Show:
Chapter 11
Chapter 12
Chapter 13
Chapter 18
Random Review
100
Describe the difference between DNA polymerase III and DNA polymerase I.
DNA pol III: synthesizes new DNA strand, builds off existing 3' end, builds on leading and lagging DNA pol I: removes RNA primers to fill in with DNA, only builds on lagging
100
Is the -35 sequence or -10 sequence more likely to be rich in two specific nucleotides? Why, and which nucleotides?
-10, b/c this is where the open complex will form and mRNA transcription occurs; high in A-T b/c less H-bonding so easier to pull apart
100
Which of the following are true concerning tRNA? Choose all that apply. A. contains the codon sequence B. contains the anticodon sequence C. it is bound to an AA that becomes part of a primary protein D. it is bound to a protein that becomes part of a quaternary protein E. mismatches can be allowed when tRNA binds to mRNA
B, C, E
100
Birthmarks are commonly manifested as different colored patches of hair or skin in an offspring that the parent does not possess. Can birthmarks be considered germ-line mutations or somatic mutations?
somatic, won't be passed on to their offspring
100
What enzyme is most well-known for being "processive"? What does it mean to be processive
DNA polymerase III, processive means that it never let's go of the DNA template
200
DNA gyrase is an enzyme necessary during: replication, transcription, or translation. Is it used in eukaryotic or prokaryotic cell types? And why, is it not used in the other?
Replication Prokaryotic not in eukaryotic b/c there is no supercoiling since it is not circular DNA strands
200
Which of the following are true concerning Rho-dependent termination? Choose all that apply. A. a stem-loop structure forms B. acts by destabilizing RNA polymerase C. a small aggregate of proteins disrupt RNA polymerase D. relies upon 3 different consensus sequences in the DNA E. contains a protein recognition site that begins termination
A, B, E
200
Name and describe the three stages of translation in order.
Initiation: assembly of ribosome complex and mRNA, initiator tRNA recognizes AUG Elongation: peptide synthesis, charged tRNA enters A site, polypeptide goes from P to E Termination: stop codon aligns with A site, release factor binds to A site
200
Name and describe three different types of DNA repair mechanisms.
Base Excision: removal of single base pair Nucleotide Excision: whole nt is removed, i.e. a thymine dimer Mis-Match Repair: recognizes mismatched nt, cleaves large DNA section and fills it back in Homologous recomb: repairs DSBs, occurs when sister chromatids are together Non-homologous end-joining: repairs DSBs, much more error prone
200
Of the types of mutations, which is the only kind that does not consist of a base substitution?
frameshift mutation; it's addition/deletion
300
If telomerase became deficient in cells which of the following physiological changes would you expect? Choose all that apply. A. longer chromosomes and increased negative supercoiling B. lose of genetic material upon division C. an increase in the progression of aging D. an increase in the likelihood of cancer occurrence E. more cells in a senescent phase
B, C, E
300
A geneticist isolates a gene for a specific trait under study. She also isolates the corresponding mRNA. Upon comparison, the mRNA is found to contain 1,000 fewer bases than the DNA sequence. Did the geneticist isolate the wrong DNA? A) yes, mRNA is made from a DNA template and should be the same length as the gene sequence B) yes, the mRNA should contain more bases than the DNA sequence because bases flanking the gene are also transcribed C) no, the final mRNA contains only exons, the introns were removed D) no, the mRNA was partially degraded after it was transcribed
C
300
Explain the roles of the A, P, and E sites during translation.
A (aminoacyl): where tRNA carrying single AA initially binds P (peptidal): contains tRNA covalently bound to growing protein construct E (exit): occupied by uncharged tRNA that has no AA anymore
300
Which of the following could be considered spontaneous mutations rather than induced? Choose all that apply. A. losing the nitrogenous base portion of a nt B. experiencing a DSB as a result of radiation C. binding of thymine to create dimers caused by UV exposure D. intrinsic conversion of an amine group to a ketone E. an unsteady equilibrium shift from a keto to an enol form
A, D, E
300
DNA polymerase is considered a high fidelity enzyme. What is meant by this? And how does it achieve it?
It does not often make mistakes 1. catalytic domain structure that catalyzes each subsequent rxn, incorrect base pairing inhibits bond formation 2. Proof-reading activity, can go back and remove incorrect nt
400
Describe the differences between the allosteric model and torpedo model of eukaryotic transcriptional termination. For the torpedo model, what would the implication be if the exonuclease had a mutation that caused it to at a slower nt/sec rate the RNA pol II?
(both have PolyA sequence) allosteric: once RNA pol II reaches sequence it's destabilize and falls off torpedo: exonuclease degrades unneeded transcript and catches up to RNA pol II to pull it off If exonuclease was slower, it wouldn't catch up to RNA pol II and transcription would not terminate resulting in an altered mRNA transcript
400
A nonsense mutation occurs at the 4th nt in the Shine-Dalgarno sequence in a bacterial mRNA transcript. Which of the following would be likely outcomes of this event? Choose all that apply. A. translation would occur sooner b/c of the shorter sequence B. translation would not occur because of this truncation C. the mRNA transcript would be unable to bind the 30S subunit of the ribosome b/c of the loss of nt D. the mRNA transcript would bind the 30S subunit with a tighter affinity b/c there are fewer nt E. no changes would be expected
B, C
400
How would each of the following types of mutations affect the amount of functional protein that is expressed from a gene? A. nonsense B. missense C. up promoter mutation D. mutation affecting splicing
A. probably inhibit function esp. if not near the innate stop sequence B. variable, depends on which AA is substituted and the region of the gene it may be found in C. increase the amount of functional protein D. variable, depends upon if the splicing alteration changes an exon in the mRNA resulting in different protein structure
400
Describe the structural features that all tRNA molecules have in common.
cloverleaf structure with three stem-loops; second stem-loop contains anticodon sequence that recognizes mRNA; at 3' end there is an acceptor stem with the sequence CCA
500
DNA polymerase sometimes makes a mistake in adding the wrong nt to a growing DNA strand. Concerning purines and pyrimidines, there are two general types. There is transition: an incorrect pyrimidine instead of the correct pyrimidine; or transversion: an incorrect pyrimidine instead of the correct purine. Although both are rare, transition is more frequent than transversion. What would be at least one explanation for why this would happen?
b/c a pyrimidine always binds with a purine (and vice versa) a transversion would cause a purine-purine or pyrimidine-pyrimidine bond disrupting the double helix another reason is that DNA pol proofreads and a pyrimidine -> purine switch (and vice versa) disrupts DNA structure much more than a pyrimidine -> incorrect pyrimidine (and vice versa)
500
The initiation phase of eukaryotic transcription via RNA pol II is considered an assembly/disassembly process. Which types of biochemical interactions (H-bonds, ionic bonds, covalent bonds, hydrophobic interactions) would you expect to drive the assembly/disassembly process? How would temp and salt conc. affect this?
primarily H-bonding because of the ease of breaking and reconstructing. High temp and low salt favor disassembly while low temp and high salt favor assembly
500
Do the following events during bacterial translation occur primarily within the 30S subunit, the 50S subunit, or at the interface between the two subunits? A. mRNA-tRNA recognition B. peptidyl transfer reaction C. exit of the polypeptide chain from the ribosome D. binding of initiation factors IF1, IF2, and IF3 E. recognition of the Shine-Dalgarno sequence
A. surface of 30S and the interface B. within the 50S C. within the 50S D. within the 30S E. within the 30S
500
In the treatment of cancer, the basis for many types of chemo and radiation is that mutagens are more effective at killing dividing cells rather than nondividing. Explain. What are harmful side effects?
Nondividing cells will harbor the mutation but will not pass them on to daughter cells b/c they are not undergoing mitosis. In dividing cells, the cells have the ability to pass it on to daughter cells resulting in an increase of the mutation occurrence to a potentially lethal level. Side effects: affecting cells other than cancerous ones to create new, unneeded mutations.
500
Describe the two major eukaryotic modifications on either end of an mRNA and their functions.
5' 7 methyl guanosine cap: allows for recognition by splicing machinery 3' PolyA tail: endonuclease recognizes to cleave RNA