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76 Cards in this Set
- Front
- Back
What is the Central Dogma?
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DNA ->/<- RNA -> Protein
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What copies DNA?
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Replication
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What allows DNA and RNA to interchange?
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Transcription and Reverse Transcription
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What takes RNA into Protein?
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Translation
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What is the DNA structure like From microscopic to macroscopic?
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-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 |
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What are the fundamental building blocks of DNA?
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-Nitrogenous bases (2 flavors)
-Sugars -Phosphate backbone |
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What are the pyrimidines?
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Cytosine
Uracil Thymine |
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What are the purines?
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Guanine
Adenine |
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What other molecules are nucleotides important building blocks of?
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-NAD+
-Coenzyme A -cAMP/cGMP -ATP/GTP -ppGpp |
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What is ppGpp?
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Guanosine tetraphosphate
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What is ppGpp important in?
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Regulating transcription in bacteria.
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What kind of bond joins the nucleotides together in DNA?
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Phosphodiester bond between the 5'-3' hydroxy groups on the phosphate backbone.
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In what direction are bases sequences written?
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5' -> 3'
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What direction are phosphodiester bonds given in?
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They're called 3'->5' phosphodiester bonds b/c the 3' OH attacks the alpha phosphate of the incoming nucleotide.
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What are the features of B-form DNA?
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-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 |
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Where in DNA are there:
-COVALENT linkages? -NONCOVALENT linkages? |
Covalent: in the phosphodiester backbone.
Noncovalent: in the base pairs |
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What are the 3 noncovalent forces holding together the DNA double strand?
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-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. |
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Why are their major and minor grooves in DNA?
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Because the glycosidic bonds of the base pairs are not diametrically opposed.
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Why are grooves in DNA useful?
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It makes the base pairs accessible for recognition and binding of other proteins.
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What is a certain cancer drug that intercalates the minor groove to exert its effect?
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Actinomycin D
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What is Actinomycin D's effect?
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Interferes w/ RNA/DNA synthesis
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So what part of DNA would bind
-Base-Specific proteins? -Nonspecific proteins? |
Base spcfc: major/minor groove
Nonspecfic: phosphate backbone |
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What is A form DNA?
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A tighter, dehydrated structure. Still right-handed like B form.
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What is the most dramatically different form of DNA?
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Z form - left handed
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What is the significance of different DNA forms?
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Regulation of the DNA within specific regions of the cell.
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What causes bent DNA?
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A string of 4-6 A with a spacer of 10 nt.
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What is the result of bent DNA?
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Distorted spacing of the major and minor grooves - which interferes with protein binding of the grooves.
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What drug induces bent DNA?
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Cisplatin
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How does Cisplatin work?
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Binds both DNA strands; induces intrastrand cross bridging.
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So what is the result of Cisplatin?
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Inhibition of cell growth
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In what type of nucleic acid is non-Watson Crick bpairing more commonly found? Why?
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RNA - because it is singled stranded and more capable of forming alternative H-bonds with non-normal bases.
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How does DNA Triple Helix formation play a role in Hereditary Persistance of fetal Hgb?
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-Naturally forming triplex in fetal Hb promotor necess to downregulate fetal Hgb;
-Mutation destabilizes helix and y-globin persists. |
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What name denotes the base pair formed in DNA triplexes?
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Hoogsteen base pairs
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What 2 variables can be used to disrupt H-bonds and denature DNA?
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1. Changes in pH
2. Changes in temp |
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What is the Tm?
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The temperature at which half the helical structure is lost.
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What increases the bond strength of a DNA helix?
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-Increased GC content - b/c it contains 3 H bonds per GC pair
-Increased salt content of solvent |
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How is DNA melting monitored?
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By measuring DNA's absorbance at 260 nm.
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How does absorbance change when DNA is melted?
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It increases - ssDNA absorbs more than dsDNA does, b/c the stacked base pairs are shielded and absorb less energy.
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What term denotes the increase in absorbance?
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Hyperchromic shift at 260 nm.
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Why does increased GC content increase the strength of a DNA double strand?
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2 reasons:
1. 3 H bonds 2. Increased Van der Waals interactions in GC base pairs |
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What would cause a decreased Tm?
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-Decreased GC content
-Decreased salt content |
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What would cause an increased?
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the opposite...
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Why does changing salt concentration change the stregnth of the DNA helix?
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-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. |
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In what 3 ways can DNA molecules be found? (states)
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-Linear
-Relaxed circular -Supercoiled circular |
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What causes
-Positive supercoiling? -Negative supercoiling? |
Pos: overwinding
Neg: underwinding |
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For every untwist of a DNA helic twist, how many supercoils are created?
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1 neg supercoil per untwist.
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What enzymes relieve the tension caused by supercoiling?
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Topoisomerases
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How does Topoisomerase I work?
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Relieves supercoils by
1. Nicks one DNA strand 2. Passes a DNA segment thru 3. Reseals the nick |
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What type of supercoiling does Topo I work on?
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Both pos and negative.
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Do topoisomerases need ATP?
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Type one, no: their action is thermodynamically favorable.
Type Two, YES. |
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How does Topo II work?
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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 |
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So in general what does Topo II do?
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Relaxes negative and positive supercoils
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What enzyme can introduce negative supercoils?
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Only prokaryotic Type II topoisomerase GYRASE.
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Eukaryotic DNA is not circular, so how do supercoils arise?
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B/c of the fact that eukaryotic DNA is packaged in nucleosomes.
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How does supercoiling affect the way DNA shows on a gel?
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It compacts it, so it moves faster
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What are the medical implications of our knowledge on superhelicity and topoisomerases?
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We can inhibit the bacterial Topo II (gyrase) and kill the bacterial cells, without affecting eukaryotic topo.
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What are two drugs that inhibit prokaryotic gyrase?
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-Novobiocin
-Ciprofloxacin |
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What is Ciprofloxacin used to treat?
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Bacillus anthracis
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What are 2 drugs that inhibit EUKARYOTIC Topo II? What are they used to treat?
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Doxorubicin + Etoposide
-Treats cancer |
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How exactly do Topo II inhibitors WORK?
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-Disable the ATPase activity
-Enhance nicking or reduce resealing, leaving permanent nicks in the DNA. |
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How do eukaryotes get ~1 meter of DNA into 1 tiny cell?
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By packaging it into chromatin.
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What is a 30 nm fiber of chromosome material made of?
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Nucleosomes
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What is a nucleosome?
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Supercoils of DNA wrapped around histones.
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What are histones?
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Positively charged basic proteins that form ionic bonds with the phosphate backbone of DNA.
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Why are histones good for DNA helix stability?
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They neutralize the large negative charge of the backbone.
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What is a nucleosome core made of?
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H2A, H2B, H3, and H4
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What links Nucleosomes?
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Linker DNA
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What stabilizes the nucleosome/linker structure?
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Histone 1 protein
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What type of structure is each part of a nucleosome core?
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a dimer - so that makes the whole nucleosome core an octomer.
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What are HATS?
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Histone Acetyl Transferases
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What do HATS do?
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Add acetyl groups to the terminal NH3+ groups of Lys residues in histone core (H3/H4)
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What does acetylation of histone core subunits do?
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Neutralizes the basicity of histones, which reduces their affinity for DNA - this OPENS UP THE DNA CHROMOSOME.
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What 2 amino acid residues are largely responsible for histone protein's basicity?
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lys and arginine
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What are HDACS?
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Histone deacetylases
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What do HDACS do?
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Repress active (open) regions of chromatin.
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What's an example of a gene that turns off chromatin opening-up?
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Sir 2
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