BMR TEST 3 Nucleic Acid Structure Flashcards
How many rings are there in each latter of the double helix and who donates what?
3 rings
2 from purines
1 from pyrimidines
What part of the nucleotide provides the backbone for the double helix?
The 5-carbon sugar
What role does the nucleotide’s phosphate play?
Energy providing molecule
Describe Chargaff’s Rules?
A=T
G=C
Purines = Pyrimidines
How does the nucleotide structure influence DNA structure?
The hydrophobic nitrogenous bases form hydrogen bonds inside the two strands and the hydrophilic 5-carbon sugar provides the external backbone
What is the Primary sequence of DNA
Covalently bonded base pair sequence.
What is the Secondary sequence of DNA?
The stable structure taken up by some or all of the nucleotides.
Do all tissues in an organism have the same base composition?
YES
Most numerous cell in the body with no DNA?
Erythrocyte, RBC
Ways to write DNA sequence?
pApTpG
dAdTdG
ATG
Number of H bonds between A and T?
2
Number of H bonds between G and C?
3
Is a DNA sequence weaker if it has a high concentration of A - T or G - C?
why?
How can this be measured?
A - T,
less hydrogen bonding.
High AT content DNA has a lower Tm point.
What forces are involved in base stacking? and is it base specific?
Dipole interactions,
Van der Walls forces,
Not base specific.
Is hydrogen bonding or base stacking stronger for DNA secondary structrure?
Base stacking.
What is the predominant form of DNA?
B form
Where is A form helices commonly seen?
RNA double helices
What is a palindrome repeat?
Repeating mirror sequence on opposite strands
What is a mirror repeat?
Repeating mirror sequence on the same strand.
Complementary repeats make what?
Hairpin structures and cruciforms
What is the role of the major groove?
Allows sequence specific trans-factors to bind by giving them easier access.
Cruciforms play what role?
Help form complex structure, and can form Epitopes which will travel along the cytoskeleton to where the mRNA is needed.
Where are cruciforms most apt to form?
5’ or 3’ ends
At what temperature does DNA completely denature?
80C
If DNA isn’t completely denatured can it reform?
Yes
What is the process for denatured DNA reforming the double helix? and how does it occur?
Annealation, it occurs spontaneously.
Is dentaturing ever good and if so when?
Yes, DNA replication can only occur when in the single stranded form.
What is the hyperchromic Effect? How is it measured?
The hyperchromic effect is the sigmoid curve of protein denaturation.
As protein denatures, it absorbs more light.
What is the Tm Melting point
The point in the Hyperchromic Effect when 50% of the protein is denatured.
What is a TATA box?
How does it work?
It is the transcription start point.
Low Tm point allows easy denaturation.
How is DNA packaged in the HSV-1 virus? Why?
Radially packaged
Saves space, can be done due to replication not occurring in the capsid.
What were the beads on a string?
Nucleosomes
Role of Topoisomerase II
Critical to maintain underwinding for this structure.
What is the centromere?
The middle of the X of the chromosome arms.
In what phase is the sister chromatid arm made?
S phase
How many core histone proteins?
8
What kind of supercoiling do the histones have?
Negative
What kind of supercoiling do the linker regions have?
Positive, due to being wrapped around the negative histone.
Role of topoisomerases in Supercoiling?
Bind to relieve engineered positive supercoiling stress.
Role of supercoiling and how it happens?
Supercoiling relieves stress imposed by underwound DNA.
DNA double helix is coiled onto itself.
If topoisomerase is inhibited what occurs?
Medical uses?
Death occurs
Quinolone Anti-biotics
Anti-cancer agents.
Epigenetics is the result of what?
Chromatin structure affecting gene expression
What are epigenetic modification?
Non-sequence based changes to DNA that are propagatable through mitosis or meiosis
Role of methylation
Sterically inhibits transfactors (Silences genes)
Though some proteins can bind to it which could activate genes.
Role of histone modifications
Effects ability of nucleosomes to interact with each other.
