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Molecular Regulation Flashcards

1
Q

Why do cells not express every gene (protein) at maximal level all the time?

A

1) Physical space limitations
2) Energy and resource conservation - takes lots of energy + resource to make proteins
3) Proteins may have CONTRADICTORY FUNCTIONS

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2
Q

(T/F) What microbes sense in their internal and external environments directs the synthesis of specific proteins.

A

True!

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3
Q

(T/F) Microbes are uncontrolled bags of enzymes.

A

False! Microbes are exquisitely tuned to their dynamic internal and external environments.

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4
Q

What are five methods (levels) of gene regulation?

A
  1. Alteration of DNA sequence
  2. Control of transcription (dna –> rna)
  3. Control of mRNA stability (mRNA degradation rate)
  4. Translational control (rna –> proteins)
  5. Post-translational control (changes in proteins)
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5
Q

(T/F) Gene regulation at the protein level is the most drastic (takes the most time and have the most impacts on cells) and the least reversible.

While gene regulation at the DNA levels is the most rapid and the most reversible.

A

False!

DNA is the most DRASTIC - it takes a while for the gene to be transcribed + translated and is PERMANENT.

Proteins are most RAPID and most REVERSIBLE.

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6
Q

What is a major site of regulatory control in bacterial cells? (i.e, where is gene regulation most exerted?)

A

Transcription initiation

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7
Q

What are DNA-BINDING REGULATORY PROTEINS? How are they affected by the changes in the environment?

A

DNA-binding regulatory proteins control initiation of transcription at gene promoters.

Changes in the internal/external environment of the cell affect the DNA-binding regulatory proteins by directing them to act or not to act.

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8
Q

Fill in the blanks:

Archaea and Eukarya have introns present in their cells, but bacteria have _______.

While archaea and bacteria have activator and repressor proteins, eukarya have ________ ________ and _________ ________.

A

Operons

Chromatin modifiers; transcription factors

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9
Q

(T/F) Plasmids are rare in eukarya and archaea, but common in bacteria.

A

False!

Plasmids are common in bacteria and archaea. They both have singular circular chromosome without a nucleus.

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10
Q

How many RNA polymerases do Eukarya have?

A

They have 3 main RNA polymerases (I, II, III).

Bacteria and archaea have a single polymerase, and the archaeal polymerase is similar to RNA pol II of eukaryotes.

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11
Q

Match the following terms to their definitions regarding RNA POLYMERASE HOLOENZYMES.

1) Sigma factor
2) Housekeeping sigma factors
3) Alternative sigma factors
4) Sigma factor in bacteria
5) Sigma factor in eukaryotes

A) bind to the RNA polymerase
B) a protein on the RNA pol holoenzyme that helps bind to certain DNA sequences and add specificity to the RNA polymerase
C) bind to DNA segments
D) responsible to direct the RNA polymerase to gene that are always expressed (tRNA, etc)
E) can direct the RNA polymerase to transcribe other genes depending on the cell’s needs

A

1) Sigma factor: a protein on the RNA pol holoenzyme that helps bind to certain DNA sequences (recognize promoter sequence) and add specificity to the RNA polymerase (needed 4 initiation of transcription)

2) Housekeeping sigma factors: responsible to direct the RNA polymerase to gene that are always expressed + needed (tRNA, etc)

3) Alternative sigma factors: can direct the RNA polymerase to transcribe other genes depending on the cell’s needs

4) Sigma factor in bacteria: bind to the RNA polymerase

5) Sigma factor in eukaryotes: bind to DNA segments

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12
Q

How do the ground states of transcription differ in bacteria and eukarya?

A

In bacteria, ground state is ON, meaning the normal state of transcription is always on unless repressed by an active repressing mechanism.

In eukarya, ground state is OFF, meaning the normal state of transcription is off, unless activated by an activating mechanism (promoters, enhancers, regulatory elements, etc).

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13
Q

How is transcription negatively regulated in prokaryotes?

A

1) Repression by repressors (brake on); transcription stopped
2) Absence of repression (neither brake or accelerator on; low levels of transcription)

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14
Q

How is transcription positively regulated in prokaryotes?

A

Activation by activators (gas on); high levels of transcription

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15
Q

Match the terms to their definitions regarding the structure of a genetic unit in prokaryotic cells:

1) Regulatory gene
2) Promoter
3) Operator
4) Control region
5) Operon

A) Binding site of RNA polymerase and transcription factors to initiate transcription.
B) Promoter and Operator
C) Activators come and bind here for positive regulation of transcription.
D) Made up of multiple structural genes and also includes the control region. Hence, it can control several genes of a metabolic pathway all at once.
E) Sits between the promoter and the structural genes. Regulators come and bind for negative regulation of transcription.

A

1) Regulatory gene: Activators come and bind here for POSITIVE regulation of transcription.

2) Promoter: Binding site of RNA polymerase to initiate transcription.

3) Operator: Sits between the promoter and the structural genes. Regulators come and bind for NEGATIVE regulation of transcription.

4) Control regions: Promoter and Operator

5) Operon: Made up of multiple structural genes and also includes the control region. Hence, it can control several genes of a metabolic pathway all at once. (V efficient)

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16
Q

Describe the differences between inducible and repressible operons.

A

Inducible operons: operon is always off (for metabolic pathways that are not always needed), so has to be INDUCED when cell wants it on.

For example, bacteria usually use glucose instead of lactose if the environment has glucose. When the environment has more lactose, the bacteria has to induce the lac gene to use lactose!

Repressible operons: operon is always on (metabolic pathway always needed) so has to be REPRESSED when cell wants it off.

For example, the metabolic pathway to make Arginine in a bacterial cell is always switched on. But when the cell has too many Arginine and does not need to make any more, the gene to make it has to be turned OFF!

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17
Q

(T/F) Changes in the extracellular conditions are detected with PLAMSA MEMBRANE-EMBEDDED SIGNALING MOLECULES.

A

True! These tell the cell what is happening outside.

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18
Q

What kind of signal transduction systems do most microbes posses?

A

A two-component signal transduction systems!

*Each system regulates a different set of genes.

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19
Q

Fill in the blank: Two-component systems are based on protein __________.

A

Phosphorylation

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20
Q

Match the following steps of the two component signal transduction system of microbes:

1) Step 1
2) Step 2
3) Step 3
4) Step 4
5) Step 5

A) Phosphate is transferred to a RESPONSE REGULATOR in the cytoplasm
B) SENSOR KINASE detects the condition outside of the cell
C) A PHOSPHATASE removes the phosphate and down-regulates the system.
D) Environmental SIGNAL binds to the sensor kinase and triggers or prevents phosphorylation (phosphate group from ATP is transferred to the kinase or to another target protein)
E) RESPONSE REGULATOR binds DNA and can stimulate or repress target genes.

A

Step 1: SENSOR KINASE detects the condition outside of the cell

Step 2: Environmental SIGNAL binds to the sensor kinase and triggers or prevents phosphorylation (phosphate group from ATP is transferred to the kinase or to another target protein)

Step 3: Phosphate is transferred to a RESPONSE REGULATOR in the cytoplasm

Step 4: RESPONSE REGULATOR binds DNA and can stimulate or repress target genes.

Step 5: A PHOSPHATASE removes the phosphate and down-regulates the system.

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21
Q

Match the following terms regarding the proteins involved in the 2 component signal transduction system:

1) Sensor kinase
2) Response regulator
3) Phosphatase

A) removes the phosphate on the cytosolic protein bound to the DNA at the end of the signalling, down regulating the system.
B) a membrane-bound enzyme that can be bound by an environmental signal which causes it to transfer a phosphate group from an ATP to itself (autophosphorylation) or another protein.
C) a CYTOSOLIC PROTEIN that is stimulated by the activated sensor kinase to bind to the DNA and alter gene expression.

A

1) Sensor kinase: a membrane-bound enzyme that can be bound by an environmental signal which causes it to transfer a phosphate group from an ATP to itself (autophosphorylation) or another protein.

2) Response regulator: a CYTOSOLIC PROTEIN that is stimulated by the activated sensor kinase to bind to the DNA and alter gene expression.

3) Phosphatase: removes the phosphate on the cytosolic protein bound to the DNA at the end of the signalling, down regulating the system.

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22
Q

What are response regulators controlled with?

A

Covalent modifications (like the addition of ATP) instead of ligands!

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23
Q

(T/F) The bacterial two-component signal transduction system has relatively slow effects.

A

False! It has very quick effects.

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24
Q

What is a REGULON? What are they controlled with? Why are they useful?

A

A regulon is a group of operons that are regulated as a unit.

Regulons are can be controlled by activators, repressors and ALTERNATIVE sigma factors!

Regulon allows the coordination of operons with differing functions to exert several responses (metabolic pathways) to a particular env condition. *when env condition requires more than just one response

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25
What are anti-sigma factors? What happens to them during stress?
Anti-sigma factors are factors bound to sigma factors to inhibit them from influencing RNA polymerase. When stressed, other proteins like PhyR can become activated that the anti-sigma factor has a higher affinity for. This frees the sigma factor and allows it to bind to the RNA polymerase holoenzyme and direct transcription to stress genes! Sometimes the opposite can be true. The anti-sigma factor can bind to the sigma factor and inhibit it as a stress response. *anti-anti-sigma factors also exist*
26
What are global control systems? Give an example.
Systems that control the EXPRESSION of MANY genes SIMULTANEOUSLY (aka regulons). Catabolite repression (starvation) is an example of global control. - controls use of carbon sources if more than 1 are present - synthesis of unrelated catabolic enzymes repressed (lactose operon) if glucose present - ensure best carbon + energy source used first
27
What is Rpos?
An alternative sigma factor that controls a stress response (starvation), by acting on multiple operons and leading to lots of different responses.
28
Match the following terms to their definitions regarding common regulation of genes AFTER transcription: 1) Attenuation 2) Riboswitches 3) Untranslated RNAs A) other regulatory RNAs influence the fates of transcribed mRNAs B) some mRNA sequence prevent their own translation into protein C) premature termination of transcription by regulatory sequences in the mRNA
1) Attenuation: premature termination of transcription by regulatory sequences in the mRNA 2) Riboswitches: some mRNA sequence prevent their own translation into protein 3) Untranslated RNAs: other regulatory RNAs influence the fates of transcribed mRNAs
29
What are second messengers? What are they involved in? Give examples.
Small molecules that do not serve as biosynthetic precursors (starting molecules/substrates) but instead have regulatory functions (change the activities of regulatory proteins and regulatory mRNAs). Often involved when environmental changes require COMPLEX PHYSIOLOGICAL RESPONSES for survival. cAMP, (p)ppGpp, and C-di-GMP are second messengers!
30
(T/F) Prokaryotes and eukaryotes share some second messengers.
True!
31
Match the following messengers to what they are involved in: 1) (p)ppGpp (alarmones) 2) cyclic diguanylate (C-di-GMP) 3) Autoinducers A) motility, cell cycle progression, biofilm formation, virulence B) quorum sensing C) stringent response, nutrient stress
(p)ppGpp (alarmones): stringent response, nutrient stress cyclic diguanylate (C-di-GMP): motility, cell cycle progression, biofilm formation, virulence autoinducers: quorum sensing
32
The stringent response is also known as the ________ response.
Stravation
33
How does ppGpp (guanosine tetraphosphate) allow cells to handle abrupt changes in nutrient availability?
Switches them from rapid growth to slower growth!
34
Which ribosomes trigger the synthesis of ppGpp? How?
Idling ribosomes (empty tRNAs). They activate RelA, which synthesizes ppGpp!
35
After ppGpp has been triggered by idling ribosomes, what does it do? How does this lead to an overall decrease in growth?
It binds to RNA polymerase and lowers it ability to transcribe ribosomal RNA (rRNA) genes! This causes a decrease in rRNA transcripts, leading to fewer ribosomes and an overall decrease in growth.
36
(T/F) The stringent response is also known as “Broadly conserved bacterial stress response that controls adaptation to nutrient deprivation, and its activation by a number of different starvation and stress signals."
True!
37
The stringent response shuts down _________ synthesis, and activates _____ _________ pathways.
Macromolecule Stress survival
38
What is shift down?
The reduction of amino acids in nutrients, that launches stringent response.
39
(T/F) After shift down, the bacterial growth is slowed down until there is a source of new nutrients.
False! The growth is slowed until bacteria can adapt to their new conditions!
40
What do alarmones (pppGpp or ppGpp) do to help bacteria survive the stress they are encountering?
1) Decrease rRNA, tRNA synthesis by inhibiting RNA pol transcription (slow growth) 2) Activate biosynthetic pathways to produce missing amino acids 3) Inhibit cell division 4) Activation of stress survival pathway (like reduction of energy available for biosynthesis)
41
(T/F) If conditions get better, tRNA and rRNA synthesis and ribosome production rapidly restarts.
False, it restarts slowly!
42
What do ppGpp and pppGpp stand for?
ppGpp - guanosine tetraphosphate pppGpp - guanosine pentaphosphate
43
(T/F) Most organisms produce alarmones as second messengers but the production of alramones may be stimulated by different signals and produce different stress responses.
True!
44
In E.Coli what molecule besides the RelA can activate the stringent response?
SpoT (goes an activates ppGpp which leads to growth arrest and stress response)
45
How and when is SpoT activated?
SpoT is activated in LIPID starvation through interactions with holo-acyl-carrier protein (Acp) and also by several different other starvation signals with unknown mechanisms.
46
Which molecule is activated by amino acid/carbon/respiration starvation in M.tuberculosis that synthesizes alarmones?
Rel instead of RelA!
47
Cells that express high levels of Rel are biased toward a ______ state, in which there is slow growth and greater resistance to antibiotics/stresses.
PERSISTER
48
What is persistence?
When a population of stress sensitive bacteria produce rare cells that are transiently tolerant to multiple stresses Stress can be antibiotics
49
What are persister cells?
Genetically identical to regularly growing bacteria but they survive lethal stresses (antibiotic treatment) in a non-growing, dormant stage. When the treatment is stopped, cells emerge from dormancy and grow, replenishing the population!
50
What is the cause of recurring Mycobacterium tuberculosis and pseudomonas aeruginosa infections?
Persister cells!
51
(T/F) The stringent response is directly linked to the TA (Toxin-Antitoxin) system!
True!
52
What are toxin-antitoxin modules? How does the toxic activity promote cellular adaption?
Genetic loci that encode a toxin whose production inhibits cell growth and an antitoxin. Toxic activity promote cellular adaption by slowing cell growth to ensure survival during stress.
53
(T/F) Toxin-antitoxin modules only found in bacteria with a role in normal physiology and pathogenicity.
False! It is found in almost all bacteria and many ARCHAEA.
54
Match the following terms to their definitions regarding a TA module that triggers persistence in E.col: 1) HipAB gene 2) HipA 3) HipB 4) PolyP 5) Lon A) Antitoxin that forms a stable complex with HipA B) Polyphosphate that are usually produced at different concentrations in bacteria C) Protease activated by polyP D) Encodes Hip A Hip B TA module that triggers persistence in E.coli E) Toxin that inhibits translation
1) HipAB gene - Encodes Hip A Hip B TA module that triggers persistence in E.coli 2) HipA - Toxin that inhibits translation 3) HipB - Antitoxin that forms a stable complex with HipA 4) PolyP - Polyphosphate that are usually produced at different concentrations in bacteria 5) Lon - Protease activated by polyP
55
If Lon is activated, HipB is _____, translation is ________, and growth _______.
Degraded; Inhibited; Arrested
56
How does HipA block translation?
It phosphorylates GLUTAMYL-tRNA-SYNTHETASE that can no longer charge amino acids, leading to ribosome stalling and activation of RelA which produces ppGpp (alarmone), inducing the stringent response pathway.
57
Cells that have triggered stringent response become ______.
Dormant. These are persister cells!
58
What is the Cyclic-di-GMP?
A second messenger used by E.coli cells to transition between a motile, single cell (planktonic) state and an adhesive multicellular (biofilm) state.
59
The transition of an E.coli from a planktonic state to a biofilm state is achieved by the synthesis and degradation of C-di-GMP. ____ C-di-GMP favours the planktonic state, while ____ C-di-GMP favours biofilm formation through inhibition of motility.
Low; high
60
(T/F) Cycli di-GMP is a second messenger found across all organisms.
False! It is only found in BACTERIA (all bacteria)!
61
Though C-di-GMP is used in biofilm formation, it also controls ________ in C.crescentus cell cycle.
MORPHOGENESIS (transition to stalked cells) Therefore, this universal bacterial second messenger is important for biofilm production and morphogenesis.
62
How is C-di-GMP involved in asymmetric division of C.crescentus?
Only stalked cells can divide and swarmer cells must turn into stalked cells to divide. C-di-GMP controls the transition of the the swarmer cell to the stalked cell. Low levels of this molecule are controlled by di-guanylate cyclases (PGCs) and phosphodiesterases (PDEs)!
63
Fill in the blanks: Autoinducer is a ________-_______ second messenger that allows cells to regulate gene expression based on the ______ of cells in the envrionment.
MEMBRANE-PERMEABLE Density
64
How does quorum sensing work in ALIIVIBRIO FISCHERI?
Quorum sensing was first discovered in ALIIVIBRIO FISCHERI, a luminescent bacterium that colonizes the light organ of the Hawaiian squid. The bacteria light up only when their cell number and the concentration of autoinducer rise above the threshold level.
65
What is POSTTRANSLATIONAL MODIFICATION? What systems does it involve? What is an example of it?
It's a modification of regulatory proteins that occurs after translation is complete that allows microbes to control their behaviours. It involves TWO-COMPONENT REGULATORY systems that control the activity of another protein (in contrast to initiation of transcription of target genes). An example of it is flagellated bacteria directing their movement through aqueous solutions using CHEMOTAXIS.
66
What are some post-translational modifications?
Phosphorylation Methylation Acetylation Ubiquitination
67
Fill in the blank: Chemotaxis allows bacteria to move ______ a chemical gradient.
Towards They move directly to the attractant chemicals, while move away from repellent chemicals.
68
How do chemotactic cells sense chemical gradients? What are they linked to? What does this do to the flagella?
RECEPTOR PROTEINS Proteins are linked to a SIGNAL TRANSDUCTION MECHANISM, that changes the direction of spin of the flagella.
69
________ rotation results in smooth swimming (run), while ________ rotation causes tumbling.
Counterclockwise Clockwise
70
(T/F) Because the natural setting of the flagella is to run, with no chemoattractant present it is always running.
False! Even though the natural setting of the flagella is to run, with no chemoattractant present it switches between runs and tumbles randomly.
71
What is the key to chemotaxis?
Suppress the number of tumbles. Balance the need for REDIRECTING TOWARDS A HIGHER GRADIENT and the need for RUNNING AS LONG AS POSSIBLE towards it when running in the right direction.
72
Match the following terms to their definitions regarding the modified two component system PART 1: 1) Methyl-accepting-chemotaxis proteins (MCP) 2) CheW 3) CheA A) Sensor kinase B) Receptor to the attractant C) Adaptor protein (between MCP and cheA)
1) Methyl-accepting-chemotaxis proteins (MCP): receptor to the attractant 2) CheW: adaptor protein (between MCP and cheA) 3) CheA: Sensor kinase (of the modified two component system)
73
What happens to CheA when a chemoattractant binds to MCP? How does this affect the flagella of the cell?
CheA is INACTIVATED when a chemoattractant binds to MCP, the flagella rotor is CCW, the cell is RUNNING!
74
MaMatch the following terms to their definitions regarding the modified two component system PART 2: 1) CheY 2) CheB and CheR 3) CheZ A) Unphosphorylates the CheY, causing the cell to RUN. B) Response regulator; when phosphorylated it binds to the flagella, cause the cell to TUMBLE. C) Sensory adaptors
1) CheY: Response regulator; when phosphorylated it binds to the flagella, cause the cell to TUMBLE. 2) CheB and CheR: Sensory adaptors 3) CheZ: Unphosphorylates the CheY, causing the cell to RUN.
75
In the absence of a ligand, MCP ______ CheA, which autophosphorylates and phosphorylates _____, which changes the rotor direction to a ______. Now the bacteria faces a new direction.
In the absence of a ligand, MCP ACTIVATES CheA, which autophosphorylates and phosphorylates CheY, which changes the rotor direction to a TUMBLE. Now the bacteria faces a new direction.
76
What is the function of CheZ? What does this do to the cell?
A negative regulation! It removes the phosphate of CheY, and CheY can no longer bind to the rotor anymore. This causes the cell to RUN, propelling the cell into a new direction.
77
What is CheB? What does it do?
CheB is a sensory adaptor, that is activated by CheA, but it actually goes and deactivates CheA in A NEGATIVE FEEDBACK LOOP!
78
Why do tumbles and runs alternate randomly in absence of chemoattractant?
No chemoattractant; CheA activated; Chey and CheB also activated. CheY leads to tumbling. CheB deactivates CheA to prevent further phosphorylation. CheY loses its phosphate (by CheZ or naturally), causing cell to RUN. CheB loses its phosphate (naturally), causing CheA to be activated again and the process continues.
79
(T/F) Bacteria always runs towards the higher gradient of chemoattractant.
False! Can run towards or against. Bacteria doesn't know where to go.
80
How does CheR (sensory adapter) causes cell to redirect itself toward a high gradient of chemoattractant?
If cell is going away from the chemogradient, CheR methylates MCP, which makes it be less responsive to chemoattractant and does not inactive CheA as normally it would. CheA phosphorylates CheY, causing CheY to bind to flagella and cause it to TUMBLE! This allows it to redirect itself toward a high gradient of chemoattractant!
81
(T/F) If there is no chemoattractant, MCP cannot be methylated by CheR!
True!
82
At high concentration of the chemoattractant, the MCP has to be __________ to prevent saturation. This is done by additional ________ by CheR. This results in the cell tumbling more and for it to run (turn off CheA), _____ ligand needs to bind!
Desensitized; Methylation More
83
At low concentration of the chemoattractant, the MCP has to be ___________. This is done by _____ demethylating the MCP. Low concentration means activation of CheA and more tumbling, which allows the cell to redirect itself to high concentration!
Resensitized; CheB
84
Match the terms to their definitions: 1) Che A 2) Che Y 3) Che Z 4) Che B 5) Che R A) Removes phosphate from CheY, allowing cell to RUN! B) Methylates MCP (in the presence of chemoattractant) to desensitize the receptor in high concentration of chemoattractant; to avoid saturation of the cell and to cause bacteria to tumble & reorient itself. C) Phosphorylated molecule binds to flagella and causes a CW motion; TUMBLING! D) When activated, inactivates CheA, allowing cell to RUN! Loses its phosphate naturally. Also demethylates MCP to resensitize receptor in lower concentrations of chemoattractant. E) Sensor kinase; activated when in absence of chemoattractant, and phosphorylates CheY and CheB!
CheA: sensor kinase; activated when in absence of chemoattractant, and phosphorylates CheY and CheB! CheY: Phosphorylated molecule binds to flagella and causes a CW motion; TUMBLING! CheZ: Removes phosphate from CheY, allowing cell to RUN! CheB: When activated, inactivates CheA, allowing cell to RUN! Loses its phosphate naturally. Also demethylates MCP to resensitize receptor in lower concentrations of chemoattractant. CheR: Methylates MCP (in the presence of chemoattractant) to desensitize the receptor in high concentration of chemoattractant; to avoid saturation of the cell and to cause bacteria to tumble & reorient itself.

z Microbiology (10 decks)

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