DNA

tanitia.dooley
Flashcards by tanitia.dooley, updated more than 1 year ago
tanitia.dooley
Created by tanitia.dooley over 6 years ago
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undergrad Chemistry Flashcards on DNA, created by tanitia.dooley on 05/15/2013.
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Question Answer
What is the axial rise of DNA? 3.4A
What form is the guanine base in B-DNA? anti
What form does the sugar adopt in B-DNA? The C2' endo south form
What form does the sugar adopt in B-DNA? The C2' endo south form
What makes the major and minor grooves equal depth? Because the base pairs sit directly on the axis
What form does the glycosidic bond adopt in B-DNA? anti
Describe the major and minor grooves in A-DNA? major-narrow and deep, minor: shallow and wide
Describe Z-DNA? left-handed helix, composed of duplexes composed of GCGC. Sugar in C3' endo conformation. Minor groove very deep and narrow
What is a hairpin? When a single strand fold back on itself if the two ends are complementary
What is thermal melting? When the 2 strands of DNA dissociate to give unstacked seperate strands
What is hypochromicity and what does it result from?? The UV absorbance of double stranded DNA is smaller than what would be predicted for the sum of their constitutent bases. This is because of coupling of the transition dipoles between neighbouring stacked bases
What happens to UV absorbance after denaturing? it increases by 20-30%
What is the melting temperature of DNA, how is this obtained? It is the temperature midpoint for the transition from a helix to single stranded. It is found by observing the UV absorbance whilst increasing the temperature
What does the melting temperature of a duplex depend on? Duplex conc, base composition, sequence, chain length, salt conc & pH of solution
Why does Tm increase with increasing salt concentration? Because the cations mask the repulsive forces of the negatively charged phosphate backbone
Why is the Tm of a hairpin independent of duplex conc? Because the duplex formation is intramolecular
What small molecules interact with DNA at the minor and major grooves? Proteins interact with DNA at the major grooves and cresent-shaped polyamides at the minor
What does intercalation of base pairs occur with? Planar polycyclic aromatics
What is the different between (-) and (+) strands in viruses? (-) strand means it is complementary, (+) means it is identical to mRNA
How is acyclovir converted from a prodrug into its active form? via herpes virus thymidine kinase which phosphorylates 5' OH and then GMP human kinase converts it into acyclovir triphosphate
How does acyclovir triphosphate terminate DNA synthesis? It is a substrate for herpes virus DNA pol- it is incorporated into DNA and because there is no 3'-OH it acts as a terminator
Why cant acyclovir triphosphate be used as the drug? It is too polar to enter cells
Why is AZT toxic? Because HIV does not have its own thymidine kinase therefore there is no selective generation of the triphosphate active form. It uses human cellular kinases to produce AZT triphosphate
How does AZT inhibit DNA synthesis? It inhibits reverse transcriptase as there is no 3' OH so the chain terminates
Describe the 5 steps in the mechaism of AZT Step 1: TrCl & pyridine to protect the OH. Step 2: MeSO2Cl and pyridine Step 3: DIPEA (a base) Step 4. LiN3 and DMF solvent step 5: Acid removes TrO group
What is a nucleoside? heterocyclic base and a sugar
What is the difference between the OH groups in RNA and DNA? Why? RNA has 2-one at 2' and one at 3'. DNA only has one at 3'. The second OH makes RNA unstable
What are the purines and what are the pyrimidines? purines: Adenine & guanine. Pyrimidines: cytosine & uracil
What replaces uracil in RNA? thymine
How is a nucleotide formed from a nucleoside? Phosphorylation of the nucleoside
At what position does the phosphate bridge in DNA and RNA? Between the 3' and 5' position of the sugars
What is the association of 2 individual strands of DNA stabilised by? 1. Watson crick base pairing- H bonds between bases 2. Hydrophobic bases on the inside and polar phosphate on the outside where they can be salvated with water to stabilise the negative charge 3. pi electrons- interactions between the bases that stock on top of each other
What is the helical turn of DNA? 10.5bp/turn
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