Class Questions Flashcards
T/F:Rotation around the N-glycosidic bond is not possible with pyrimidines, due to the steric hindrance between the carbonyl group on the nitrogen-rich base and the oxygen in the furanose
sugar ring
True
Which one of the following is the largest
contributor to DNA double helix stability?
A. The hydrophobic effect
B. Metal ion stabilization
C. Base stacking forces
D. Hydrogen-bonds between bases
C. Base stacking forces
T/F: Non-canonical base-pairing in a double stranded helix is possible,
but relies on covalent bonds between the canonical bases
False
T/F: DNA has a very regular and symmetric 3D structure, whereas
RNA, has little to no defined 3D structure
False
What is the impact of making a modification
to a nitrogen-rich base?
A. It can chance the nucleotides with which it can interact
B. It can promote the folding of a nucleotide polymer into a specific
conformation
C. It can increase the number of nucleotides with which it can make
hydrogen bonds
D. All the above
D. All the above
You have a molecule that is a DNA-RNA hybrid and subject it to
heat denaturation. At a certain point Tm the mixture is half
annealed and half denatured
A. This would have a higher Tm than a comparable solution of DNA
molecules (same length and base ID except T instead of U)
B. This would have a lower Tm than a comparable solution of DNA
molecules (same length and base ID except T instead of U)
C. This would have the same Tm as a comparable solution of DNA
molecules (same length and base ID except T instead of U)
D. Not given enough information in the question to solve this problem
A. This would have a higher Tm than a comparable solution of DNA
molecules (same length and base ID except T instead of U)
Which one of the following statements about
post-translational modifications of histone
proteins is false?
A. Different modifications can change chromatin from a closed
inactive structure to an open active one
B. Modifications to the acidic patch will drive clustering of the
nucleosome forming a closed conformation
C. Histone tails can be modified with several different chemical
modifications, including acetylation and methylation
D. Histone tails stick out from the core nucleosome particle
structure enabling them to form a chemically distinct
binding platform for other protein complexes to silence or
activate specific regions of the genome
B. Modifications to the acidic patch will drive clustering of the
nucleosome forming a closed conformation
Which one of the following statements about
protein phase separation is false?
A. Protein phase separation can occur through pi-stacking, often through
phenylalanine residues in low-complexity regions
B. One protein will self-solubilize and exclude all other biological molecules to
generate a spatial-temporally controlled compartment
C. Protein phase separation can occur through interactions between
complementary domains, forming an interlocking mesh-network of protein
D. Protein phase separation is a reversible biophysical phenomena, with proteins
undergoing transitions between aqueous solubility and self-solubility
B. One protein will self-solubilize and exclude all other biological molecules to
generate a spatial-temporally controlled compartment
You are interested in understanding where a
particular gene is in relationship to a nuclear body.
The experiment you would preform is:
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A. PCR
B. Immunofluorescence experiment
C. FISH and Immunofluorescence experiment
D. Cannot determine both of these properties simultaneously
C. FISH and Immunofluorescence experiment
After the Kronberg lab discovered DNA polymerase, an E. coli strain with a mutation in DNA Pol I rendering it non-functional was discovered. When they performed their DNA synthesis assess with a whole extract of this E. coli they were able to synthesize acid-insoluble DNA. What can you conclude about this observation?
A. This mutant strain of E. coli is not viable (can’t live)
B. Another DNA polymerase must be present – otherwise replication wouldn’t be feasible
C. The acid insoluble component is just free nucleotide – so this indicates that the purified extract did not in fact contain the polymerase
D. Not given sufficient amounts of information to answer the question
B. Another DNA polymerase must be present – otherwise replication wouldn’t be feasible
Which of the following represents the second step that occurs during DNA polymerization?
- Nucleophilic attack from 3’ OH to alpha phosphate
- Stabilization of the incoming nucleotide and the active 3’OH by magnesium
- Formation of Watson-Crick hydrogen bonds between the incoming nucleotide and the template strand
- Generation of the phosphodiester bond and formation of a new substrate for polymerization
- Stabilization of the incoming nucleotide and the active 3’OH by magnesium
T/F: A mutation that renders the protein non-function in either the clamp or the clamp loader would have the same effect – it would reduce the processivity of DNA polymerase
True
Which one of the following statements accurately matches the protein involved in replication with it’s function
A.Helicases stabilize single-stranded DNA which is a required template of DNA polymerase
B.Clamp loading protein is an ATP-independent complex which is in a triplex to facilitate the trombone mechanism
C.Ligase is required to seal up gaps at the ends of the DNA and RNA primer after lagging strand synthesis
D.Pol I performs nick translation to remove the RNA/DNA hybrids that are generated by primase
D.Pol I performs nick translation to remove the RNA/DNA hybrids that are generated by primase
A cytosine residue undergoes spontaneous deamination. After one
round of replication (S-phase) what is the base pair composition in the
two daughter strands?
A. C-G and A-T
B. C-G and A-U
C. A-T and A-U
D. Not enough information given in the question
B. C-G and A-U
Given what you know about the mechanism of DNA polymerase – what would happen when DNA pol III encountered UV-photo cross-linked
damage?
A. Replication stalling
B. Mutations potentially depending on whether the cross-linked
nucleotides were As or Gs
C. This damage would not likely cause any issues for DNA polymerase
D. Would induce rotation around the N-glycosidic bond and potentially
introduce a mutation if new h-bonds could be formed
A. Replication stalling
