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