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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
Question: What are the specific sites on the promoter where RNAP binds during transcription initiation?
Answer: The -35 and -10 sites are the locations on the promoter where RNAP binds.
26
Question: What is formed when the RNAP holoenzyme binds to the promoter?
Answer: The formation of the closed complex occurs when the RNAP holoenzyme binds to the promoter.
27
Question: What happens during the open complex formation in transcription initiation?
Answer: RNAP unwinds DNA to form the open complex.
28
Question: When does RNA synthesis begin during transcription initiation?
Answer: RNA synthesis begins after the formation of the open complex.
29
Question: What happens after the initiation of RNA synthesis? (sigma factor)
Answer: The Sigma factor leaves the complex.
30
Question: Where are the new nucleotides (NTPs) added during transcription elongation?
Answer: NTPs are added to the 3′ end of the RNA in the RNA-DNA hybrid.
31
Question: What is the nature of the nucleotides added during transcription elongation concerning the template strand (DNA)?
Answer: The nucleotides added during transcription elongation are complementary to the template strand (DNA).
32
Question: What happens to the DNA during the progress of RNA polymerase (RNAP) during transcription elongation?
Answer: The DNA is rewound as RNAP progresses in the process of transcription elongation.
33
Question: What is the role of RNA polymerase (RNAP) in transcription termination?
Answer: RNAP stops at terminators during transcription termination.
34
Question: What are factor-dependent terminators in transcription termination?
Answer: Factor-dependent terminators are termination sites that require additional proteins or factors for efficient termination.
35
Question: Which protein is involved in separating the RNA-DNA hybrid during transcription termination?
Answer: Rho factor is the protein that separates the RNA-DNA hybrid during transcription termination.
35
Question: What characterizes intrinsic terminators in transcription termination?
Answer: Intrinsic terminators are characterized by a specific DNA sequence: an inverted repeat followed by a poly(T) tract.
36
Question: How does the Rho factor contribute to transcription termination?
Answer: The Rho factor separates the RNA-DNA hybrid, facilitating the termination of transcription.
37
Question: What is the structural feature of DNA that indicates an intrinsic terminator?
Answer: Intrinsic terminators are identified by the DNA sequence: an inverted repeat followed by a poly(T) tract.
37
Question: What structural feature is formed in mRNA during the formation of an intrinsic terminator?
Answer: An inverted repeat forms a hairpin (or stem) loop in mRNA during the formation of an intrinsic terminator.
38
Question: What is the role of poly(U) in the formation of an intrinsic terminator?
Answer: With poly(U), it forms a terminator in mRNA during transcription termination.
39
Question: How does the loop formed behind RNA polymerase (RNAP) affect transcription?
Answer: The loop formed behind RNAP causes it to stall during transcription.
40
Question: What is the nature of base pairing between U and A in the hairpin loop of an intrinsic terminator?
Answer: The base pairing between U and A is weak in the hairpin loop of an intrinsic terminator.
41
Question: What happens to the RNA-DNA hybrid during transcription termination at intrinsic terminators?
Answer: The RNA-DNA hybrid dissociates during transcription termination at intrinsic terminators.
42
Question: What leads to the departure of RNA polymerase (RNAP) during transcription termination at intrinsic terminators?
Answer: The dissociation of the RNA-DNA hybrid leads to the departure of RNAP, and transcription stops.
43
Question: What characterizes constitutive genes in terms of transcription?
Answer: Constitutive genes are always transcribed, and their expression is constant.
44
Question: Provide an example of an essential protein encoded by constitutive genes.
Answer: Essential proteins, such as those involved in central metabolism, are encoded by constitutive genes.
45
Question: What are the two mechanisms by which transcription can be regulated?
Answer: Transcription can be regulated by DNA-binding proteins, which control initiation, and by mRNA structure, which affects elongation and termination.
45
Question: How is the transcription of genes like β-galactosidase (involved in lactose catabolism) regulated?
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
Question: Why do bacteria use multiple promoters?
Answer: Bacteria use multiple promoters because different genes require different regulatory signals. Multiple promoters allow for the precise control of gene expression.
47
Question: What is the role of sigma factors in transcription initiation?
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
Question: What is the main function of sigma factors in the context of gene transcription?
Answer: Sigma factors control which genes are transcribed during the initiation phase of transcription.
48
Question: How does altering sigma factor levels impact transcription?
Answer: Changing sigma factor levels leads to variations in transcription levels, influencing the expression of specific sets of genes.
49
Genes controlled by a sigma factor often have what?
often have related functions
50
Where do repressor proteins bind? What is this binding controlled by?
They bind to operator region, and binding is controlled by ligands
50
What do repressor proteins do in terms of initiation? What type of control is this?
they block initiation, and this is negative transcriptional control
51
Question: How are some repressor-controlled genes inducible?
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
What happens if lactose is present in terms of regulation of lac operon?
- 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
Question: How does transcription occur in repressor-controlled genes that are repressible?
Answer: In repressible genes, the repressor, by itself, cannot bind to the operator, allowing transcription to proceed.
53
Question: What is the mechanism by which repressor-controlled genes become repressed?
Answer: Repressible genes are turned off when a co-repressor ligand helps the repressor bind to DNA, preventing transcription.
53
What happens if lactose is NOT present in terms of regulation of lac operon?
-allolactose is not made -LacI can bind to operator (lacO) -operon is NOT transcribed -enzymes for lactose catabolism not made
54
What is the function of co-repressor ligands?
helps repressor bind to DNA, which turns off transcription
55
Question: In conditions of low tryptophan, what happens to the transcription of the trp operon?
Answer: In conditions of low tryptophan, the trp operon is transcribed, as more tryptophan is needed.
56
Question: Describe the transcription status of the trp operon in conditions of high tryptophan.
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
What is the function and control type of activator proteins?
help RNAP initiate transcription, and it is a positive transcriptional control
58
Where does the activator bind, and what is this controlled by?
activator binds to activator-binding site (ABS), and the binding is regulated by ligands
59
What does it mean that most activator controlled genes are inducible?
activator can't bind to ABS by itself, which means transcription is off. An inducer ligand increases activator binding, which turns on transcription
60
In terms of the ara operon, which is regulated by AraC, what happens when arabinose is present?
arabinose binds to AraC, enhancing initiation
61
When do both transcription and translation occur?
They occur at the same time
61
In terms of the ara operson, which is regulated by AraC, what happens when arabinose is NOT present?
AraC dimer bends DNA, preventing initiation
62
Question: How do ribosomes and RNA polymerase (RNAP) work in relation to each other?
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
Question: What is the consequence of ribosome stalling during mRNA translation?
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
Question: What is attenuation, and how does it relate to ribosome stalling and transcription?
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
Question: How does low amino acid abundance affect attenuation?
Answer: Low amino acid abundance causes the ribosome to stall during translation, leading to attenuation.
66
Question: Describe the impact of ribosome stalling on the transcription of the operon.
Answer: Ribosome stalling increases the transcription of the operon as a regulatory response.
67
Question: What is unique about the leader region in the trp operon?
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
Question: Why is the presence of multiple tryptophan (Trp) codons in the trpL gene significant?
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
Question: What is the consequence of a limited amount of tryptophanyl-tRNATrp in the cell?
Answer: The limited availability of tryptophanyl-tRNATrp can lead to ribosome stalling at Trp codons in the trpL gene.
70
Question: How does ribosome stalling at Trp codons contribute to transcription attenuation?
Answer: Ribosome stalling at Trp codons allows the formation of a specific secondary structure in the mRNA leader region, contributing to transcription attenuation.
71
Question: Describe the secondary structure formed in the mRNA leader region when trpL mRNA is not being translated by ribosome.
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
Question: What is the role of the terminator formed in the mRNA leader region during transcription attenuation?
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
Question: In conditions of low tryptophan levels, how does ribosome stalling affect the pairing of bases 1 and 2 in the mRNA leader region?
Answer: Ribosome stalling at Trp codons in low tryptophan levels blocks the pairing of bases 1 and 2.
74
Question: What happens to bases 2 and 3 in the mRNA leader region when ribosome stalls at Trp codons during low tryptophan levels?
Answer: In low tryptophan levels, bases 2 and 3 pair together, forming an anti-terminator. This prevents the formation of the terminator structure.
74
Question: What is the consequence of the anti-terminator formation in the mRNA leader region during low tryptophan levels?
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
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?
Answer: Ribosome stalling at the trpL stop codon in high tryptophan levels blocks the pairing of bases 2 and 3.
75
Question: In conditions of high tryptophan levels, how does ribosome stalling differ from low tryptophan levels?
Answer: In high tryptophan levels, ribosome translates Trp codons but stalls at the trpL stop codon.
76
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?
Answer: In high tryptophan levels, bases 3 and 4 pair together, forming a terminator structure.
77
Question: What is the consequence of the terminator formation in the mRNA leader region during high tryptophan levels?
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
What is a riboswitch?
mRNA leader region that can adopt two different conformations
79
What is the function of the two different conformations for a riboswitch?
one allows transcription to continue, the other one terminates transcription
80
What is riboswitch conformation controlled by?
ligands
81
What does a riboswitch often regulate?
metabolic genes
82
Question: How are riboswitches that are normally off regulated in terms of transcription termination?
Answer: Terminators are present in the DNA sequence, and transcription is normally stopped at the poly(T) tract.
83
Question: What activates riboswitches that are normally off, and how does this activation affect transcription termination?
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
Question: What is the consequence of the formation of an anti-terminator in riboswitches that are normally off?
Answer: The formation of an anti-terminator prevents the terminator from forming, allowing transcription to continue beyond the poly(T) tract.
85
Question: How are switches that are normally on regulated in terms of transcription termination?
Answer: Transcription does not stop at the poly(T) tract in switches that are normally on.
86
Question: What turns off switches that are normally on, and how does this affect transcription termination?
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
Question: What happens if the anti-antiterminator does not form in switches that are normally on?
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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