Term
| What is the transcription cycle in bacteria? |
|
Definition
RNAP binds σ(sigma) factor to form a holoenzyme, then locates a promoter
RNAP σ factor unwinds DNA at start site, opening the complex. Trancsription begins.
After transcribing about 10 nucleotides, the sigma factor dissociates and RNAP clamps down on the DNA. Transcription continues without releasing the substrate until termination signals in the DNA form a structure in the RNA that destabilizes RNAP interaction with mRNA, allowing the RNAP to bind another sigma factor. |
|
|
Term
| What occurs during initiation in bacteria? |
|
Definition
| Sigma factor binds to RNAP. Promoter sequence is located by sigma factor, RNAP forms complex with DNA at the site of the promoter. DNA is unwound, forming an open complex known as the transcription bubble. The first few mRNA nucleotides are formed (known as aborive initiation). The sigma factor must then be ejected as it binds too strongly to the promoter to allow the RNAP to move along the DNA. |
|
|
Term
| What subunits make up RNAP? |
|
Definition
| Alpha, beta, beta prime, omega, and sigma when in holoenzyme form |
|
|
Term
| What do the RNAP subunits do? |
|
Definition
Alpha- initiation and interaction with regulators
Beta and beta prime - catalysis
Omega - stability
Sigma - binding to promoter |
|
|
Term
| What is the standard sigma factor in bacterial cells? |
|
Definition
|
|
Term
| How does the sigma factor recognise promoters?` |
|
Definition
| Via direct read out - side chains of amino acids in the sigma factor recognise specific bases in the promoter. |
|
|
Term
| What is indirect read out? |
|
Definition
| When the side chains of the sigma factor interact with the DNA backbone |
|
|
Term
| What happens to the RNAP when the sigma factor binds to a promoter? |
|
Definition
| A structure called a crab claw in the RNAP closes around the DNA. around 14 bases are melted to form the open complex, which gives the RNAP access to the rest of the DNA. The sigma factor must also be ejected because it blocks the exit channel for the mRNA. |
|
|
Term
| What is 6SRNA and how does it work? |
|
Definition
| A regulator of RNAP the mimics an open promoter complex. It can associate with up to 75% of RNAP sigma factor 70. The 6SRNA:RNAPsigma70 complex is verystable, preventing the sigma factor from leaving. It is released when nucleotide triphosphate levels rise high enough for RNAP to synthesize the 6SRNA. The produce binds to the 6SRNA and releases the sigma factor. |
|
|
Term
| How does transcription switch to elongatin mode? |
|
Definition
Sigma factor dissociates
Crab claw closes
Flap at the back of RNAP closes to form exit tunnel for new mRNA
Closing of crab claw clamps RNAP to DNA |
|
|
Term
| How many nucleotides are synthezised a second in elongation mode? |
|
Definition
|
|
Term
| What is the two-metal ion mechanism used by RNAP? |
|
Definition
| Two Mg2+ ions in an active centre catalyse a Sn2+ nucleotide attack by the 3'OH group on an alpha phosphate of an incoming NTP. After phosphodiester bind formation, pyrophosphate (PPi) is released and the elongation complex translocates one base pair down DNA complex |
|
|
Term
| What are the two moving parts of RNAP, and what do they do? |
|
Definition
| The bridge helix (F bridge) and trigger loop/helix (g loop). THey select and bind the correct NTP. The NTP binds to the RNAP pre-insertionally and posttranslocationally. The trigger loop is closed at this point as the chemical nature of the NTP is monitored. Folding of the trigger loop/helix brings the two Mg2+ ions together. If this does not happen then the NTP is not inserted. |
|
|
Term
| What do antibiotics such as rifampicin rely on? |
|
Definition
| Th elongation complex stalling or arresting if modified bases are in the DNA. |
|
|
Term
| What is intrinsic termination and how does it work? |
|
Definition
| Termination of the RNAP elongation complex via formation of a hairpin structure that wedges open the flap on RNAP and releases the mRNA from the exit tunnel. |
|
|
Term
| What is Rho dependant termination and how does it work? |
|
Definition
| Rho is found in all bacteria. it acts as an ATP dependant 5-3 helicase. It moves rapidly along the RNA, and when it reaches the RNAP it effectively knocks it off the mRNA. The Rho protein binds as a heximer to specific recognition sequences in an unstructured transcript segment and progresses in a 3-OH direction on the transcript. if it enounters polymerase it directs the RNAP to stop transcription and release the transcript. |
|
|
Term
| What are anti-terminators? |
|
Definition
| Molecules that modify RNAP to allow it to bypass intrinsic termination sites and rho-dependant sites |
|
|
Term
| Which sigma factors are expressed during exponential phase? |
|
Definition
| sigma70, sigma54, sigma28 |
|
|
Term
| Which sigma factors are expressed during stationary phase? |
|
Definition
| sigma70, sigma54, sigma38, sigma28 |
|
|
Term
| What do the various sigma factors do? |
|
Definition
sigma 70 - growth related
sigma 54 - nitrogen regulated/stress response genes
sigma 38 - stationary phase/stress response
sigma 32 - heat shock/ stress resoibse
sigma 28 - chemotaxis
sigma 24 - extreme heat shock
sigma fecl - ferric citrate transport |
|
|
Term
| How is sigma38 kept around during stationary phase? |
|
Definition
| Usually it is quickly degraded by ClpP, but ClpP is inhibited during stationary phase. |
|
|
Term
|
Definition
| A single nucleotide that makes promoter escape difficult. It is also known as alarmone, as it co-ordinates a stringent response to amino acid starvation by inhibiting transcription of regular translation, and promoting transcription of amino acid biosynthesis. It couples transcription to DNA repair. It is induced by DNA damage, and required for efficient NER repair of UV damage |
|
|
Term
| What is DksA and how does it work? |
|
Definition
| A small protein that regulates transcription by binding to RNAP but not DNA, trapping the trigger loop in a conformation that destabilizes promoter complexes. |
|
|
Term
| Is ppGpp absolutely required for sigma 38? |
|
Definition
| No, it can also be caused by overproduction of Rsd, an anti-sigma 70 protein, mutations, or underproduction of sigma 70 |
|
|
Term
|
Definition
|
|
Term
| Divergent promoters point: |
|
Definition
Away from each other
<- -> |
|
|
Term
| Convergent promoters point; |
|
Definition
|
|
Term
| Why is RNA polymerase so important in microbial gene regulation |
|
Definition
| it is in short supply, and cannot transcribe all genes at once |
|
|
Term
| What are the four molecular mechanisms for prudent distribution of RNAP? |
|
Definition
The closer the promoters are to consensus, the more efficiently they function.
Sigma factors.
Transcription factors.
Small ligands. |
|
|
Term
| What are the main recognition elements in sigma 70 specific promoters? |
|
Definition
|
|
Term
| How do two component sensor regulators work, and what are they made of? |
|
Definition
| They are made of a sensor, comprised of a sesnsor domain and a kinase doman, and a receiver, comprised of a receiver and regulator domain. First, the sensor is activated by a stimulus, which causes a conformational change in the kinase, which autophosphorylates itself using phosphate from ATP. They then phosphorylate onto a histidine residue. The regulator is then phosphorylated by the kinase on a conserved aspartate residue. This occurs when the kinase and receiver domains collide. Phosphorylation changes the shape of the regulator, usually to allow dimerization. It then collides and binds with promoters to alter transcription. |
|
|
Term
| What is a second site suppressor study? |
|
Definition
| Mutagenising one of the two genes encoding a protein, stopping it interacting and signalling, then looking at the compensatory the partner two component protein-gene. |
|
|
Term
| What do Methyl-accepting chemotaxis proteins (MCPs) do? |
|
Definition
| If stimulated, use CheA and CheY proteins to singal to the flagellar motor |
|
|
Term
| What are the four types of gene control circuits? |
|
Definition
Negatively controlled inducible - a repressor is normally active, an inducer can repress the repressor.
Negatively controlled repressible - An apo-repressor and co-repressor are both active
Positively controlled inducible - apo-activator and co-activator are both active
Positively controlled repressible - inhibitor and activator |
|
|
Term
| What comprises the lac operon? |
|
Definition
lacZ - which codes for beta galactosidase
lacY - which codes for permease to transport lactose into the cell
lacA - which encodes for transacetylase - not required for lactose metabolism. |
|
|
Term
| What controls the lac operon? |
|
Definition
| A repressor coded for by lacl, which binds the operon. Lactose modifies the lacl repressor, acting as an inducer. |
|
|
Term
| Helix-turn helix motifs are common in... |
|
Definition
|
|
Term
| What does the lac repressor allosteric site do? |
|
Definition
| Binds inducers. Occupancy of the allosteric site alters the ability of the lac repressir to bind DNA at the operator. |
|
|
Term
| What additional control system is superimposed over the lac repressor-operator system, and what does it favour? |
|
Definition
| catabolite repression, the uptake of glucose over lactose |
|
|
Term
|
Definition
| any cell growth characterized by two phases - normally caused by presence of two sugars, one of which is easier to metabolise |
|
|
Term
| How is the lac operon regulated? |
|
Definition
| If glucose is present, then cAMP is low, and cannot bind CAP. As well as this, if lactose is not present, then the repressor is bound to the operator. If glucose and lactose are both present, the repressor does not bind, but cAMPis still low, so the CAP-cAMP complex is not binding the promoter. If lactose is present but glucose is not, cAMP is high, and the repressor cannot bind, so the cAMP-CAP complex binds the promoter and the repressor does not bind the operator, allowing high transcription of the lac operon |
|
|
Term
| Why does the cAMP-CAP complex increase transcription of the lac operon? |
|
Definition
| it binds to the promoter, binding the DNA by 90degrees to increase the affinity of RNA polymerase for the lac promoter |
|
|
Term
| induction of the lac operon is... |
|
Definition
|
|
Term
| How many lac operators are there, and which need to be present for repression of the lac operon? |
|
Definition
| There are three lac operons, and O1, AND O2 OR O3 |
|
|
Term
| How does the lac repressor work? |
|
Definition
| it forms a tetramer, and binds O1, and either O2 or O3, and DNA looping brings the operators close enough for it to bind both. Partial dissociation leads to rapid rebinding, complete dissociation leads to induction. |
|
|
Term
| Trptophan biosynthesis is controlled on which levels? |
|
Definition
A repressor that negatively regulates transcription
Feedback inhibition
Transcription attenuation |
|
|
Term
| What is transcription attenuation (tryptophan example)? |
|
Definition
The first 141bp of the leader region of the trp gene are not transcribed at the maximum rate, even at high typtophan levels. Base 130-160 is deleted in some mutants of trp. This is called the attenuator. It does not prevent initiation of transcription, but acts as an mRNA chain terminator when tryptophan is present. Part of the leader is translated to produce a 14 amino acid peptide. The trp leader RNA can form a variety of secondary structures. If tryptophan is abundant, segment 2 is sequestered in the ribosome, and segments 3 and 4 pair, forming a stem loop. This terminates transcription. If tryptophan is scarce, the ribosome stalls in segment 1, as it has two tryptophan codons, segment 2 is therefore free to pair with segment 3, preventing segment 3 and 4 forming the stem-loop, so transcription continues.
Example of a positively controlled repressible system. |
|
|
Term
| How do bacteria grow? (per individual cell) |
|
Definition
| Maintain a slightly higher intracellular osmotic pressure on the inside of the cell, pushing the cell wall out |
|
|
Term
| What are the two porins in E. coli, and when are they expressed? |
|
Definition
| OmpC, which is small and used in the digestive tract so as not to allow in damaging substances such as bile salts, and OmpF which is large and used when free-living in water to ensure enough food is taken up |
|
|
Term
| How are the two porins in E. coli controlled? |
|
Definition
|
|
Term
| What does the EnvZ/OmpR sensor do? |
|
Definition
| EnvZ has two activities at high or low osmolarity. it is not known how it senses this. When the osmolarity is high, EnvZ conformation changes, it becomes active as a kinase and phosphorylates a histidine residue. The phosphate is then passed to OmpR, creating high levels of OmpR-P. OmpR-P binds the ompC promoter, and activates transcription. High levels of ompR-P also bind to low affinity regions in the ompF promoter, enhancing looping and repressing ompF transcription. Low levels of OmpR-P ( which are around when EnvZ is not acting as a kinase) bind to high affinity areas in the ompF promoter and activate transcription. |
|
|
Term
|
Definition
| to the DNA of promoters of porin genes AND to RNA polymerase to recruit it to transcribe mRNA from those genes |
|
|
Term
| What does ompR regulate apart from ompF and ompC? |
|
Definition
| omrA and omrB, which are also osmoregulators |
|
|
Term
|
Definition
|
|
Term
| What system measures osmolarity? |
|
Definition
|
|
Term
| What systems measure oxygen? |
|
Definition
| ArcAB, FNR, FixLJ and RegAB |
|
|
Term
| How do bacillus species sense oxygen? |
|
Definition
| Directly, with haem containing domains that alter the conformation if oxygen binds. |
|
|
Term
| What are the two more common methods of sensing oxygen? |
|
Definition
| Redox state of a metal, or build up of metabolic intermediates |
|
|
Term
| How does the ArcAB system work? |
|
Definition
| ArcA is the regulator and ArcB the sensor kinase. ArcB senses aerobic condition by the binding of metabolite intermediates, which build up under anaerobic conditions and change the conformation of ArcB. ArcB has three autophosphorylation sites for intramolecular phosphate transfer. It autophosphorylates its first Hi, then the phosphate is passed to an Asp residue. Here, if the conditions are aerobic, it is lost. If the conditions are anaerobic it is passed to the final His residue. This then phosphorylates the D domain on ArcA. |
|
|
Term
| how do quinones affect ArcB? |
|
Definition
| If the environment is aerobic, there will be quinones being rapidly oxidised by oxygen. They will therefore be looking to take electrons from more sources, such as ArcB. When ArcB is oxidised, disulfide bonds form, turning off its kinase activity |
|
|
Term
| What are the types of quinones in e. coli and what are they used for? |
|
Definition
| Menaquinone for low oxygen conditions and ubiquinone for high oxygen |
|
|
Term
| What happens when ArcA is phosphorylated? |
|
Definition
| it dimerises and frees its DNA binding domain, allowing it to bind to promoters, repress the TCAcycle and induce fermentative genes and cydAb (a gene encoding a high oxygen affinity cytochrome for low oxygen conditions. |
|
|
Term
| What is used to sense oxygen in Sinorhizobium? |
|
Definition
|
|
Term
| What is the FixLJ system. |
|
Definition
| FixLJ is used to sense oxygen for nitrogen fixation. FixL is an amino acid membrane protein that senses oxygen by it binding a haem domain. this causes an inactive FixL conformation. without oxygen, FixL autophosphorylates, then phosphorylates FixJ, which binds to promoters of nitrogen fixation genes and recruits RNAP |
|
|
Term
| How does Rhodobacter regulate photosynthesis? |
|
Definition
| The RegAB system. This regulates the pufBALM, pucBA and puhA genes/ pufLM and PuhA make the reaction centre and BA encodes light harvesting proteins. RegA-P binds at the puf and puc promoters and activates their transcription. RegA-P is produced by RegB acting as a kinase. Oxidised ubiquinone inhibits RegB as a kinase, so when oxygen is high, photosynthesis does not occur. |
|
|
Term
| How does the FNR system work? |
|
Definition
| It turns off cytochromeD promoters under anaerobic conditions, When it gains 4 Fe ions in its iron sulfur clusters it can dimerise. However, in aerobic conditions it cannot keep all Fe ions, and so must monomerise again. it is also vulnerable to proetolytic degredation in aerobic environment. It is a one component sensor regulator, and cannot recruit RNAP unless dimerised |
|
|
Term
| What can block FNR binding? |
|
Definition
| Nuclear Associated proteins (NAPs) which support the regulation of trancription factor binding |
|
|
Term
| When do bacteria form spores? |
|
Definition
| After the stationary phase if it is not enough, or when under serious threat |
|
|
Term
| What are the key stages of sporulation/ |
|
Definition
| Filamentation - > asymmetric division -> prespore - > englufment - > cortex synthesis -> coat synthesis and maturation -> lysis to release spore |
|
|
Term
| When is the decision to sporulate taken? |
|
Definition
| in the transition phase between exponential and stationary growth |
|
|
Term
|
Definition
| An unstable repressor stationary phase genes such as spo0H |
|
|
Term
|
Definition
| it encodes sigmaH sporulation signal factor |
|
|
Term
|
Definition
| a global repressor of early stationary phase and sporulation genes, which binds GTP to become a repressor. The more GTP around, the more nutrients. |
|
|
Term
| What is Spo0A and what does it do? |
|
Definition
| the master regulator of sporulation. It is activated by a phosphorelay - five sensor histidine kinases feed phosphoyl groups into a phosphorelay. The Phosphoryl group passed to aspartic acid in Spo0F relay protein, then to histidine in Spo0B, eventually to aspartic acid residue in Spo0A. Once a certain threshold of Spo0A is reached sporulation is inevitable. |
|
|
Term
|
Definition
Rap A, B, E proteins are phosphatases that dephosphorylate Spo0F~P
This prevents the flow of phosphate to Spo0A
Rap phosphatases are antagonised by cognate secreted pentapeptides
Pentapeptides function as cell density signals |
|
|
Term
| What is SpoA-P dephosphorylated by, end when does this happen? |
|
Definition
Spo0A~P itself is dephosphorylated by Spo0E
Expression of spo0E is repressed by AbrB
Spo0E is not particularly active
Spo0E ensures that Spo0A~P only accumulates when phosphorelay is active |
|
|
Term
| What are Sda, SirA and Spo0A required for, and what do they individually do? |
|
Definition
Regulating DNA replication during sporulation. Sda inhibits auto-phosphorylation of KinA, preventing sporulation in replicating cells.SirA displaces DnaA initiator from origin of replication oriC, prevents re-initiation in sporulating cells
Spo0A binds to specific sites in oriC region, directly controls chromosome copy number |
|
|
Term
| How much of a chromosome is present in the prespore/ |
|
Definition
|
|
Term
|
Definition
| Transfers DNA into the prespore compartment, and forms the spore to allow it to enter, strips DNA of proteins , transcription factors and RNAP |
|
|
Term
| What occurs to DNA during the translocation of the chromosome into the prespore? |
|
Definition
| All proteins are stripped off and displaced. |
|
|
Term
| What is the housekeeping sigma factor in bacillus? |
|
Definition
|
|
Term
| What is the order of sigma factor change in the mother and prespore of bacillus? |
|
Definition
| sigmaH in prespore replaced by sigmaF, after an hour sigmaF replaced by sigmaG. In mother cell, sigma A replaced by sigmaE, after an hour replaced by sigmaK |
|
|
Term
| What does SpollAB do and how does it work? |
|
Definition
It is n anti-sigma factor, which holds sigmaF. his inhibition is reversed in the prespore by the anti-anti-sigma factor SpoIIAA
SpoIIAA activity is regulated by phosphorylation
SpoIIAA is inactive when phosphorylated by SpoIIAB (which is also a kinase)
SpoIIAA is active when dephosphorylated by SpoIIE (which also interacts with FtsZ) |
|
|
Term
| How many molecules of SpollAb form a complex with sigma F? |
|
Definition
|
|
Term
|
Definition
| Proteolytic cleavage from SpollGA - which is activated by binding of SpollR - the promoter of SpollR is recognised by sigmaF - sigmaE activation requires sigmaF |
|
|
Term
|
Definition
Where the mother cell cytoplasm engulfs the prespore,The cell wall at material at the septum is degraded by SpoIIB Membrane movement requires SpoIID, SpoIIM and SpoIIP - spoIID, spoIIM and spoIIP genes are transcribed by RNAP-σE - spoIIQ is transcribed by RNAP-σF
Membrane fusion at the cell apex requires SpoIIIE (DNA translocase) - The prespore is now a free protoplast within the mother cell |
|
|
Term
| What are the final stages of spore formation? |
|
Definition
| Synthesis of proteins to coat and protect DNA, production of dipicolinic acid in mother cell which is taken up by the spore to dehydrate and mineralise it, sigma E and K assemble protective layers, the first being the cortex, and the second being a multilayered protein coat. |
|
|
Term
| How can ArcB be silenced? |
|
Definition
| Autophosphorylation of ArcB is inhibited by ubiquinone, but not menaquinone, it is due to oxidation rather than allosteric binding. |
|
|
Term
| Which systems regulate cholera virulence? |
|
Definition
|
|
Term
| What is the process by which cholera causes disease? |
|
Definition
Vibrio cholerae ingested, senses change in environment and derepresses virulence gene expression
Adheres to mucosal epithelial cells of small intestine, grows and colonizes
Toxin produced which is taken up by host cells
V. cholerae bind to GM1 gangliosides
Cholera toxin injected into epithelium activates adenyl cyclase in gut cells altering gut transporter activity
Sodium uptake blocked, chloride pumping to lumen
Osmotic balance upset: too many ions in gut lumen; massive water pumping from blood to try to equilibrate & wash ions out. Hence dehydration & ion loss
Death due to dehydration |
|
|
Term
| What needs to be expressed for cholera to be virulent? |
|
Definition
Flagellar motility and chemotaxis, required for colonization of small intestine, bacterium swims into intestinal mucous layer. (Non motile mutants are avirulent)
Accessory colonization factors (acfs), haemagglutinins (HAs), Toxin Coregulated Pili (TCP pili) required for adherence and colonization of intestinal epithelial cells
TCP minus cells (e.g tcpA minus) are avirulent
ACFs & HAs form tighter links to epithelial cells of host mucosa after TCP mediated binding. This is required for toxin delivery
TCP pili also allow bacterial aggregation on gut epithelium. |
|
|
Term
| How is the main cholera toxin activated? |
|
Definition
| The pretoxin is nicked to make the toxin. The TcpG -DsbA homologue ensures the correct protein folding the periplasm. |
|
|
Term
| Which cholera subunit does the damage, and which delivers the toxin? |
|
Definition
| A is the toxin, B is the deliverer |
|
|
Term
| How does the cholera toxin work? |
|
Definition
| The toxin binds to GM1 gangliosides on inestinal mucosal cells, the B sununits create a pore in the membrane vesicle through which A can enter the cell. The A subunit locks G proteins into a permanently active state, continually stimulates adenylate cyclase to create cAMP. This causes phosphorylation of transport proteins that lead to an influx of chloride and sodium ions. The body tries to balance this by secreting water, which causes diarrhea |
|
|
Term
|
Definition
| activates transcription of ctxAB and tcp genes. |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| ToxPH expression is regulated by... |
|
Definition
|
|
Term
| AphAB controlled genes are activated under... |
|
Definition
| conditions of low pH and anaerobiosis |
|
|
Term
|
Definition
| protect TcpP from proteolytic degredation |
|
|
Term
| What does ToxR do, and how does it work? |
|
Definition
| It is a membrane promoter that binds as a dimer to repeats in the toxT promoter and porin gene regulators. It is stabilized by Tox S. once ToxT is expressed the virulence genes are activated. It is activated by bile salts which bind to the ToxR membrane domain. |
|
|
Term
| How do bile salts activate ToxR? |
|
Definition
| They cause isomerization which causes an intermoleculear disulfide bond between two subunits of tcpP. the now dimer can bind to the ToxT promoter and stimulate gene expression. |
|
|
Term
| Which two systems are involved in ToxT activation? |
|
Definition
|
|
Term
|
Definition
| regulate its own expression. |
|
|
Term
| Why is it useful for cholera to be able to sense a quorum? |
|
Definition
| So they know when it is efficient to move |
|
|
Term
| What is the basic idea behind quorum sensing? |
|
Definition
| All bacteria secrete a small amount of quorum molecules, and can sense the levels of them |
|
|
Term
| What is the model behind quorum sensing? |
|
Definition
| At low levels of the of the quorum sensing compound, the LuxO sensor represses the activity of HapR, (a regulator of gene expression). When HapR is active, it represses TcpPH (and therefore ToxT). At higher cell densities, LuxO stops repressing HapR, decreasing virulence. When the bacteria move, the cell density is lower, and they can express the virulence factors again |
|
|
Term
| What regulates cyclic GMP signalling? |
|
Definition
| Diguanylate cyclase proteins. |
|
|
Term
|
Definition
| an icosahedral tailed virus that infects E. coli. |
|
|
Term
| What are the two different lifestyles of bacteriophage lambda? |
|
Definition
| Actively replicating lytic state and a dormant lysogenic state |
|
|
Term
| What does bacteiophage lambda eat? |
|
Definition
|
|
Term
| What is the difference between lysogenic plaques and lytic plaques? |
|
Definition
| Lytic are clear, lysogenic are turbid |
|
|
Term
| What is the lytic cycle for bacteriophage lambda? |
|
Definition
Chromosome circulised upon injection into E.coli
This helps protect λDNA from host exonucleases, and brings together groups of genes transcribed together
Different groups of genes are expressed at different times in the life cycle, co-ordinated regulation of genes in contigous blocks encode related functions
Regulatory proteins are vital to determine which pathways are taken
N, Cro and Q are required for lytic growth, while N, cll, clll and cl are required for lysogenic growth |
|
|
Term
| What do PL and PR promoters do? |
|
Definition
| They are recognised by host RNA polymerase, which starts transcription until the terminators tLI and tRI are reached, which encode the early regulatory proteins N and Cro |
|
|
Term
|
Definition
| it turns on genes to the left of N and the right of cro. It is an antiterminator, which modifies RNAP at N utilisation (Nut) sites, to allow it to ignore tLI and tRI termination sites. N anti-termination is also effective against rho-independant terminators |
|
|
Term
| What Nus factors are there and one do they do? |
|
Definition
NusA: moderates transcription elongation, pausing, termination
NusB, essential for growth at low temperatures
NusD, termination factor
NusE, ribosomal protein that enhances Rho activity |
|
|
Term
| What does PL do with N anti termination? |
|
Definition
| transcribes clll, involved in lysis vs. lysogeny decision, and xis and int, site-specific recombination system for integration/excision of λ into E. coli chromosome |
|
|
Term
| What does pR do with N anti termination? |
|
Definition
| transcribes cll, which determines lysis vs lysogeny decision, O and P, involved in initiating DNA replication of the λ genomes, and Q, another anti-terminator that is needed for activation of late gene expression |
|
|
Term
|
Definition
transcription of late genes.
E. coli RNA polymerase synthesises a small mRNA from PR and stalls at tR
Q acts at qut (q-utilisation) sites to anti-terminate the short mRNA
The qut site is located between the -10 and -35 sequences of PR
In contrast to N anti termination, Q only needs NusA
Transcription of head and tail genes leads to production of λ coat proteins |
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Term
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Definition
| prevents synthesis of repressor (cI), and transcription from PL and PR - Cro binds to operator sites, preventing access to PL and PR (and PRM) promoters by RNA polymerase |
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Term
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Definition
Facilitates RNA polymerase binding and transcription at PRE and PI promoters.
cll is unstable. It promotes lysogeny |
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Term
| What do PRE and PI promoters do? |
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Definition
PI directs transcription of int, for integration of λ into E. coli chromosome
PRE (promoter for repressor establishment) directs transcription of cI, the λ repressor |
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Term
| What protects cll from degredation? |
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Definition
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Term
| How does starvation lead to active cll levels? |
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Definition
| low protease levels stop cll being degraded so quickly. |
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Term
| How is lambda integrated into E. coli genome? |
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Definition
| Site-specific recombination between attP and attB, which requires Int protein. It generates two hybrid att sites are generated that flank the integrated phage chromosome. |
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Term
| What is required for excision, and how does it work? |
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Definition
| Both Int and Xis proteins, The P int promoter lies within the xis gene.Xis production is stimulated by cll. |
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Term
| What is required for lytic growth over lysogenic? |
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Definition
| More Xis than Int to be synthezised |
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Term
| Where is cl transcribed from to establish and maintain lysogeny? |
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Definition
| To establish, PRE, to maintain, PRM |
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Term
| What do repressor dimers bound to OR1 and 2do? |
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Definition
| Increases the affinity of RNA polymerase for PRM. Transcription from PRM leads to more repressor synthesis, repressors bound to OR1 and 2 prevents RNA polymerase binding to PR, preventing lytic cycles beginning, so preventing further infection |
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Term
| How does repressor binding work with OR1, 2 and 3? |
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Definition
| OR1 binds the repressor most strongly, after OR1 is bound, the affinity OR2 has for the repressor increases. If OR1 and 2 have repressors bound to them cl transcript is stimulated. If OR3 is bound, RNA polymerase binding to PRM is blocked |
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Term
| What happens when OR1, 2 and 3 have Cro bound? |
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Definition
| It is a negative regulator, it binds to the same sites that the repressor does, but with the opposite order of affinity, with OR3 being the most affinitive |
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Term
| What do the lambda repressor and Cro have in common? |
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Definition
| They both contain helix-turn-helix motifs that aid with binding to OR2 and 3 |
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Term
| Lysogens are induced by... |
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Definition
| UV light. UV induced damage modifies the DNA repair protein RecA to become a highly specific protease. Activated RecA cleaves repressor monomers in the linker between amino and carboxyl domains. Seperated domains cannot dimerise, in the absence of the repressor, the lytic cycle starts. RecA cleaves other repressors too |
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Term
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Definition
| EAL or HD-GYP, are c-di-GMP degrading proteins, also called phosphodiesterases (PDEs). |
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Term
| What aids synthesis of c-di-GMP? |
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Definition
| They are Di guanylate cyclase (DGC) proteins with a GGDEF (Duf1) domain (called as it was previously a conserved domain of unknown function). |
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Term
| How are GGDEF proteins with a receiver domain activated, and what does that activation do? |
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Definition
| A histidine in the receiver domain is phosphorylated, and it activated or diactivates the synthesis of c-di-GMP |
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Term
| What does the I site in the GGDEF proteins do? |
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Definition
RxxD, also binds c-di-GMP, blocks catalysis by the DGC when levels of c-di-GMP are high
product inhibition –limits the amount of time c-di-GMP that is
produced – downstream signalling modulation
I-sites found in ~50% all known DGCs |
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Term
| How is c-di-GMP degraded by EAL proteins? |
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Definition
| First it is degraded to pGpG, then oligoribonucleases in the cytoplasm completes the transformation to GMP. It is the DUF2 domain that does this. |
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Term
| What do bacteria synthesize to be sessile or use pili or flagella? |
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Definition
| Extracellular polysaccharide |
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Term
| What does high c-di-GMP normally cause? |
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Definition
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Term
| What does c-di-GMP binding to specific PilZ receptors do to the flagellar rotation? |
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Definition
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