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microbio unit 2 > week 6 > Flashcards

week 6 Flashcards

1
Q

activator

A
  • positive control
  • The protein binds upstream of the promoter and encourages RNAP binding
  • Example: mismatch in -35, but a transcription factor can make up that deficit under certain environmental conditions.
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2
Q

repressor

A
  • negative control
  • The protein binds to the operators to block RNAP binding (lac)
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3
Q

operator

A
  • segment of DNA in operon to which the repressor binds.
  • It controls teh expression of genes adjacent to it.
  • Downstream of promoter
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4
Q

promoter

A

is located at the start of the gene (recognition/binding site for RNAP/Oreinets polymerase)

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5
Q

RNAP

A

RNA polymerase, an enzyme that catalyzes the synthesis of RNA

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6
Q

sigma factor? What role does the sigma factor play in the initiation of transcription?

A
  • a protein that helps bacterial RNAP core enzymes recognize the promoter at teh start of the gene (Critical for initiation )
  • First, it recognizes the -35 sequence and directs the RNAP to sit on that promoter region.
  • Sigma and RNAP undergo a conformational change that causes DNA in the -10 region to separate.
  • Creates an open complex for transcription to occur
  • Changing sigma factors changes the presence of where RNAP needs to go
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7
Q

leader sequence

A
  • in DNA transcribed into mRNA but not amino acids (folding)
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8
Q

inducer? corepressor?

A
  • inducer binds to repressors causing them to change shape and be unable to bind DNA, this turns on gene expression
  • co-repressor binds to repressors and keeps gene expression off
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9
Q

what are teh two kinds of regulations?

A
  • constitutive genes - housekeeping genes) - constant supply needed (central metabolic pathway ) - always on
    = give off basal expression
  • expression is regulated - some enzymes are only needed during specific conditions/environments.
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10
Q

How do bacteria regulate their response to external stimuli (three broad ways)?

A
  1. Transcriptional - initiation or elongation (regulation in the step that involves making mRNA from DNA)
  2. Translational regulation (regulation on mRNA/ribosome to control the amount of protein being made)
  3. Posttranslational modifications (modifications on protein to increase or decrease their activity)
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11
Q

What is regulation always about? (pathway)

A
  • Signal -> sensor -> amplifier-> effector (acts on a genetic switch)
  • A lot of stuff happens in bacteria that happens all at once, so they need to be quick about it
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12
Q

when are RNA products regulated in transcription?

A
  • Initiation (activator/repressor binds to promoter)
  • Elongation (attenuation)
  • Termination (termination/ antitermination loops)
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13
Q

How does environmental signaling influence bacterial transcription elongation?

A
  • When environmental conditions change, such as an influx of a certain substance, bacteria can receive a new signal that prompts them to alter what mRNA they are producing. This allows the bacteria to quickly adjust their gene expression in response to changes in their surroundings
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14
Q

What role does the mRNA leader region play in the regulation of transcription termination?

A
  • The mRNA leader region is typically long and can form specific RNA folding patterns.
  • These folding patterns influence transcriptional termination, meaning they can determine whether transcription is terminated early or allowed to continue, thereby regulating gene expression at the elongation phase.
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15
Q

What is attenuation ? how can it happen?

A
  • Is the termination of transcription within the leader region
  • happens through a stem-loop structure in the leader RNA depending on the level of trp (high trp means that there is one and stops transcription)
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16
Q

What is a riboswitch?

A
  • It is a specialized form of transcription attenuation that is found in bacteria and archaea.
  • Folding of the RNA leader sequence determines if transcription will occur or terminate and is a response to the effector molecule binding to teh RNA
17
Q

What are RNA thermometers, and how do they regulate translation? How do RNA thermometers use temperature to influence ribosome binding?

A
  • RNA thermometers are RNA secondary structures located in the leader sequence of mRNA that regulate translation in a temperature-dependent manner.
  • The RNA thermometer folds into a structure to prevent access of the ribosome to the Shine-Dalgarno (SD) sequence within the mRNA at lower temperatures.
18
Q

How are genes organized and regulated in an operon, and how does this differ between prokaryotes and eukaryotes?

A
  • Organized 3-4 regions: leader first, then coding region, then spacer (if polycistronic), more coding regions, and finally a trailer at the 3’ end
  • Eukaryotes are monocentric = one gene in 1 RNA, resulting in 1 protein
19
Q

What is repressible control? How does the presence of tryptophan regulate transcription in the trp operon?

A
  • Turns transcription OFF by the presence of specific molecules
  • In the trp operon, the presence of tryptophan acts as a co-repressor, meaning that when tryptophan is abundant, it binds to the repressor protein, enabling it to bind to the operator and block transcription.
  • When tryptophan levels are low, the repressor is inactive, allowing transcription of the genes responsible for synthesizing tryptophan to occur.
20
Q

What is diauxic growth, and how does it relate to the regulation of the lac operon? catabolite repression?

A
    • Catabolite repression is a global regulatory mechanism where glucose inhibits the lac operon’s expression, even if lactose is present.
  • Diauxic growth refers to the biphasic growth pattern in which a cell preferentially uses glucose as its carbon source first.
  • Biphasic growth pattern - preferential use of one carbon source over another (glucose first)
  • Once glucose is exhausted, there is a lag phase - where now lactose is being used ( after the preferred substrate is used growth will resume using the second carbon source)
21
Q

What are the four scenarios of lactose and glucose interaction that regulate lac operon transcription?

A
  1. Lactose but no glucose: Allolactose binds to the inactive repressor, and with high cAMP levels activating CAP, transcription occurs.
  2. Lactose + glucose: The repressor is inactive due to allolactose, but low cAMP results in inactive CAP, and transcription does not occur.
  3. Neither lactose nor glucose: The repressor remains active, and transcription is repressed.
  4. Glucose but no lactose: The repressor binds to the operator, CAP is inactive due to low cAMP, and no transcription occurs.
22
Q

What is the two-component system? sensor kinase?

A
  • Direct line for a bacterial system
  • In the two-component system, a sensor kinase (e.g., EnvZ) spans the plasma membrane, detecting environmental changes such as osmolarity.
  • The sensor kinase phosphorylates itself and then transfers the phosphate to a response regulator in the cytoplasm.
  • The response regulator undergoes a conformational change, which triggers transcriptional changes, allowing the bacteria to respond to the detected environmental signal.
23
Q

what are alternate sigma factors ? what do these help with?

A
  • these change the expression of many genes, directing RNAP to specific subsets of bacteria promoters.
  • These help bacteria control which genes should be turned on or off in response to different conditions
  • -Crucial contributor to facilitating engagement of RNA polymerase with a gene, to initiae transctiption. Different sigma factors have differing affinities for different DNA sequences, so alternate
    sigma factors immediately change expression of many genes as they direct RNA polymerase to specific
    subsets of bacterial promoters,
    e.g. to change growth phase, metabolic modes, response to heat shock stress
24
Q

What are second messengers? what cellular process can be effected?

A
  • Small molecules respond to a signal outside the cell. (Receptors and signals that are relayed into the cell and impact gene expression through transduction can change form. )
  • Allows for the cell cycle progression, biofilm formation, virulent gene expression, etc
25
Q

what is a stringent response?

A
  • second messangers
  • Amino acid starvation decreases the production of tRNA and rRNA in cells while increasing the transcription of amino acid genes.
    Protein RelA produces pppGpp when an uncharged tRNA enters the ribosome.
26
Q

What is chemotaxis? porcess?

A
  • Movement in response to chemical stimulus
  • MCP/ methyl-accepting chemotaxis protein = chemoreceptors in the membrane will bend to environmental chemicals, initiating phosphorelay towards cheY, which governs flagella rotation
27
Q

what is quorum sensing?

A
  • Cell-to-cell communication
28
Q

How do regulatory proteins control transcription initiation, and what structural feature helps them interact with DNA?

A
  • by binding to the promoter region and positioning RNA polymerase (RNAP) for transcription.
  • A key structural feature of these proteins is the helix-turn-helix motif, which allows them to interact with the grooves of the DNA, similar to a “cowboy on a horse.” This interaction can alter the DNA’s topology or flip regions to either promote or inhibit transcription
29
Q

what are the three genes for lactose uptake and metabolism?

A
  1. lacZ - encodes for an enzyme that cleaves disaccharides to release two monomers for consumption
  2. B-galactosidase - hydrolyzes lactose into galactose and glucose
  3. Lac repressor (lacL) binds the operator and inhibits transcription when no lactose
30
Q

what are the four types of regulations that global regulatory systems use?

A

Two-component signal transduction systems
Phophorelays system
Sigma factors
Second messengers

31
Q

What is the global regulatory system? how do they help bacteria adapt to changing conditions? regulon?

A
  • are regulatory networks that can simultaneously affect many genes, operons, and pathways, allowing bacteria to adapt to changing environmental conditions.
  • regulon genes or operons controlled by a common global regulatory protein
32
Q

How does the lac repressor regulate transcription in the presence and absence of lactose?

A
  • In the absence of lactose, the lac repressor binds to the operator and creates DNA loops to prevent RNAP and sigma factors from accessing the promoter, inhibiting transcription. (negative control - repressor prevents gene expression )
  • lactose is present, lactose permease brings lactose into the cell, and β-galactosidase converts lactose to allolactose, which will bind to the repressor, preventing the repressor form from binding to the operator = allowing transcription from happening (induces the expression of the operon)
33
Q

How does the Catabolite Activator Protein (CAP) regulate transcription in response to glucose levels?

A
  • regulates transcription based on glucose levels (second messenger)
  • When glucose levels are low, ATP is converted to cAMP, which binds and activates CAP = transcription
  • CAMP is not produced when glucose levels are high, leaving CAP inactive and preventing transcription activation.
34
Q

what do cyclic dinnucleotides act as? two classes? in high concnetrations what happens?

A
  • act as key signaling molecules in bacteria by binding to effector molecules in the cytoplasm.
  • Two classes of enzymes control their synthesis and degradation. These molecules regulate essential cellular processes, such as transitioning from a motile (swimming) state to a sessile (stationary) state.
  • In higher concentrations, cyclic dinucleotides trigger the production of polysaccharides, leading to the formation of biofilms.
35
Q

What is the role of the restriction-modification system in bacteria? Restriction endonucleases?

A
  • The restriction-modification system in bacteria is an innate defense mechanism used to restrict the growth of viruses.
    -it is encoded in the bacterial genome and expressed at low levels.
  • which recognize specific DNA sequences in foreign viral DNA and cut it, preventing viral replication and growth.
36
Q

CRISPR/Cas system ? process?

A
  • adaptive immunity
  • Adaptation stage - occurs upon infection by a virus
  • If the cell survives, it adds pieces of the viral genome to its Casper array
  • Expression stage - CRISPR region transcribed to yield a precursor RNA (Cas protein processes this into mature CRISPR RNAs (crRNAs) )
  • Interface stage - during viral infection, the cas-crRNAs block VIRAL DNA/mRNA

microbio unit 2 (6 decks)

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