

Question: When does RNA synthesis begin during transcription initiation?

A

Answer: RNA synthesis begins after the formation of the open complex.

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29
Q

Question: What happens after the initiation of RNA synthesis? (sigma factor)

A

Answer: The Sigma factor leaves the complex.

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30
Q

Question: Where are the new nucleotides (NTPs) added during transcription elongation?

A

Answer: NTPs are added to the 3′ end of the RNA in the RNA-DNA hybrid.

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31
Q

Question: What is the nature of the nucleotides added during transcription elongation concerning the template strand (DNA)?

A

Answer: The nucleotides added during transcription elongation are complementary to the template strand (DNA).

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32
Q

Question: What happens to the DNA during the progress of RNA polymerase (RNAP) during transcription elongation?

A

Answer: The DNA is rewound as RNAP progresses in the process of transcription elongation.

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33
Q

Question: What is the role of RNA polymerase (RNAP) in transcription termination?

A

Answer: RNAP stops at terminators during transcription termination.

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34
Q

Question: What are factor-dependent terminators in transcription termination?

A

Answer: Factor-dependent terminators are termination sites that require additional proteins or factors for efficient termination.

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35
Q

Question: Which protein is involved in separating the RNA-DNA hybrid during transcription termination?

A

Answer: Rho factor is the protein that separates the RNA-DNA hybrid during transcription termination.

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35
Q

Question: What characterizes intrinsic terminators in transcription termination?

A

Answer: Intrinsic terminators are characterized by a specific DNA sequence: an inverted repeat followed by a poly(T) tract.

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36
Q

Question: How does the Rho factor contribute to transcription termination?

A

Answer: The Rho factor separates the RNA-DNA hybrid, facilitating the termination of transcription.

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37
Q

Question: What is the structural feature of DNA that indicates an intrinsic terminator?

A

Answer: Intrinsic terminators are identified by the DNA sequence: an inverted repeat followed by a poly(T) tract.

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37
Q

Question: What structural feature is formed in mRNA during the formation of an intrinsic terminator?

A

Answer: An inverted repeat forms a hairpin (or stem) loop in mRNA during the formation of an intrinsic terminator.

38
Q

Question: What is the role of poly(U) in the formation of an intrinsic terminator?

A

Answer: With poly(U), it forms a terminator in mRNA during transcription termination.

39
Q

Question: How does the loop formed behind RNA polymerase (RNAP) affect transcription?

A

Answer: The loop formed behind RNAP causes it to stall during transcription.

40
Q

Question: What is the nature of base pairing between U and A in the hairpin loop of an intrinsic terminator?

A

Answer: The base pairing between U and A is weak in the hairpin loop of an intrinsic terminator.

41
Q

Question: What happens to the RNA-DNA hybrid during transcription termination at intrinsic terminators?

A

Answer: The RNA-DNA hybrid dissociates during transcription termination at intrinsic terminators.

42
Q

Question: What leads to the departure of RNA polymerase (RNAP) during transcription termination at intrinsic terminators?

A

Answer: The dissociation of the RNA-DNA hybrid leads to the departure of RNAP, and transcription stops.

43
Q

Question: What characterizes constitutive genes in terms of transcription?

A

Answer: Constitutive genes are always transcribed, and their expression is constant.

44
Q

Question: Provide an example of an essential protein encoded by constitutive genes.

A

Answer: Essential proteins, such as those involved in central metabolism, are encoded by constitutive genes.

45
Q

Question: What are the two mechanisms by which transcription can be regulated?

A

Answer: Transcription can be regulated by DNA-binding proteins, which control initiation, and by mRNA structure, which affects elongation and termination.

45
Q

Question: How is the transcription of genes like β-galactosidase (involved in lactose catabolism) regulated?

A

Answer: The transcription of genes like β-galactosidase is regulated based on the need. For example, in the absence of lactose, there are fewer copies ( < 5 copies/cell), but in the presence of lactose, there are more copies (~3000 copies/cell).

46
Q

Question: Why do bacteria use multiple promoters?

A

Answer: Bacteria use multiple promoters because different genes require different regulatory signals. Multiple promoters allow for the precise control of gene expression.

47
Q

Question: What is the role of sigma factors in transcription initiation?

A

Answer: RNAP requires sigma factors to recognize promoters during initiation. Different sigma factors bind to different promoters, facilitating the specificity of transcription initiation for various genes.

48
Q

Question: What is the main function of sigma factors in the context of gene transcription?

A

Answer: Sigma factors control which genes are transcribed during the initiation phase of transcription.

48
Q

Question: How does altering sigma factor levels impact transcription?

A

Answer: Changing sigma factor levels leads to variations in transcription levels, influencing the expression of specific sets of genes.

49
Q

Genes controlled by a sigma factor often have what?

A

often have related functions

50
Q

Where do repressor proteins bind? What is this binding controlled by?

A

They bind to operator region, and binding is controlled by ligands

50
Q

What do repressor proteins do in terms of initiation? What type of control is this?

A

they block initiation, and this is negative transcriptional control

51
Q

Question: How are some repressor-controlled genes inducible?

A

Answer: Inducible repressor-controlled genes can be turned on. The inducer ligand prevents the repressor from binding to the operator, allowing transcription to proceed.

52
Q

What happens if lactose is present in terms of regulation of lac operon?

A
  • allolactose is made
    -allolactose binds to repressor LacI
    -LacI does not bind to operator (lacO)
    -operon is transcribed
    -enzymes for lactose catabolism are made
52
Q

Question: How does transcription occur in repressor-controlled genes that are repressible?

A

Answer: In repressible genes, the repressor, by itself, cannot bind to the operator, allowing transcription to proceed.

53
Q

Question: What is the mechanism by which repressor-controlled genes become repressed?

A

Answer: Repressible genes are turned off when a co-repressor ligand helps the repressor bind to DNA, preventing transcription.

53
Q

What happens if lactose is NOT present in terms of regulation of lac operon?

A

-allolactose is not made
-LacI can bind to operator (lacO)
-operon is NOT transcribed
-enzymes for lactose catabolism not made

54
Q

What is the function of co-repressor ligands?

A

helps repressor bind to DNA, which turns off transcription

55
Q

Question: In conditions of low tryptophan, what happens to the transcription of the trp operon?

A

Answer: In conditions of low tryptophan, the trp operon is transcribed, as more tryptophan is needed.

56
Q

Question: Describe the transcription status of the trp operon in conditions of high tryptophan.

A

Answer: In conditions of high tryptophan, the trp operon is not transcribed. This is because tryptophan acts as a co-repressor, and when present in abundance, it prevents transcription by binding to the trpR repressor.

57
Q

What is the function and control type of activator proteins?

A

help RNAP initiate transcription, and it is a positive transcriptional control

58
Q

Where does the activator bind, and what is this controlled by?

A

activator binds to activator-binding site (ABS), and the binding is regulated by ligands

59
Q

What does it mean that most activator controlled genes are inducible?

A

activator can’t bind to ABS by itself, which means transcription is off. An inducer ligand increases activator binding, which turns on transcription

60
Q

In terms of the ara operon, which is regulated by AraC, what happens when arabinose is present?

A

arabinose binds to AraC, enhancing initiation

61
Q

When do both transcription and translation occur?

A

They occur at the same time

61
Q

In terms of the ara operson, which is regulated by AraC, what happens when arabinose is NOT present?

A

AraC dimer bends DNA, preventing initiation

62
Q

Question: How do ribosomes and RNA polymerase (RNAP) work in relation to each other?

A

Answer: Ribosomes and RNA polymerase (RNAP) work in close proximity, sharing the same mRNA. They are involved in the processes of transcription and translation concurrently.

63
Q

Question: What is the consequence of ribosome stalling during mRNA translation?

A

Answer: Ribosome stalling during mRNA translation can impact RNAP activity. The slowdown or pause in translation can influence the efficiency of RNA polymerase and overall gene expression.

64
Q

Question: What is attenuation, and how does it relate to ribosome stalling and transcription?

A

Answer: Attenuation is a regulatory mechanism where ribosome stalling during translation impacts transcription. It is involved in the regulation of some amino acid biosynthetic operons.

65
Q

Question: How does low amino acid abundance affect attenuation?

A

Answer: Low amino acid abundance causes the ribosome to stall during translation, leading to attenuation.

66
Q

Question: Describe the impact of ribosome stalling on the transcription of the operon.

A

Answer: Ribosome stalling increases the transcription of the operon as a regulatory response.

67
Q

Question: What is unique about the leader region in the trp operon?

A

Answer: The leader region, situated between the operator and structural genes in the trp operon, contains trpL, a short gene that encodes a leader peptide with no functional role.

68
Q

Question: Why is the presence of multiple tryptophan (Trp) codons in the trpL gene significant?

A

Answer: The trpL gene having multiple Trp codons is significant because Trp codons are usually rare in genes. This abundance of Trp codons contributes to ribosome stalling during translation.

69
Q

Question: What is the consequence of a limited amount of tryptophanyl-tRNATrp in the cell?

A

Answer: The limited availability of tryptophanyl-tRNATrp can lead to ribosome stalling at Trp codons in the trpL gene.

70
Q

Question: How does ribosome stalling at Trp codons contribute to transcription attenuation?

A

Answer: Ribosome stalling at Trp codons allows the formation of a specific secondary structure in the mRNA leader region, contributing to transcription attenuation.

71
Q

Question: Describe the secondary structure formed in the mRNA leader region when trpL mRNA is not being translated by ribosome.

A

Answer: In the absence of ribosome translation;
- bases 1 and 2 pair together
- bases 3 and 4 pair together (forming poly(U) sequence and a hairpin loop, which act as a terminator)

72
Q

Question: What is the role of the terminator formed in the mRNA leader region during transcription attenuation?

A

Answer: The terminator formed by the poly(U) sequence and the hairpin loop causes RNA polymerase (RNAP) to stop transcribing DNA at the poly(T) tract, leading to transcription attenuation.

73
Q

Question: In conditions of low tryptophan levels, how does ribosome stalling affect the pairing of bases 1 and 2 in the mRNA leader region?

A

Answer: Ribosome stalling at Trp codons in low tryptophan levels blocks the pairing of bases 1 and 2.

74
Q

Question: What happens to bases 2 and 3 in the mRNA leader region when ribosome stalls at Trp codons during low tryptophan levels?

A

Answer: In low tryptophan levels, bases 2 and 3 pair together, forming an anti-terminator. This prevents the formation of the terminator structure.

74
Q

Question: What is the consequence of the anti-terminator formation in the mRNA leader region during low tryptophan levels?

A

Answer: The formation of the anti-terminator prevents the terminator from being formed, allowing RNA polymerase (RNAP) to transcribe genes beyond the poly(T) tract.

75
Q

Question: What is the impact of ribosome stalling at the trpL stop codon during high tryptophan levels on the pairing of bases 2 and 3 in the mRNA leader region?

A

Answer: Ribosome stalling at the trpL stop codon in high tryptophan levels blocks the pairing of bases 2 and 3.

75
Q

Question: In conditions of high tryptophan levels, how does ribosome stalling differ from low tryptophan levels?

A

Answer: In high tryptophan levels, ribosome translates Trp codons but stalls at the trpL stop codon.

76
Q

Question: What occurs between bases 3 and 4 in the mRNA leader region when ribosome stalls at the trpL stop codon during high tryptophan levels?

A

Answer: In high tryptophan levels, bases 3 and 4 pair together, forming a terminator structure.

77
Q

Question: What is the consequence of the terminator formation in the mRNA leader region during high tryptophan levels?

A

Answer: The terminator formation leads to the termination of transcription by RNA polymerase (RNAP), preventing the transcription of genes beyond the poly(T) tract.

78
Q

What is a riboswitch?

A

mRNA leader region that can adopt two different conformations

79
Q

What is the function of the two different conformations for a riboswitch?

A

one allows transcription to continue, the other one terminates transcription

80
Q

What is riboswitch conformation controlled by?

A

ligands

81
Q

What does a riboswitch often regulate?

A

metabolic genes

82
Q

Question: How are riboswitches that are normally off regulated in terms of transcription termination?

A

Answer: Terminators are present in the DNA sequence, and transcription is normally stopped at the poly(T) tract.

83
Q

Question: What activates riboswitches that are normally off, and how does this activation affect transcription termination?

A

Answer: Switches that are normally off are turned on by a metabolite or ligand. The binding of the metabolite or ligand promotes the formation of an anti-terminator, preventing the terminator from forming.

84
Q

Question: What is the consequence of the formation of an anti-terminator in riboswitches that are normally off?

A

Answer: The formation of an anti-terminator prevents the terminator from forming, allowing transcription to continue beyond the poly(T) tract.

85
Q

Question: How are switches that are normally on regulated in terms of transcription termination?

A

Answer: Transcription does not stop at the poly(T) tract in switches that are normally on.

86
Q

Question: What turns off switches that are normally on, and how does this affect transcription termination?

A

Answer: Switches that are normally on are turned off by a metabolite. The binding of the metabolite promotes the formation of an anti-antiterminator, preventing the formation of the anti-terminator.

87
Q

Question: What happens if the anti-antiterminator does not form in switches that are normally on?

A

Answer: If the anti-antiterminator does not form, the terminator is allowed to form, leading to transcription stopping at the poly(T) tract.

MICR 221 (12 decks)

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