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BCHM 4360 EXAM 2 (ACTUAL EXAM 2025 ) | ALL
QUESTIONS AND CORRECT ANSWERS |
VERIFIED ANSWERS | GRADED A+ | NEWEST
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What is the main difference between the many bacterial sigma factors? ----- ----CORRECT ANSWER-----------------Each has a preferred binding sequence and preferred spacing between the - 35 and - 10 elements How do the sigma factor preferred spacings help regulate transcription? ---- -----CORRECT ANSWER-----------------The closer the sequences and spacing are to the preference for a particular sigma factor, the tighter the sigma factor will bind, giving higher transcription rates What are most common for strong promotion of expression of genes? ------- --CORRECT ANSWER-----------------Consensus sequences What does Domain 2 of the RNA Polymerase holoenzyme bind to and what is its function? ---------CORRECT ANSWER------------------10 region, helps separate duplex DNA (promoter melting) What does Domain 3 of the RNA Polymerase holoenzyme bind to and what is its function? ---------CORRECT ANSWER-----------------two bases of the extended - 10 region What does Domain 4 of the RNA Polymerase holoenzyme bind to and what is its function? ---------CORRECT ANSWER------------------35 element,
attached to flexible part of core enzyme which may let it accomodate different - 35 to - 10 spacings What are pro and anti sigma factors? ---------CORRECT ANSWER------------ -----Pro-sigma factors have inhibitory domains that must be cleaved before the sigma can associate with the core enzyme. Anti-sigma factors are proteins that bind to sigma factors and inhibit their function Explain the example of how anti-sigma factors are involved in the regulation of flagellum assembly in S. typhimurium. ---------CORRECT ANSWER-----------------1. While the proteins that form the flagellum base are being synthesized, the anti-sigma binds to the sigma factor, preventing it from binding to the holoenzyme
- The sigma factor promotes transcription of genes that are needed for completion of flagellum assembly
- In the late stages of flagellum protein synthesis, the anti-sigma factor is exported from the cell so the sigma factor can promote assembly gene transcription, allowing the flagellum to be put together. Eukaryotic and archaeal promoters also need extra proteins to target the core enzyme to promoters: _______ _____________ _______. --------- CORRECT ANSWER-----------------general transcription factors The TFII complex works with RNA Polymerase ___ to form the ___- _________ complex. ---------CORRECT ANSWER-----------------II, pre- initiation What happens with regards to Cro if there is insufficient cI production? ------ ---CORRECT ANSWER-----------------Cro accumulates and binds with greatest affinity to OR3, blocking Prm and suppressing cI synthesis. More
What are riboswitches and what are their two components? --------- CORRECT ANSWER-----------------portions of a transcript that can directly bind a small molecule that controls the RNA secondary structure, regulating transcription or translation, aptamer and expression platform Give an example of a riboswitch. ---------CORRECT ANSWER----------------- The bacterial adenine riboswitch that regulates adenine synthesis and transport What are mitogens? ---------CORRECT ANSWER-----------------extracellular signals that promote entry into mitosis What is ELK1 and what happens to it in the absence of mitogens? --------- CORRECT ANSWER-----------------DNA-binding protein that recruits mediator, in absence of mitogen it binds to serum response factor but doesn't activate transcription because it can't recruit mediator Describe how galactose metabolism in yeast is regulated. --------- CORRECT ANSWER-----------------Gal4 activates transcription by binding to UAS sequence. Gal4 activity is regulated by Gal3 and Gal80, which respond to galactose in the cell.
- In absence of galactose, nothing to be metabolized so Gal80 binds to Gal4 to prevent transcription.
- In presence of galactose, Gal3 binds to Gal80 so it can't bind to Gal4, and therefore Gal4 recruits SAGA and Mediator, and transcription continues regularly.
What is Ume6? ---------CORRECT ANSWER-----------------a protein in yeast that can activate or repress transcription in response to nutritional cues What is Rpd3? ---------CORRECT ANSWER-----------------a histone deacetylase, promotes more compact chromatin which represses transcription What is Isw2? ---------CORRECT ANSWER-----------------nucleosome remodeling enzyme, which helps establish the altered chromatin pattern, repressing transcription How does Ume6 respond to the presence and absence of nitrogen and carbon in the cell? ---------CORRECT ANSWER-----------------In presence, Ume6 binds DNA and recruits co-repressors such as Rpd3 and Isw2. In absence, Ume6 is phosphorylated, Sin3 and Rpd3 dissociate, and a co- activator, Ime1 is recruited Why would RNA Polymerase sometimes stall after transcribing the first few dozen nucleotides with regards to Hsp70? ---------CORRECT ANSWER----- ------------This is used to prime hsp70 for rapid transcription in response to heat shock At normal temperatures, the hsp70 polymerase complex is not phoshporylated enough so transcription stalls. What happens with a sudden rise in temperature? ---------CORRECT ANSWER----------------- Heat-shock factor trimerizes and binds to heat shock elements, which then interact with mediator and recruits a kinase, which phosphorylates the CTD and allows transcription to continue
True or False: MCM1 activates transcription of alpha-specific genes, alpha- specific genes are not transcribed in a cells ---------CORRECT ANSWER---- -------------False, reverse, MCM1 activates transcription of a-specific genes, a-specific genes are not transcribed in alpha cells True or False: alpha1 activates transcription of a-specific genes in alpha cells, while a2 represses alpha-specific gene transcription --------- CORRECT ANSWER-----------------False: pay attention to a's and alpha's. alpha1 activates transcription of alpha-specific genes in alpha cells, while alpha2 represses a-specific gene transcription True or False: in a/alpha diploid cells, the a1 and alpha2 proteins combine to form a heterodimer, thus repressing haploid specific genes --------- CORRECT ANSWER-----------------True What is the main function of human interferon-Beta? ---------CORRECT ANSWER-----------------viral defense Nuclear ________ proteins respond specifically to __________. Nuclear receptors have a ___ binding domain and a _______ binding domain. ------- --CORRECT ANSWER-----------------receptor, effectors, DNA, ligand What are the three steps of transcription? ---------CORRECT ANSWER------ -----------initiation, elongation, termination
True or False: The transcription bubble is just as big as the replication bubble. ---------CORRECT ANSWER-----------------False, replication bubble is much larger because it requires two machines at once. When does transcription officially start? ---------CORRECT ANSWER--------- --------when RNA Polymerase binds to the promoter What is the first base to be transcribed known as and how is it denoted? --- ------CORRECT ANSWER-----------------the transcription start site (TSS) and
Which direction is RNA transcribed in? ---------CORRECT ANSWER---------- -------5' to 3' On RNA, bases 3' of a site are __________ while bases 5' of a site are _________. ---------CORRECT ANSWER-----------------downstream, upstream When the RNA is a sufficient size, the RNA Polymerase moves past the ________ and changes ____________ to be more stably associated with the DNA. ---------CORRECT ANSWER-----------------promoter, conformation How does the RNA Polymerase maintain the transcription bubble along the DNA? ---------CORRECT ANSWER-----------------unwinds the DNA ahead of the bubble and the DNA re-pairs behind the enzyme
Bacteria are _______ than eukaryotes and thus operate mainly on _____ factors. ---------CORRECT ANSWER-----------------simpler, sigma Which domain has the smallest RNA Polymerase and approximately what size is it? ---------CORRECT ANSWER-----------------Bacteria, 400kD How many subunits are in the bacterial RNA Polymerase? --------- CORRECT ANSWER----------------- 5 What shape do bacterial RNA Polymerase subunits assemble into? --------- CORRECT ANSWER-----------------jaw-like lobes Between Pol I, II, and III, which subunits are common? ---------CORRECT ANSWER-----------------Rbp5, 6, 8, 10, and 12 What is an additional function of RNA Polymerase II? ---------CORRECT ANSWER-----------------couples transcription to processing of RNA transcript True or False: RNA core sequences can synthesize RNA, but cannot recognize promoter sequences. ---------CORRECT ANSWER----------------- True What does the core bacterial enzyme require in order to recognize promoter sequences? ---------CORRECT ANSWER-----------------Sigma factor
Core polymerase (bacteria) + sigma factor =___________ --------- CORRECT ANSWER-----------------holoenzyme Bacterial promoters generally have which two elements? ---------CORRECT ANSWER------------------35 and - 10 Are the - 35 and - 10 elements upstream or downstream of the TSS? --------- CORRECT ANSWER-----------------upstream Why would having two contact points for sigma factors be beneficial to transcription? ---------CORRECT ANSWER-----------------Makes a much more stable process than if just one contact point What is the function of TFIIA? ---------CORRECT ANSWER----------------- stabilizes binding of TBP and TFIIB What is the function of TFIIB? ---------CORRECT ANSWER----------------- promoter recognition, stabilizes early transcription complex What is the function of TFIID? ---------CORRECT ANSWER----------------- promoter recognition, DNA bending interacts with regulatory factors
How does TFIID bind to the TATA box? ---------CORRECT ANSWER--------- --------Via TBP, which binds to the minor groove of DNA, which induces strong distortions in the DNA and causes local DNA unwinding Some other components of TFIID, called TBP-_________ factors (TAFs) mediate recognition of other promoter elements like ___ and ___. --------- CORRECT ANSWER-----------------associated, INR, DPE What is the next step in transcription initiation after TFIID has associated with DNA? ---------CORRECT ANSWER-----------------TFIIB is recruited. This recognizes the BRE promoter element and binds asymmetrically, helping to determine the transcription direction. What is the next step in transcription initiation after TFIIB has bound? ------- --CORRECT ANSWER-----------------TFIIA binds and stabilizes the TBP- DNA interactions. What is the next step in transcription initiation after TFIIA binds? --------- CORRECT ANSWER-----------------TFIIE and TFIIH bind, which catalyze ATP-powered unwinding of DNA What are the two main components of the pre-inititation complex? --------- CORRECT ANSWER-----------------RNA Polymerase II and general transcription factors True or False: The pre-initiation complex is good enough to initiate transcription in vitro and in vivo. ---------CORRECT ANSWER----------------- False, in vivo requires additional protein complexes
Another large complex, ________, is needed to activate many Polymerase II transcribed genes. ---------CORRECT ANSWER-----------------mediator What are the main similarities between Pol I, II, and III? ---------CORRECT ANSWER-----------------Core subunits are similar, all three use TBP to initiate transcription What are the main differences between Pol I, II, and III? ---------CORRECT ANSWER-----------------TBP is part of different complexes in each enzyme, each use different proteins to initiate transcription, recognize different promoters, and have different general transcription factors Once RNA Polymerase is in position, the complex of polymerase and promoter is called a ______ complex. ---------CORRECT ANSWER----------- ------closed Approximatel how many bp of duplex DNA (transcription bubble) does RNA Polymerase open up? ---------CORRECT ANSWER-----------------14bp True or False: ATP is required to open up the transcription bubble in all three RNA Polymerases ---------CORRECT ANSWER-----------------False, only Pol II requires ATP The RNA Polymerase bound to an open region of DNA is called the ____ complex. ---------CORRECT ANSWER-----------------open
How do magnesium ions work with RNA Polymerase? ---------CORRECT ANSWER-----------------activate the 3' OH and stabilize a negative charge on the leaving oxygen Bacterial _____ ______ and eukaryotic ____ are involved in abortive initiation. Both proteins have a ____ that extends into the RNA Polymerase active site region ---------CORRECT ANSWER-----------------sigma factor, TFIIB, loop How does the loop in abortive initiation function? ---------CORRECT ANSWER-----------------It is in position to block the elongating transcript, so the loop must be moved in order for transcription to continue. Displacement of the loop is thought to help the polymerase break away from the promoter
- promoter clearance During promoter clearance, RNA Polymerase undergoes a ____________ change that associates it very ______ with DNA, and _______ its grip on initiation factors. ---------CORRECT ANSWER-----------------conformational, stably, loosens What is characteristic of the switch from initiation to elongation? --------- CORRECT ANSWER-----------------Dissociation of the general transcription initiation factors RNA Polymerase remains associated with DNA and adds _________ or ________ of bases to growing RNA at about - nucleotides per second. ---------CORRECT ANSWER-----------------hundreds, thousands, 20- 50
What is transcriptional pausing? ---------CORRECT ANSWER----------------- RNA Polymerase pauses due to physical obstructions. This can occur when the RNA has short complementary sequences that can form a hairpin, or by a weak DNA-RNA hybrid within the bubble When does transcriptional arrest occur? ---------CORRECT ANSWER-------- ---------When RNA Polymerase cannot result RNA synthesis following transcriptional pausing Transcriptional pausing can be relieved or enhanced by what? --------- CORRECT ANSWER-----------------elongation factors RNA Pol II makes mRNA, but his is not usually in the final active form, so it is called the _________. ---------CORRECT ANSWER-----------------pre- mRNA True or False: Transcriptional elongation is coupled to mRNA processing in eukaryotes. ---------CORRECT ANSWER-----------------True The phosphorylated ___ region of the ____ subunit of RNA Pol II is involved in processing. ---------CORRECT ANSWER-----------------CTD, Rbp The _____ ______ in the CTD heptad repeat is phosphorylated as RNA Pol II clears the _______ region. ---------CORRECT ANSWER----------------- fifth serine, promoter
What is a proposed mechanism for how transcript cleavage factors work? -- -------CORRECT ANSWER-----------------Transcript cleavage factors are thought to position a metal ion at the active site, which activates a water molecule for hydrolysis of the phosphodiester bond How doe eukaryotes solve the problem of nucleosomes hindering RNA Polymerase? ---------CORRECT ANSWER-----------------use histone chaperones to remove nucleosomes ahead of RNA Polymerase, and reassemble them behind the polymerase What are the three main histone chaperones in eukaryotes? --------- CORRECT ANSWER-----------------FACT (Facilitates Chromatin Transcription), Asf1, and Spt Changes in supercoiling caused by the transcription bubble could cause stalling of RNA Polymerase, and the tension must be relieved by ______________. ---------CORRECT ANSWER----------------- topoisomerases In bacteria, DNA _______ removes the ________ supercoils and DNA ____________ I removes the ________ supercoils. ---------CORRECT ANSWER-----------------gyrase, positive, topoisomerase, negative What are the two main classes of bacterial terminators? ---------CORRECT ANSWER-----------------Intrinsic and Rho-dependent Intrinsic, or ______, terminators end transcription in the _______ of any other factors ---------CORRECT ANSWER-----------------simple, absence
What are the two main features of bacterial intrinsic terminators? --------- CORRECT ANSWER-----------------1. An inverted repeat sequence that, when transcribed, forms a step-loop in the RNA.
- A string of 8-10 angstrom residues. This pairs with the transcribed poly-U in the transcription bubble (a weak, unstable structure) The weak base pairing in the transcription bubble is thought to _______ transcription and the RNA hairpin is thought to interact with the RNA Polymerase and help ____ the RNA ___ of the active site. --------- CORRECT ANSWER-----------------arrest, pull, out When entering into transcription termination, a lot of ___ residues must be present to have the temperature high enough. ---------CORRECT ANSWER-----------------G-C In bacteria, certain genes need the ___ protein to terminate transcription. -- -------CORRECT ANSWER-----------------Rho True or False: Rho-dependent genes have the hairpin and poly-A structures that are found in intrinsic terminators. ---------CORRECT ANSWER-----------------False, rho-dependent genes do not have these structures Rho is a _________ ATP-ase with a ____ structure. It binds to ______ areas of RNA ---------CORRECT ANSWER-----------------hexameric, ring, C- rich
