03a: DNA Flashcards
The bases are attached to which atom of nucleotide?
C1
Difference between ribose and deoxyribose configuration.
Ribose has hydroxyl on C2
Phosphate group attached to which atom on nucleotide?
C5
Complementary sequence to ACTGCT.
AGCAGT
Number of hydrogen bonds between A and T.
2
Number of hydrogen bonds between G and C.
3
Distance between adjacent bare pairs in DNA is (constant/variable) at around:
Constant; 0.34 nm
Width of DNA double helix is:
2 nm
Describe Pauling and Corey DNA model, called (X).
P-form DNA
Bases on outside, backbone on inside. Not probable (backbone negatively charged, so repulsion)
In wet environment, which DNA form is found?
B form
In low humidity environment, which DNA form is found?
A form
What does Z form DNA code for?
Non-coding area (spacer)
Z form DNA nucleotide sequence is composed of:
Repeating GC units
Z form DNA is (RH/LH).
LH helix
B form DNA is (RH/LH).
RH
A-form DNA is (RH/LH).
RH
(A/B)- form DNA is more tightly wound.
A-form
T/F: once denatured, DNA strands cannot be renatured.
False
What are the stabilizing factors in secondary DNA structure?
- Hydrogen bonds
- Van der waals
- Ions in cells
What are the destabilizing factors in secondary DNA structure?
Electrostatic repulsion (P has negative charge at phys pH)
(Single/double) stranded DNA absorbs more light.
Single-stranded (more exposed)
Tm, aka (X), depends on:
X = temperature at which half DNA denatured
Depends on % AT and GC base pairs
DNA with higher percent AT base pairs will have (higher/lower) Tm compared to DNA with higher GC base pairs.
Lower
Template for reverse transcriptase.
RNA
Drugs that block HIV RNA from being reverse transcribed into DNA.
Nucleoside reverse transcriptase inhibitors (NRTIs)
Drugs that cut up proteins needed to create new HIV virus.
Protease inhibitors
Drugs that prevent HIV entry into cell.
Entry inhibitors
Drugs that prevent HIV from inserting its genetic code into human cell genome.
HIV integrase inhibitors
AZT, a drug that treats (X), has which MOI?
X = HIV
Thymine analog that is incorporated into growing DNA; lack of OH at 3’ position prevents addition of NT
Quinolones are drugs used to combat (X). What’s the MOI?
X = infectious agents
Bind to topoisomerase and inhibit ligase domains (leads to DNA fragmentation)
Type 1B topoisomerases cut (1/2) strand(s) and introduce (X) number of supercoils at a time.
1 strand;
X = 1
Type 1B topoisomerases rely on E from:
Strained DNA
Which end of DNA strand(s) rotate(s) when acted on by type 1B topoisomerase?
Free 3’ end of nicked strand
Type II topoisomerases cut (1/2) strand(s) and introduce (X) number of supercoils at a time.
2 strands;
X = 2
Type II topoisomerases rely on E from:
ATP
In nature, Type II Topoisomerases usually introduce (positive/negative) supercoils.
Negative
T/F: Certain topoisomerases affect bacteria and not eukaryotes.
True
Histones are rich in which AA? Why?
Lys and Arg;
Positive charges bind tightly to negative DNA backbone
List the histones in (X) core.
X = nucleosome
H2A, H2B, H3, H4
Which histone is associated with linker DNA (not part of nucleosome core)?
H1
Nucleosome formation gives about (X)-fold shortening, allowing (positive/negative) supercoiling in (euk/prok).
X = 6-7
Negative; eukaryotes
Solenoid formation gives about (X)-fold shortening.
X = 35-40
How many nucleosomes per turn in solenoid formation?
6 nucleosomes per turn
In prokaryotes, how does the mRNA sequence compare to the template stand? And non-template strand?
Complementary to template strand; IDENTICAL to non-template (unlike eukaryotes, due to introns)
In (eukaryotes/prokaryotes), DNA and protein are colinear.
Prokaryotes
T/F: In eukaryotes and prokaryotes, size of genome doesn’t correspond to number of genes
False - it does, but only in prokaryotes
In (eukaryotes/prokaryotes), gene sequences are unique/single copy.
Prokaryotes
T/F: In eukaryotes and prokaryotes, most DNA is functional.
False - in eukaryotes, most DNA is non-functional
In eukaryotes, about (X)% of genome codes for proteins.
X = 10
Highly repetitive sequences (are/aren’t) transcribed.
Aren’t
Highly repetitive sequences are usually composed of which nucleotides?
Short, tandem AT-rich repeats
Highly repetitive sequences are present at (X) copies/genome.
X = >300,000
T/F: Some highly repetitive sequences have functions.
True - telomeres
Telomeres are examples of (highly/moderately/non)-repetitive sequences.
Highly repetitive
Moderately repetitive sequences are derived from:
transposons
Moderately repetitive sequences (are/aren’t) transcribed.
Usually are
Moderately repetitive sequences (are/aren’t) translated.
Aren’t
Moderately repetitive sequences are present at (X) copies/genome.
X = 2-300,000
Moderately repetitive sequences code for:
Highly used genes (histones, rRNA, tRNA), but most non-functional
Most of genome composed of (highly/moderately/non)-repetitive sequences.
Non-repetitive (unique/single-copy)
In any one cell, about (X)% of genome made into protein, except for (Y).
X = 1
Y = housekeeping genes (universally required)
Advantages of nucleosome folding:
- Pack lots of DNA into small nucleus
- Negative supercool opens DNA up for use
- Distant linear regulatory sequences brought closer together
