Category - Definitions

Query - What definition best describes the term below?

Reversal

Category - Term Recognition

Query - What term does the description below refer to?

(Terms are shown on left, descriptions in middle, figures on right)

-10 region (also called the Pribnow box) | A region in prokaryotic DNA sequences about 10 base pairs ahead of the transcriptional start sequence which contains the consensus sequence, TATAAT. | Figure 26.11 | -35 Region | A region in prokaryotic DNA sequences about 35 base pairs ahead of the transcriptional start sequence which contains the consensus sequence, TTGACA. | Figure 26.11 | Actinomycin D | A molecule that inhibits transcription by intercalating between adjacent GC base pairs in DNA. | Figure 26.4 | Adenylate cyclase | An enzyme that catalyzes synthesis of cAMP when glucose levels drop in E. coli. |  | -amanitin | A toxin from Amanita mushrooms that inhibits eukaryotic RNA polymerase II at low concentrations and RNA polymerase III at high concentrations. | Figure 26.4 | Antisense RNA | An RNA molecule that is complementary to an mRNA; it can block translation of the mRNA by forming a duplex with it. Gene expression can be regulated by the production of antisense RNAs. |  | araC | A regulatory protein of the E. coli arabinose operon that activates transcription of the operon when it binds arabinose and represses transcription when no arabinose is bound. | Figure 26.39 | Attenuation | A transcriptional regulatory mechanism in bacteria in which the deficiency of an amino acid slows translation and ultimately stops transcription. |  | cAMP Receptor Protein (CRP) | An E. coli protein that interacts with cAMP and undergoes a conformational change that increases its affinity for several DNA sequences, including a site in the lac operon adjacent to the RNA polymerase binding site | Figure 26.19 | cI | A repressor encoded by phage that along with cro, binds to each of the six operator sites of the virus with varying efficiencies. The protein can also act as a transcriptional activator, under certain conditions. | Figure 26.23, Figure 26.27 | Cis-Dominant | Mutations occurring in a genome that only affect gene expression in that one. An example is a mutation in a regulatory sequence of a promoter that affects transcription only of that promoter. |  | Closed Promoter Complex | A complex produced as a result of the initial interaction between RNA polymerase and promoter. | Figure 26.6 | Consensus Sequence | For a group of nucleotide or amino acid sequences that show similarity but are not identical (for example, the sequences for a family of related regulatory gene sequences), an artificial sequence that is compiled by choosing at each position the residue that is found there most often in the sequences under study. |  | Cordecypin | A transcriptional chain terminator, due to its lack of a 3' hydroxyl group. |  | Cro | A repressor encoded by phage that acts as both a repressor and as an antirepressor, antagonizing the action of cI in a very specific way. | Figure 26.23, Figure 26.27 | Downstream | A term used to indicate "in the 3' direction of." |  | Factor Independent Termination | A transcriptional termination process that relies on base pairing of a GC-rich sequence near the 3' ends of many genes. | Figure 26.15 | Factor-Dependent Termination | A transcriptional termination mechanism in E. coli that employs a factor called (rho), which works by binding the RNA near the 3' end and unwinds the RNA strand from the DNA strand, causing release of the transcriptional complex. | Figure 26.16 | galR | The structural gene for the gal repressor that negatively regulates the gal operon of E. coli. |  | Guanosine 3',5'-tetraphosphate (ppGpp) | A molecule that accumulates during the bacterial stringent response. |  | Helix-Turn-Helix Motif | A protein structure found in the CRP-cAMP-DNA complex by x-ray crystallography. It is a common structure in DNA-binding regulatory proteins. |  | Inducer | In the lac operon system, for example, a molecule, such as allolactose or IPTG, which binds to the repressor and inactivates it, thus removing a barrier to transcription. | Figure 26.18 | Intron Splicing | A posttranscriptional processing event of RNAs that occurs almost exclusively in eukaryotes. |  | Isopropyl Thiogalactoside (IPTG) | A synthetic inducer of the lactose operon. |  | Lac Repressor | The 'i' gene product of the lac operon. It is a macromolecular repressor which, in the active form, binds to the operator, blocking transcription of the operator. | Figure 26.18 | Lactose Operon | An E. coli operon that consists of the three linked structural genes that encode enzymes of lactose utilization, plus adjacent regulatory sites | Figure 26.17 | Messenger RNA (mRNA) | The form of RNA that is translated into protein by the ribosomes. | Figure 26.2 | NusA | A protein that may be involved in recognition of -dependent termination sites. |  | Open Promoter Complex | A complex produced as a result of a highly temperature-dependent unwinding of several base pairs of DNA by RNA polymerase during transcriptional initiation. | Figure 26.6 | Operator | A DNA site where a repressor protein binds to block the initiation of transcription from an adjacent promoter. | Figure 26.2 | Operon | A set of contiguous prokaryotic structural genes that are transcribed as a unit, along with the adjacent regulatory elements that control their expression. | Figure 26.2 | Operon Model | A model originally proposed by Jacob and Monod that was a unifying hypothesis of transcription in prokaryotic organisms. | Figure 26.2 | Polycistronic Messenger RNA | A messenger RNA molecule carrying coding sequences for more than one polypeptide sequence. |  | PRM | A 'maintenance' promoter from which cI gene is transcribed during maintenance of lysogeny. |  | Promoter | A DNA sequence recognized by RNA polymerase, resulting in the initiation of transcription. |  | Regulon | A group of unlinked (nonadjacent) genes that are all regulated by a common mechanism. |  | Repression | The turning off of the transcription of a gene or genes. |  | Repressor | A protein that inhibits the transcription of a gene by binding to an operator. | Figure 26.2 | Ribonuclease III | An enzyme that cuts rRNAs in the stem loops during processing of the message made by the operon. It also performs posttranslational processing on some phage mRNAs. | Figure 26.41 | Ribosomal RNA (rRNA) | The form of RNA found in the ribosomes. |  | Rifampicin | An inhibitor of the prokaryotic RNA polymerase. | Figure 26.4 | RNA Polymerase | An enzyme that makes RNA using DNA as a template. |  | Stringent Response | A response to amino acid starvation in E. coli that inhibits synthesis of rRNA and tRNA. |  | T7 RNA Polymerase | A prokaryotic RNA polymerase composed on a single polypeptide subunit. |  | Trans-Dominant | Mutations that happen in one genome which can affect gene expression in others. An example is a mutation in the lac repressor gene which affects sequences to which the repressor binds. |  | Transcription | The process whereby RNA is made, using DNA as a template. |  | Transfer RNA (tRNA) | The form of RNA that provides translation between the three base codon sequence in the mRNA and amino acid cOResponding to it. |  | trp Repressor | A 58-kilodalton protein encoded by the nonadjacent trpR gene that is activated by binding tryptophan. Bound to tryptophan, it can bind to the trp operator and block transcription. |  | Upstream | A term used to indicate "in the 5' direction of." |

Category - General

Query - Is contained in the left column below, solution in middle, figure on right

Reversal - there is no reversal

Besides rRNAs, what else is encoded in the E. coli rRNA operons? | One to four tRNA molecules. |  | Besides the tryptophan operon, what other bacterial operons use attenuation as a mechanism of regulating the operon? | In E. coli, the leucine operon (with four adjacent leucine codons in the leader sequence) and histidine (with 7). In Bacillus subtilis, synthesis of tyrosyl-tRNA synthetase is activated by an antitermination mechanism that allows transcription to proceed past a potential termination site in a leader region. Termination proceeds efficiently when most of the appropriate tRNA is charged with tyrosine, and there is no need to synthesize more of the aminacyl-tRNA synthetase |  | From which end does degradation of bacterial mRNAs begin? | From the 5' end. |  | How are bacterial genes with common functions organized? | In clusters under common regulation |  | How are variations in the rate of transcription explained? | By variations in the sequence of the promoters. |  | How does bacterial RNA polymerase find promoters? | The holoenzyme binds nonspecifically to DNA, with low affinity, and then slides along the DNA, without dissociation from it, until it reaches a promoter sequence, to which it binds with much higher affinity. | Figure 26.6 | How does bending of the DNA by the CRP-cAMP complex facilitate initiation of transcription? | It may bring DNA sequences farther upstream into direct contact with the promoter or transcriptional start site |  | How does binding of Cro to OR1, OR2, and OR3 compare with binding of cI to the same sites? | The affinity of Cro for the sites is the reverse that of cI. Thus, in decreasing order, the affinity is OR3>OR2=OR1. Cro binds the sites less tightly than cI and the binding is not cooperative. |  | How does cI bind to operators OR1, OR2, and OR3? | It binds most tightly to them in decreasing affinity as OR1>OR2>OR3. Binding is cooperative. |  | How does rapid turnover of bacterial mRNAs fit in with the organisms' life cycles? | It provides rapid adaptation to environmental change and ensures that proteins for metabolic pathways are present only when the precursors for the pathway are available. |  | How does the location of the gal repressor with respect to the operon it regulates differ from that of the lac repressor? | The gal repressor is unlinked to the structural genes. |  | How does the sequence of the RNA in the region of the trpL gene affect attenuation? | Four oligonucleotide sequences in the trp leader region are capable of base-pairing to form stem–loop structures in the RNA transcript (Figure 26.35). | Figure 26.35 | How is coding of the individual 16S, 23S, and 5S rRNAs organized? | Each E. coli rRNA operon encodes in a single transcript one copy each of these rRNAs. |  | How is lysogeny established for phage ? | cII protein binds specifically at the -35 region of PRE, stimulating transcription of a longer cI mRNA (more efficiently translated), providing sufficient cI repressor to bind all three sites in OR and block transcriptional events. Binding of cI in this manner inhibits transcription of Cro from its own promoter and activates transcription of itself. | Figure 26.27 | How is the cI repressor inactivated under conditions of DNA damage? | The E. coli SOS system produces a protease that cleaves cI |  | How is the lysogenic state broken? | cI repressor is inactivated and the OR sites become unoccupied. Cro is transcribed from PR and the Cro protein blocks further transcription of cI. Simultaneously, leftward transcription from PLL generates the N protein, blocking transcriptional termination at sites TR1 and TL. Leftward transcription produces genes Int and Xis, necessary for prophage excision. Rightward transcription generates O and P, necessary for DNA replication. Q protein activates transcription of late-acting genes (strucural proteins of the virus). Early gene transcription is suppressed by Cro. cI transcription from PRM is blocked, leading to activation of Cro transcription from PR. | Figure 26.27 | How is the lysogenic state of phage maintained in the host cell? | By repressing nearly all of the viral genes via binding of a -induced repressor to two operators in the sequence | Figure 26.23, Table 26.2 | How many base pairs are unwound in the transcriptional bubble? | About 18 |  | How many base pairs of newly made RNA are hybridized to DNA during transcription? | About 8 |  | How many copies of cI are found in -infected cells during the lysogenic state? | About 200 |  | How many different nucleotide binding sites does RNA polymerase have? | Two - one for elongation and one for initiation. |  | How many genes of tryptophan biosynthesis are located in the trp operon? | Five | Figure 26.33 | How many molecules of RNA polymerase are present in an E. coli cell? | About 3000 |  | How many operons does the E. coli genome have for rRNAs? | Seven |  | How many structural genes are in the E. coli arabinose operon? | Three, araB, araA, and araD | Figure 26.39 | In binding a promoter, what contacts does RNA polymerase make with DNA? | It contacts DNA from about nucleotide -55 to -5, where +1 is the first nucleotide transcribed. |  | In what way is RNA polymerase postulated to bind DNA? | On one side of the helix. |  | Most transcriptional initiations abort with release of oligonucleotides of what length? | 2 to 9 |  | The loop that forms in the arabinose operon during conditions of low arabinose occurs between araC molecules on which sites in the arabinose operon? | araO2 and araI | Figure 26.39 | What activities does the termination protein possess? | It is an RNA-DNA helicase and contains a nucleoside triphosphatase activity activated by binding to polynucleotides. |  | What are the common structural motifs found in proteins that bind to DNA? | Helix-turn-helix, helix-loop-helix, leucine zipper, and zinc finger. |  | What are the control elements of the E. coli SOS Regulon? | The genes, lexA and RecA | Figure 26.32 | What are the extracellular and intracellular inducers of the lactose operon? | Extracellular - lactose; Intracellular - allolactose (Gal--(1->)Glc |  | What are the promoters of the E. coli gal operon called? | S1 and S2 | Figure 26.38 | What are the rates of transcription of various E. coli genes? | They range from one initiation every 10 seconds to once per generation (30-60 minutes) |  | What are the structural genes in the lactose operon? | -galactosidase (z), -galactoside permease (y), and thiogalactoside transacetylase (a) | Figure 26.17 | What are the two possible outcomes of phage infection of an E. coli cell? | 1. A lytic cycle of growth 2. Lysogenization, in which the viral chromosome circularizes and undergoes site-specific integration into the host-cell chromosome. |  | What are three distinct phases of transcription? | Initiation, elongation, and termination |  | What cellular processes are operating during attenuation of the trp operon? | Transcription and translation |  | What common DNA-binding motif is found in Cro and cI? | Helix-turn-helix | Figure 26.29 | What common DNA-binding motif is found in the structure of the trp operon? | Helix-turn-helix |  | What controls transcription of araC, the repressor of the arabinose operon? | araC itself. | Figure 26.39 | What DNA binding proteins discussed in the text have a helix-turn-helix binding motif? | cI, Cro, lac rePRessor, and trp repressor |  | What DNA sequences can the araC repressor of the E. coli arabinose operon bind within the operon? | araO2, araO1, and araI | Figure 26.39 | What does RecA do upon binding to single-stranded DNA? | Proteolytically cleaves LexA. |  | What does the core RNA polymerase enzyme do to DNA during elongation? | It simultaneously unwinds the DNA in advance of the progression and rewinds the template behind the growing RNA chain. |  | What E. coli gene is implicated as the source of the antisense RNA regulating ompF? | micf | Figure 26.40 | What effect does binding of cII protein to the -35 region of PRE have on cI production? | It increases it because it makes an mRNA that is longer and more efficiently translated than the one made from PRM |  | What effect does binding of the CRP-cAMP complex to the lac operon have on the system? | Binding facilitates transcription of the lac operon by stimulating the binding of RNA polymerase to form a closed-promoter complex. |  | What effect does cleavage of LexA by RecA have in the E. coli cell? | RecA protein accumulates in large amounts and all genes under control of LexA start transcribing. | Figure | What effect does superhelicity have on transcription? | For some genes, increasing superhelicity increases transcription. For others, transcription is inhibited. |  | What effect on the DNA does binding of the CRP-cAMP complex have? | It causes the DNA to bend quite sharply. |  | What function does protein N have? | It interacts with the E. coli NusA gene to prevent termination of transcription of selected genes. |  | What functions related to proofreading do GreA and GreB do? | They catalyze the hydrolytic cleavage of nucleotides at the 3' ends of nascent RNA molecules |  | What genes discussed in the text use antisense RNA in a regulatory way? | ompF (an outer membrane protein), CRP (cAMP receptor protein), and the transposase of Tn10 |  | What geometric structure is formed in the E. coli arabinose operon under conditions of low arabinose? | A loop | Figure 26.39 | What governs which promoter is used in the gal operon of E. coli? | Transcription from the S1 promoter requires cAMP-CRP. Transcription from S2 occurs when glucose is present. | Figure 26.38 | What happens to the DNA in the transition between the closed-promoter complex and the open promoter complex? | It is bent. |  | What happens to the tryptophan operon if a ribosome does not bind to the mRNA? | Duplexes form between regions 1-2 and 3-4. The latter duplex causes transcriptional termination. |  | What happens when RNA polymerase reaches DNA sequences that are difficult to transcribe (as measured in vitro)? | It pauses and may sit at the site for several minutes. |  | What happens when the duplex between regions 3 and 4 forms during translation of the trp operon? | Termination of transcription | Figure 26.35 | What intracellular metabolite must increase in E. coli before the lactose operon is turned on? | cAMP | Figure 26.21 | What is a major difference in the template requirements of RNA polymerases and DNA polymerases? | RNA polymerases do not require a template to initiate strand synthesis. |  | What is known about the various subunits of the E. coli RNA polymerase? | is the target for rifampiciin inhibition, plays a role in transcription initiation, and is the catalytic site for chain elongation. subunit - promoter recognition; beta' - DNA binding; - unknown, - chain initiation, interaction with regulatory proteins. | Table 26.1 | What is suspected as the trigger of the E. coli SOS system? | Single-stranded DNA. |  | What is the advantage of using IPTG to induce the lactose operon? | IPTG induces the operon, but is not cleaved by -galactosidase, so its concentration does not change during the experiment. |  | What is the difference between RNA polymerases in eukaryotes and prokaryotes? | Eukaryotes have three RNA polymerases. Prokaryotes have only one RNA polymerase. |  | What is the difference between the nucleotides used to make RNA versus DNA? | 1. Ribonucleoside triphosphates are used. 2. The bases of the ribonulceoside triphosphates are adenine, guanine, uracil (in place of thymine), and cytosine. |  | What is the direction of transcription? | 5' to 3' |  | What is the effect of adding rifampicin during transcription elongation? | Nothing. Rifampicin only inhibits initiation |  | What is the effect of backward movement of RNA polymerase during transcription? | The 3' end tail may be unpaired from the DNA and exposed to the GreA and GreB proteins, which can cleave it. |  | What is the effect of decreasing superhelicity on transcription of the genes for DNA gyrase subunits? | The transcriptional efficiency is increased. |  | What is the error rate of RNA polymerase? | About 1 per 105 nucleotides. |  | What is the function of the Q protein? | Activation of late transcription. |  | What is the function of the trpL sequence at the beginning of the E. coli tryptophan operon? | It provides two consecutive tryptophans for translation. If tryptophan is in short supply, the ribosome will pause at that point. | Figure 26.35 | What is the half-life of most bacterial mRNAs? | 2-3 minutes |  | What is the most efficient spacing region between the -10 region and the -35 region? | 17 nucleotides |  | What is the name of E. coli mutant that does not make ppGpp and thus does not exhibit a stringent response? | Relaxed |  | What is the nature of the motion of the RNA polymerase through the DNA during transcription? | It advances discontinuously, holding its position for several cycles of nucleotide addition and then jumping forward by several base pairs along the template. |  | What is the relationship between the consensus sequence of the -35 and -10 regions and the efficiency of transcriptional initiation? | The more closely a promoter matches the consensus sequence, the more efficient the promoter is in initiating transcription. |  | What is the size of the transcript made from each E. coli rRNA operon? | 30S | Figure 26.41 | What is the subunit structure of the E. coli RNA polymerase? | Two copies of the subunit, one copy each of , beta', , and , giving a Mr of about 450,000 for the holoenzyme. |  | What is the transcriptional rate in E. coli? | About 50 nucleotides per second. |  | What levels of expression of lexA and RecA occur in healthy cells? | Low levels, but sufficiently high for LexA protein to turn off synthesis of the other SOS genes (except RecA) completely. |  | What nucleotides are preferentially bound by the nucleotide binding site used by RNA polymerase in initiation? | ATP or GTP |  | What other gene systems besides the lac operon does the CRP-cAMP complex bind to? | All of them involve energy generation, including operons for utilization of other sugars, including galactose, maltose, arabinose, and sorbitol, and several amino acids. |  | What percent of the total DNA of the E. coli genome is taken up by coding for rRNA and tRNA? | Less than 1% |  | What percentage of the total RNA does mRNA constitute in bacteria? | 1% to 3% |  | What percentage of the total RNA in a bacterial cell is rRNA and tRNA? | About 98% |  | What region of the ompF mRNA is targeted by the antisense RNA? | The translation initiation region. | Figure 26.40 | What regulatory complex used by the lac operon of E. coli is also used by the gal operon? | CRP-cAMP |  | What regulatory factors in the lac operon are positive effectors and which are negative? | Positive - CRP; Negative - Lac Repressor |  | What regulatory gene binds arabinose and activates transcription of the arabinose operon? | araC | Figure 26.39 | What site in the arabinose operon of E. coli does the araC-arabinose complex bind to initiate transcription? | araI | Figure 26.39 | What sites in the arabinose operon of E. coli does araC bind to repress transcription? | araO2 and araO1 | Figure 26.39 | What specificity does the elongation nucleotide binding site have on RNA polymerase? | Any of the four ribonucleotides can bind. |  | What structure does the nucleotide at the 5' end of an RNA molecule have that is different from all the other nucleotides in the chain? | It has three phosphates |  | What subunit of bacterial RNA polymerase is essential for the polymerase finding a promoter? |  |  | What two mechanisms does E. coli use to control the trp operon? | 1. A repressor that is activating by bindingtryptophan 2. Early termination of transcription by attenuation. |  | What two proteins in E. coli are implicated in transcriptional error correction? | GreA and GreB |  | What two types of termination events are known in E. coli? | Factor (rho) independent events and factor (rho) dependent events. |  | When are the repressor-operator and the attenuation regulatory mechanisms functional in regulating the E. coli trp operon? | At low tryptophan concentration the repressor–operator interaction is the principal regulatory mechanism, whereas the effects of attenuation are more significant at moderate to high tryptophan levels. |  | When do the GreA and GreB transcriptional proofreading proteins gain access to the unpaired 3' end of a newly made RNA? | At pause sites. |  | When does attenuation of the E. coli trp operon occur? | When tryptophan levels are high. |  | When E. coli are grown in media containing both glucose and -galactosides, which one is used first? | Glucose |  | When tryptophan levels in the cell are high, which duplexes in the operon form? | 1-2 and 3-4 | Figure 26.35 | When will an RNA polymerase move backwards on a DNA strand? | During pausing |  | Where in the trp operon is transcription stopped by attenuation? | 131 nucleotides from the 5' end of the trpL sequence |  | Which genes stimulate synthesis of cI? | cII and cIII |  | Which genes are involved in excision of the prophage from the genome? | int, xis, and att |  | Which genes function in initiation of DNA replication? | O and P |  | Why is attenuation not a mechanism of regulating eukaryotic genes? | Because transcription and translation occur in physically different regions of the cell, in contrast to prokaryotes where they occur almost simultaneously. |  | Why is it important that bacterial mRNA degradation begins at the 5' end? | If degradation were to start from the 3' end, a ribosome starting from a 5' end might never reach an intact 3' end. |  | Why is translation an essential component of attenuation of the trp operon? | Because it is the position of the ribosome on the mRNA that determines which regions of the RNA form helices. If tryptophan is in short supply, the ribosome stalls in region 1, preventing the 1-2 region from pairing, and allowing the 2-3 region to pair. Thus, the 3-4 region cannot pair and transcriptional termination does not occur. On the other hand, if tryptophan levels are high, the ribosome does not pause in region 1 and quickly moves to region 2, allowing the region 3-4 duplex to form and terminate transcription. |  | With which RNA polymerase subunit does NusA compete for binding to the polymerase? |  |

What four distinct patterns of gene expression must maintain for its four physiological states? | 1. Infection leading to lytic growth. 2. Infection leading to establishment of lysogeny. 3. Long-term maintenance of lysogeny. 4. Breaking of lysogeny with subsequent lytic growth. |  | What are the steps in maturation/processing of a tRNA in E. coli? | 1. An endonuclease cleaves at a stem–loop structure on the 3' side of the tRNA sequence. 2. Ribonuclease D carries out exonucleolytic cleavage to a point two nucleotides removed from the CCA sequence at the 3' end. 3. The 5' end is created by ribonuclease P, which cleaves to leave a phosphate on the 5' terminal G.

4. Ribonuclease D removes the remaining two nucleotides from the 3´ end.

5. Creation of the modified bases common to tRNAs occurs at the final stage, including methylations, thiolations, reduction of uracil to dihydrouracil, and so forth.

Figure 26.42
How does factor-independent termination work?

Two symmetrical GC-rich segments in the transcript have the potential to form a stem–loop structure.

RNA polymerase slows down, or pauses, when it reaches the first GC-rich segment, because the stability of G-C base pairs makes the template hard to unwind.

Pausing gives time for the complementary GC-rich parts of the nascent transcript to base-pair with one another, causing the downstream GC-rich segment of the transcript to be displaced from its template.

The ternary complex of RNA polymerase, DNA template, and RNA is weakened. Further weakening, leading to dissociation, occurs when the A-rich segment is transcribed to give a series of AU bonds (very weak), linking transcript to template.

Figure 26.15

Category - General

Query - What is the status of the lac operon under the following conditions?

Reversal - there is no reversal.

(Conditions on left, status in middle, figure on right)

No -galactosides | Off |  | Glucose plus -galactosides available | Off |  | Only -galactosides are available for energy | On |