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88 Cards in this Set

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Replication is regulated by....
ATP levels (DnaA) and GATC methylation at the oriC
Transcription is regulated by...
activators/repressors at initiation;
attenuation affects premature termination.
Negative regulation of transcription is carried out by....
DNA binding proteins called repressors.
Genes are not transcribed when...
repressors bind to operators (DNA sites) and inhibit RNAP activity.
Explain negative control of an inducible gene.
Transcription can occur like normal until a repressor protein is formed. It then binds to the operators and stops the activity of the RNAP.
Repressors act by preventing either....
initiation of elongation of transcription.
What are corepressors?
They are ligands that bind to repressors to regulate repressor activity under different conditions.
Corepressors are used for genes involved in...
anabolic or biosynthetic reactions.
Inducers are used for...
catabolic reaction genes.
Positive regulation of transcription is carried out by....
DNA-binding proteins called activators.
Genes that are positively regulated are only transcribed when.....
activators bind to DNA and facilitate RNAP activity at the promoters.
Activators act by....
helping RNAP or other activators bind at promoters.
Activators bind........under different conditions.
ligands that regulate DNA binding activity
Catbolic pathways use ______ and a have _____ control.
repressors and inducers (inducers signal that substrates are present)
Biosynthetic pathways use.....
repressors and co-repressors (end product is often co-repressors).
Biosynthetic pathways also use other transcriptional controls like....
attenuation and translational and post-translational controls.
In the lac operon, the gene products control....
the entry and catabolism of lactose as an alternate energy source when the preferred sugar, glucose, is unavailable.
Small amounts of lactose that enter the cells are converted to ______ in a side reaction.
allolactose
Allolactose does what to the gene expression of lactose?
it is an inducer that inactivates the lacI repressor leading to full gene expression.
WHat does lacI do?
It encodes for the repressor that binds to DNA in the absence of lactose/allolactose and blocks the binding of RNAP.
All DNA binding proteins have "off rates" which means...
they occasionally come off DNA and allow a transcript to be made if CAP-cAMP is bound.
In regulation of the lac operon, optimal RNAP binding requires....
depression by allolactose and positive action of CAP-cAMP (Catabolite activator protein).
CAP-cAMP regulates...
many genes (approx. 200), signaling that alternate fuel sources are needed.
The lac promoter has a -35 region. What does this mean?
binding of RNAP requires prior binding of the CAP-cAMP to the adjacent site and interactions with the alpha subunit of RNAP to compensate.
CAP-cAMP can stabilize....
binding of other adjacent activators.
CAP only binds to DNA when...
cAMP levels are high.
cAMP levels are...
inversely related to glucose levels.
How is the cAMP formed?
By adenylate cyclase and ATP.
Glucose down regulates cAMP, how?
By down regulating the adenylate cyclase activity via PTS
Biosynthetic operons contain genes that...
encode enzymes for the production of a specific building block.
In tryptophan and other building blocks, the end products can function as...
co-repressors that turn off transcription of the operon when the end product accumulates (some use attenuation, some only use attenuation).
In attenuation, .........can form when end products accumulate.
alternate RNA structures of leader genes/sequences
In attenuation, explain what happens when product levels are high?
conditions favors the formation of the hairpin structures that causes ρ-independent transcription termination.
In attenuation, explain what happens when product levels are low?
the terminator hairpin doesn't form and the termination of transcription doesn't occur.
What is the regulation of gene expression by a riboswitch?
a specialized form of attenuation or translational regulation that occurs when end products of biosynthetic pathways bind to mRNA sequences to effect transcription termination or prevent translation
Two examples of a riboswitch.
1. Inhibition of translation by Shine Dalgarno sequence occlusion.
2. Attenuation (transcription doesn't proceed).
What are riboswitches used for?
AA and vitamin biosynthetic pathways.
sRNAs are also called...
siRNA, sRNAs, ncRNAs,
sRNAs can be....
either positive or negative regulators.
How do anti-sense RNAs work?
they typically bind to leader sequence and block translation by blocking access of mRNA to ribosome, but some sRNAs promote ribosome binding.
How are housekeeping enzymes regulated?
by allosteric (non-covalent) ligands that transiently control activity by changing the conformation of the enzyme (catalytic site).
Allosteric regulation is not limited by....
biochemistry since covalent bonds not used. This means that almost anything can be allosterically inhibited.
Biosynthetic pathways use many ____.
enzymes.
In biosynthetic pathways, the activity of the first enzyme...
is often feed-back regulated using the end product as an allosteric effector.
The two forms of phosphorylation and the uses for them.
Kinase puts it on, phospatase takes it off.
Used in 2-component and phosphorelay systems.
The two forms of methylation and the uses for them.
Methylase puts it on, demethylase takes it off.
Used for chemotaxis and other taxes.
Explain what these put on and what they are used for: adenylylation, ADP ribosylation, uridylylation.
These are all ways to covalently modify proteins via covalent attachment.
adenylyation attaches AMP.
ADP ribosylation attaches ADP.
Uridylylation attaches uridine.
Control of enzymatic activity (gln synthetase).
The two forms of acetylation and the uses for them.
Acetylase puts it on, deactylase takes it off.
Controls charges on NH2 groups (DNA-binding).
What is an operon?
A set of genes found on a polycistronic mRNA, its promoter region and sometimes a regulatory protein.
What is a regulon?
a set of operons that all have the same set of transcriptional regulators.
The ara regulon is comprised of three operons: ___, ___, & ___. These are all regulated by ___ & ___.
araBAD, araE, & araFGH; araC & CAP-cAMP.
What is a modulon?
a set of regulatons/operons that share a common element of regulation.
(ex: the CAP modulon contains all regulons/operons, including the lac operon and ara regulon, that are all regulated by CAP/cAMP.....but each operon has other regulators as well).
How many sigma factors are in E. coli? In B. subtilis?
7; 14
The extras are for sporulation. Each has its own -35 sequence.
What sigma is responsible for heat shock?
sigma 32
Nitrogen utilization uses....
sigma factors + other control.
In 2-component systems, sensors are often...
integral membrane proteins. They are also kinases that autophosphorylate when the signal binds.
In the 2-component system that was given as an example, what was the sensor kinase, and what did it do?
EnvZ. It sensed hypertonic conditions. It phosphorylated His-P.
The phosphorylated kinase transfers the P to..
an asparartic acid (aspartate) on the next component (usually a response regulator) that controls target genes.
What happens to the regulator once it gets phosphorylated?
it can become an activator or repressor.
The 2-component system is absent in...
strictly parasitic bacteria.
Sporulation is an example of...
a phosphorelay system when there are >2 components.
What regulates when the cell begins the sporulation process?
Spo0A-P levels
When the activation of sporulation begins, what occurs?
kinA gets activated by starvation and Spo0F gives a P to Spo0B--->Spo0A. So a buildup of Spo0A-P occurs.
What occurs at low levels of Spo0A-P?
Survival responses activate. Formation of antibiotics, toxins, competence factors, chemotaxis factors. Phosphotases then reset the system.
What occurs at high levels of Spo0A-P?
induces sporulation by activation of 100sof genes and alternate sigma factors.
In Chemotaxis, sensory proteins (MCPs) are found ____ and bind _____.
in the membrane; chemoattractants/repellents.
What is the phosphotase in Chemotaxis that resets the system?
CheZ
What happens when MCPs are bound to repellents?
MCPs interact with CheA/CheW (sensory kinase) which results in autophosphorlyation and an increase in levels of Che-P.
What happens when MCPs are bound to attractants?
CheA-P is decreased.
CheA-P transfers is P to..
CheY
What is CheY-P and what does it do?
It is a response regulator that interacts with flagellar motion to induce clockwise rotation and tumbling.
What does CheY do if not phosphorylated?
It doesn't make a tumbling move, it just makes it move forward.
What happens with no attractants/repellents?
The CheA has intermediate levels of autophosphorylation. This results in a back & forth type of movement. It goes forward, changes direction the goes forward again.
In adaptation, each MCP binds to..
a variety of attractants/repellents.
In adaptation, the MCPs are...
continuously methylated by CheR.
What happens when CheA phosphorylates CheB?
A demethylase is formed and it removes methyl groups for the MCPs.
What happens with fully methylated and fully unmethylated MCPs?
Fully methyl, they do not respond.
Fully unmethyl, they are super sensitive.
What is quorom sensing?
a form of intecellular communication that allows cells to know when its population is concentrated enough for group activity.
In quorom sensing, each cell..
makes and secretes its own autoinducer to induce the genes, but not enough to turn its own cell on. Only when many cells come together within a population can the levels combine and be enough to turn on.
The Lux operon produces....
AHL (acyl homoserine lactone) synthase from the Lux I gene and enzymes (Lux A-E and G leads to bioluminescence).
What happens as cell density increases?
Levels of AHL increase which leads to the activation of LuxR and induction of high lux operon expression. ----> Bioluminescence.
sigma 70
needed during exponential growth
sigma S
needed during the general stress response and during stationary phase
sigma E
needed to restore membrane integrity and the proper folding of membrane proteins
sigma H (or sigma 32)
needed to protect against heat shock and other stresses including genes encoding chaperones that help maintain or restore proper folding of cytoplasmic proteins and proteases that degrade damaged proteins.
Fecl sigma
encode the iron citrate transport machinery in response to iron starvation and the availability of iron citrate
sigma F (or sigma 28)
flagellum assembly
sigma 60
involved in nitrogen metabolism