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76 Cards in this Set

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What is the Central Dogma?
DNA ->/<- RNA -> Protein
What copies DNA?
Replication
What allows DNA and RNA to interchange?
Transcription and Reverse Transcription
What takes RNA into Protein?
Translation
What is the DNA structure like From microscopic to macroscopic?
-DNA helix
-Chromatin - beads on string
-Chromatin makes up fibers
-Fibers form loops (75000 bp)
-6 loops make up one rosette
-30 rosettes stacked = 1 coil
-10 coils like a phone cord = 1 chromatid
What are the fundamental building blocks of DNA?
-Nitrogenous bases (2 flavors)
-Sugars
-Phosphate backbone
What are the pyrimidines?
Cytosine
Uracil
Thymine
What are the purines?
Guanine
Adenine
What other molecules are nucleotides important building blocks of?
-NAD+
-Coenzyme A
-cAMP/cGMP
-ATP/GTP
-ppGpp
What is ppGpp?
Guanosine tetraphosphate
What is ppGpp important in?
Regulating transcription in bacteria.
What kind of bond joins the nucleotides together in DNA?
Phosphodiester bond between the 5'-3' hydroxy groups on the phosphate backbone.
In what direction are bases sequences written?
5' -> 3'
What direction are phosphodiester bonds given in?
They're called 3'->5' phosphodiester bonds b/c the 3' OH attacks the alpha phosphate of the incoming nucleotide.
What are the features of B-form DNA?
-Antiparallel strands
-Bases inside, backbone out
-Bases stacked, perpendicular to helical axis.
-10.5 nt / turn
-Hydrogen bp hold structure together
-Base sequence is unrestricted
Where in DNA are there:
-COVALENT linkages?
-NONCOVALENT linkages?
Covalent: in the phosphodiester backbone.
Noncovalent: in the base pairs
What are the 3 noncovalent forces holding together the DNA double strand?
-Hydrogen bonding btwn base pairs
-Hydrophobic effect (all hydrophobic uncharged bases hide from water)
-Electrostatic force arising from base stacking and Van der Waal interactions.
Why are their major and minor grooves in DNA?
Because the glycosidic bonds of the base pairs are not diametrically opposed.
Why are grooves in DNA useful?
It makes the base pairs accessible for recognition and binding of other proteins.
What is a certain cancer drug that intercalates the minor groove to exert its effect?
Actinomycin D
What is Actinomycin D's effect?
Interferes w/ RNA/DNA synthesis
So what part of DNA would bind
-Base-Specific proteins?
-Nonspecific proteins?
Base spcfc: major/minor groove
Nonspecfic: phosphate backbone
What is A form DNA?
A tighter, dehydrated structure. Still right-handed like B form.
What is the most dramatically different form of DNA?
Z form - left handed
What is the significance of different DNA forms?
Regulation of the DNA within specific regions of the cell.
What causes bent DNA?
A string of 4-6 A with a spacer of 10 nt.
What is the result of bent DNA?
Distorted spacing of the major and minor grooves - which interferes with protein binding of the grooves.
What drug induces bent DNA?
Cisplatin
How does Cisplatin work?
Binds both DNA strands; induces intrastrand cross bridging.
So what is the result of Cisplatin?
Inhibition of cell growth
In what type of nucleic acid is non-Watson Crick bpairing more commonly found? Why?
RNA - because it is singled stranded and more capable of forming alternative H-bonds with non-normal bases.
How does DNA Triple Helix formation play a role in Hereditary Persistance of fetal Hgb?
-Naturally forming triplex in fetal Hb promotor necess to downregulate fetal Hgb;
-Mutation destabilizes helix and y-globin persists.
What name denotes the base pair formed in DNA triplexes?
Hoogsteen base pairs
What 2 variables can be used to disrupt H-bonds and denature DNA?
1. Changes in pH
2. Changes in temp
What is the Tm?
The temperature at which half the helical structure is lost.
What increases the bond strength of a DNA helix?
-Increased GC content - b/c it contains 3 H bonds per GC pair
-Increased salt content of solvent
How is DNA melting monitored?
By measuring DNA's absorbance at 260 nm.
How does absorbance change when DNA is melted?
It increases - ssDNA absorbs more than dsDNA does, b/c the stacked base pairs are shielded and absorb less energy.
What term denotes the increase in absorbance?
Hyperchromic shift at 260 nm.
Why does increased GC content increase the strength of a DNA double strand?
2 reasons:
1. 3 H bonds
2. Increased Van der Waals interactions in GC base pairs
What would cause a decreased Tm?
-Decreased GC content
-Decreased salt content
What would cause an increased?
the opposite...
Why does changing salt concentration change the stregnth of the DNA helix?
-Higher ionic strength shields the negatively charged phosphate backbone;
-Lower strength allows the charges to predominate and pull charge away from the interior H bonds of the base pairs, decreasing stability.
In what 3 ways can DNA molecules be found? (states)
-Linear
-Relaxed circular
-Supercoiled circular
What causes
-Positive supercoiling?
-Negative supercoiling?
Pos: overwinding

Neg: underwinding
For every untwist of a DNA helic twist, how many supercoils are created?
1 neg supercoil per untwist.
What enzymes relieve the tension caused by supercoiling?
Topoisomerases
How does Topoisomerase I work?
Relieves supercoils by
1. Nicks one DNA strand
2. Passes a DNA segment thru
3. Reseals the nick
What type of supercoiling does Topo I work on?
Both pos and negative.
Do topoisomerases need ATP?
Type one, no: their action is thermodynamically favorable.
Type Two, YES.
How does Topo II work?
Relieves supercoils by
1. Binds One DNA coil/2 ATP
2. Cleaves one dsDNA coil
3. Passes other strand thru
4. Reseals complete DNA coil
So in general what does Topo II do?
Relaxes negative and positive supercoils
What enzyme can introduce negative supercoils?
Only prokaryotic Type II topoisomerase GYRASE.
Eukaryotic DNA is not circular, so how do supercoils arise?
B/c of the fact that eukaryotic DNA is packaged in nucleosomes.
How does supercoiling affect the way DNA shows on a gel?
It compacts it, so it moves faster
What are the medical implications of our knowledge on superhelicity and topoisomerases?
We can inhibit the bacterial Topo II (gyrase) and kill the bacterial cells, without affecting eukaryotic topo.
What are two drugs that inhibit prokaryotic gyrase?
-Novobiocin
-Ciprofloxacin
What is Ciprofloxacin used to treat?
Bacillus anthracis
What are 2 drugs that inhibit EUKARYOTIC Topo II? What are they used to treat?
Doxorubicin + Etoposide
-Treats cancer
How exactly do Topo II inhibitors WORK?
-Disable the ATPase activity
-Enhance nicking or reduce resealing, leaving permanent nicks in the DNA.
How do eukaryotes get ~1 meter of DNA into 1 tiny cell?
By packaging it into chromatin.
What is a 30 nm fiber of chromosome material made of?
Nucleosomes
What is a nucleosome?
Supercoils of DNA wrapped around histones.
What are histones?
Positively charged basic proteins that form ionic bonds with the phosphate backbone of DNA.
Why are histones good for DNA helix stability?
They neutralize the large negative charge of the backbone.
What is a nucleosome core made of?
H2A, H2B, H3, and H4
What links Nucleosomes?
Linker DNA
What stabilizes the nucleosome/linker structure?
Histone 1 protein
What type of structure is each part of a nucleosome core?
a dimer - so that makes the whole nucleosome core an octomer.
What are HATS?
Histone Acetyl Transferases
What do HATS do?
Add acetyl groups to the terminal NH3+ groups of Lys residues in histone core (H3/H4)
What does acetylation of histone core subunits do?
Neutralizes the basicity of histones, which reduces their affinity for DNA - this OPENS UP THE DNA CHROMOSOME.
What 2 amino acid residues are largely responsible for histone protein's basicity?
lys and arginine
What are HDACS?
Histone deacetylases
What do HDACS do?
Repress active (open) regions of chromatin.
What's an example of a gene that turns off chromatin opening-up?
Sir 2