DNA structure Flashcards
What force contributes the most stability to DNA?
Hydrophobic interactions between adjacent stacked base pairs (van der Waals)
How many hydrogen bonds form between G and C?
3
How many hydrogen bonds form between A and T?
2
What end is the phosphate attached to?
5’
What is the destabilizing force in DNA structure?
Repulsion between the negative charges of the phosphate backbone.
What is the complementary sequence to ACCGTATTC?
5’-GAATACGGT-3’
What forms are the adenine and cytosine bases in order for correct base pairing to occur?
Amino (as opposed to imino)
What form at the guanine and thymine bases?
Keto (as opposed to enol)
How wide is the secondary structure of DNA?
2 nm
How tall is each turn (B form)? How many base pairs per turn?
3.4 nm and 10 base pairs per turn (.34 nm between adjacent stacked base pairs)
What handedness is the DNA helix (B form)
right-handed
How are base pairs oriented to the helix axis (B form)?
Flat and perpendicular
What does the major groove allow when DNA needs to be used?
Proteins to gain access to the bases
What environment is A form DNA found in?
Dehydrated
How many base pairs per turn of A form DNA?
11
What is the structure for dsRNA and RNA-DNA hybrid?
A form
How is the backbone oriented in Z DNA? Why?
Zig zag due to alternating purine and pyrimidine sequences (first isolated as repeating dGdC)
How is the helix oriented in Z DNA (handedness)?
Left handed
How many base pairs per turn in z DNA?
12
Where do other forms of DNA involving 3 or 4 strands appear?
Sites important for initiation or regulation of DNA metabolism, such as replication and transcription.
What is hyperchromicity?
The phenomenon of increased UV absorption as strands of the double helix separate. Bases absorb UV light at 260 nm
What occurs at the Tm?
Half of DNA has melted (denatured)
What factor of DNA composition influences Tm?
Concentration of AT to GC. More GC pairs will make DNA more stable so it will have a higher melting point.
Where is circular DNA found in eukaryotes?
mitochondria
What are 4 ways to interrupt the HIV life cycle (HAART therapy)?
Inhibit: 1) reverse transcriptase; 2) HIV entry into the host cell; 3) protease that cleaves proteins HIV needs to make new viral particles; 4) inhibit integrase
What is AZT?
An NRTI. It is a thymidine analogue that lacks a 3’ hydroxyl group. Terminates chain elongation.
What does acyclovir do?
It goes through a series of conversions to eventually resemble dGTP, but it lacks a 3’ OH group so it prevents attachment of additional nucleosides.
What type of drug is Cipro and what does it inhibit?
Antibiotic. Topoisomerase inhibitor.
What other type of therapy uses topoisomerase inhibitors?
Antineoplastic (chemotherapy)
What supercoiled state is DNA normally in? How is this advantageous for transcription?
Negative. This rotation opposes the double helix twisting, so DNA is easier to open and utilize.
How do type Ia topoisomerases work?
Cut one strand and passes the unbroken strand through the cut, then rejoins. Strand must have tension from a supercoiled state to provide energy.
How to type Ib topoisomerases work?
Cuts one strand and lets the other strand rotate around before rejoining.
What type of supercoil can type Ia TI relax?
negative
What type of supercoil can type Ib TI relax?
- or +
How do prokaryotes introduce negative supercoiling into newly synthesized DNA?
Type II topoisomerase
What can type II topoisomerases relax?
Negative or positive supercoils
What do eukaryotes use to introduce negative supercoils?
Histones. We don’t use topoisomerase II for nuclear DNA.
What amino acids are histones rich in?
Lysine and arginine. so basic
What is the full structure of nucleosome?
Octamer of two identical tetramers (H2A, H2B, H3, and H4)x2. DNA wrapped around 1 and 3/4 time.
Where does histone 1 come in?
Associated with linker DNA. Helps form higher order structures.
What is the level of structure above nucleosome?
Solenoid
How many nucleosomes per solenoid turn? What is the shortening ration?
- Provides 35-40 fold shortening of DNA.
How many turns are taken out of DNA by wrapping around a histone?
one
What is the packing efficiency of condensed DNA?
10,000 times shorter
Highly repetitive sequences
Not transcribed, tandem repeats, usually 10% or less of genome
Moderately repetitive sequences
Derived from transposon, usually transcribed but not translated, 25-45% of genome
How frequently repeated are sequences for histones, tRNA, rRNA?
Moderately
Single copy DNA
Most genes, 40-60% of genome, one type of unique gene exists with gene families
