Molecular Regulation Flashcards
Why do cells not express every gene (protein) at maximal level all the time?
1) Physical space limitations
2) Energy and resource conservation - takes lots of energy + resource to make proteins
3) Proteins may have CONTRADICTORY FUNCTIONS
(T/F) What microbes sense in their internal and external environments directs the synthesis of specific proteins.
True!
(T/F) Microbes are uncontrolled bags of enzymes.
False! Microbes are exquisitely tuned to their dynamic internal and external environments.
What are five methods (levels) of gene regulation?
- Alteration of DNA sequence
- Control of transcription (dna –> rna)
- Control of mRNA stability (mRNA degradation rate)
- Translational control (rna –> proteins)
- Post-translational control (changes in proteins)
(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.
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.
What is a major site of regulatory control in bacterial cells? (i.e, where is gene regulation most exerted?)
Transcription initiation
What are DNA-BINDING REGULATORY PROTEINS? How are they affected by the changes in the environment?
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.
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 _________ ________.
Operons
Chromatin modifiers; transcription factors
(T/F) Plasmids are rare in eukarya and archaea, but common in bacteria.
False!
Plasmids are common in bacteria and archaea. They both have singular circular chromosome without a nucleus.
How many RNA polymerases do Eukarya have?
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.
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
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
How do the ground states of transcription differ in bacteria and eukarya?
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).
How is transcription negatively regulated in prokaryotes?
1) Repression by repressors (brake on); transcription stopped
2) Absence of repression (neither brake or accelerator on; low levels of transcription)
How is transcription positively regulated in prokaryotes?
Activation by activators (gas on); high levels of transcription
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.
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)
Describe the differences between inducible and repressible operons.
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!
(T/F) Changes in the extracellular conditions are detected with PLAMSA MEMBRANE-EMBEDDED SIGNALING MOLECULES.
True! These tell the cell what is happening outside.
What kind of signal transduction systems do most microbes posses?
A two-component signal transduction systems!
*Each system regulates a different set of genes.
Fill in the blank: Two-component systems are based on protein __________.
Phosphorylation
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.
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.
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.
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.
What are response regulators controlled with?
Covalent modifications (like the addition of ATP) instead of ligands!
(T/F) The bacterial two-component signal transduction system has relatively slow effects.
False! It has very quick effects.
What is a REGULON? What are they controlled with? Why are they useful?
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
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
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
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.
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
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!
(T/F) Prokaryotes and eukaryotes share some second messengers.
True!
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
The stringent response is also known as the ________ response.
Stravation
How does ppGpp (guanosine tetraphosphate) allow cells to handle abrupt changes in nutrient availability?
Switches them from rapid growth to slower growth!
