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44 Cards in this Set

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What is the Griffith experiment?
Mixer of virulent heat killed bacteria and live nonvirulent bacteria was pathogenic.

Furthermore, live non virulent bacteria and DNA isolated from virulent heat killed bacteria was also pathogenic.

Conclusion is that the transforming agent was DNA.
What is the Hershey-Chase experiment?
Radioactive DNA (not radioactive protein) results in radioactive progeny viruses.
Whats the linkage of the DNA polymers?
Phosphodiester bond linked from 5 to 3.
What forms the backbone of DNA?
Phosphodiester bonds.
Which base pairs are stronger?
G to C or C to G
In B form DNA, how would describe the major groove?
The major groove is wide and shallow.
In B form DNA, how would describe the minor groove?
The minor groove is narrow and deep.
In A form DNA, how would describe the major groove?
The major groove is narrow and deep.
In A form DNA, how would describe the minor groove?
The minor groove is wide and shallow.
What are the differences between A and B form helix?
The A from is more compressed and dehydrate. It's adopted by RNA.

The B form is the most stable form and is found in solution.
What stabilizes the DNA structure?
Base pairing
Stacking interactions
How can we measure the level of denaturation of DNA?
Denaturation increases UV absorbance due to the distruption of base stacking interactions (hyperchronic effect)
What is Tm? and how does it relate to GC concentration.
Temperature at which half of the DNA is random coil (non-helical).

Tm increases with the % of GC.
How do we distinguish the major and minor groove?
The side with the larger angel between the two riboses is the major groove side.
What is the advantage of binding to the major groove?
Space to access the interior of the helix.

Higher specificity: at the major groove we can discriminate between AT, TA, GC, CG whereas at the minor groove we can only discriminate AT/TA vs. GC/CG.
How are specific DNA sequences recognized?
Hydrogen bonding (AA side chains and bases)
Major groove interactions.
What are the major DNA Binding motifs?
HTH
Zinc Finger (helix coordinated by Zn ion)
Homeodomain
Leucine Zipper
BHLB
Which of the motifs are dimers?
Leucine Zipper (Leucine is in the zipper which holds the 2 subunits together through hydrophobic interactions)

BHLH (interacts with two major grooves)
What causes positive supercoiling?
Overwinding
What causes negative supercoiling?
Underwinding
Why is the most of cellular DNA unwound?
Underwinding facilitates strand separation?
How many bases/turn in relaxed DNA?
10.5 bases/turn
What is the linking number (Lk)?
The number of helical turns in a closed circular DNA.

= (# of bp) / (bp/turn)
What is the linking number if there is a nick in strand?
The linking number is undefined.

They are no longer topological joined.
What is superhelical density?
(Change Lk)/(Original Lk)
What is the relationship between negative and positive supercoils?
They are opposite handed.
What are tropoisomers?
Two forms of circular DNA that differ only in a topology property such as linking number.
Which type of topoisomerase can introduce negative supercoils?
Type II
What kind of topoisomerase is DNA gyrase?
Type II
Mechanism of type I tropoisomerase
Bind DNA (closed conformation)
Cleave one strand (Tyrosine attacks phosphodiester linkage)
Pass single branch through the break (open conformation)
Religate DNA (attack from 3' hydroxyl)
What happens when you treat highly coiled DNA with topoisomerase in gel electrophoresis?
As the DNA becomes closer to relaxed, it moves slower through the gel because its less compact.
Mechanism of topoisomerase type II?
Bind two distal segments of DNA
Cleave both strands
Passes one segment through the other break
**REQUIRES ATP HYDROLYSIS**
What are the two types of supercoling? What's their difference?
Plectonemic - less compact and more more linear. DNA in solution

Solenoidal - more compact. DNA found in cells
How does solenodial supercoil occur?
Histone protein (wrapped 2 solenodial supercoils) which form the core of the nucelosome particle.
Where are each of the histones found?
Histone core is made up of 2 copies of 2A, 2B, 3, 4.

Linker histone (H1) is located on the outside and seals the nucleosome.
What helps curve the DNA around the DNA around the histone core?
High concentration of A=T paris.
How does the packaging of nucleosome facilitate supercoiling?
Binding of histone core makes negative solenodial supercoil. This induces an unbounded positive plectonemic supercoil.

Relax DNA with topoisomerase I leaving one net negative supercoil.
What is a 30 nm fiber?
100 fold compaction.

Solenoid supercoil of nucleosomes in solenoid supercoils.
What's the highest order currently known to us?
Nuclear scaffold.
What is the structure of DNA?
DNA is a right handed double helix.
What are the possible secondary structures of RNA?
It can form a harpin or internal loops.
How do the different types of tropisomerase change the linking number?
Type I - changes in increments of one

Type II - changes in increments of two
What kind of amino acids are histones made of?
Negatively charged amino acids which makes them attracted to teh negatively charge phosphate backbone of DNA.
Why are tropisomerase essential for DNA compaction?
They reduce strain caused by underwinding DNA.