Term
| What is another name for thymine? |
|
Definition
|
|
Term
| In all naturally occuring nucleotides and nucleosides the nitrogenous base is linked to the ___ atom (which is called a ________ bond) |
|
Definition
|
|
Term
| If the phosphate group is absent, the compound is known as a _________ |
|
Definition
|
|
Term
| The purines form glycosidic bonds to ribose via their ___ atoms |
|
Definition
|
|
Term
| Pyrimidines form glycosidic bonds to ribose via their ___ atom |
|
Definition
|
|
Term
| Are phosphodiester groups acidic of basic? |
|
Definition
|
|
Term
| What are chargaffs rules? |
|
Definition
|
|
Term
| In humans ___ stores information and __ transmits information |
|
Definition
|
|
Term
| ____ is more stable than ___ |
|
Definition
|
|
Term
| nucleotides are made up of..? |
|
Definition
| a Nitrogenous base, a sugar and a phosphate group |
|
|
Term
| nucleic acids are polymers made up of what monomers? |
|
Definition
|
|
Term
| another name for adenine is |
|
Definition
|
|
Term
| the pKa of guanine is about..? |
|
Definition
|
|
Term
| Nitrogenous bases are called bases because they can be..? |
|
Definition
|
|
Term
| the pKa of adenine is about..? |
|
Definition
|
|
Term
| The pKa of cytosine is about..? |
|
Definition
|
|
Term
| before titration of adenine can occur what process must take place? |
|
Definition
|
|
Term
| The pKa of the enol form of thymine is about..? |
|
Definition
|
|
Term
| The reactivities of the nitrogenous bases are very similar to their ability to _______ |
|
Definition
|
|
Term
| Nucleophilicity is very similar to _______ |
|
Definition
|
|
Term
| A base reacting with a sufficently electrophilic alkyl group such as : CH3I can lead to..? |
|
Definition
| alkylation.. in this case methylation at the same places where the bases are protonated |
|
|
Term
| Bases are are aromatic so their electrons are ________ and their shape is ________ |
|
Definition
|
|
Term
| What for of ribose is used in DNA? |
|
Definition
|
|
Term
| What form of sugar is used in RNA? |
|
Definition
|
|
Term
| What two carbons are involved in the phosphodiester bond? |
|
Definition
|
|
Term
| what is the most unstable phosphoester? |
|
Definition
|
|
Term
| what are the two stable phosphoesters? |
|
Definition
|
|
Term
| A term for a short polymer of nucleotides |
|
Definition
|
|
Term
| a term for a long chain of nucleotides? |
|
Definition
|
|
Term
| what aspects of biochem make it distinct from regular o-chem and give biochem its "magic" |
|
Definition
| folding up of macromolecules into 3D structures which interact w/ other molecules with great specificity |
|
|
Term
| What kind of interactions is folding dependant on? |
|
Definition
|
|
Term
| what are the three types of weak interaction we looked at? |
|
Definition
Electrostatic
H-bonding
Hydrophobic |
|
|
Term
| What are the two main aspects of hydrophobic interactions? |
|
Definition
1. non-interferance w/ water structure
2. Van der Waals interactions |
|
|
Term
| What is the equation for change in gibbs free energy? |
|
Definition
| (delta)G=(delta)H-T(delta)S |
|
|
Term
| in the equation for gibbs free energy what is the form of degrees used ? |
|
Definition
|
|
Term
| What equation relates change in free energy to the equilibrium constant? |
|
Definition
|
|
Term
| What equation relates change in free energy of activation to the rate constant constant? |
|
Definition
| (delta)G(activation)=-RTlnk(rate constant) |
|
|
Term
| how do enzymes speed a reaction? |
|
Definition
| lower the free energy of activation |
|
|
Term
| What is the appx free energy of a C-C single bond? |
|
Definition
|
|
Term
| what is the appx free energy of a C=C dbl bond? |
|
Definition
|
|
Term
| What is the range of free energies for weak interactions? |
|
Definition
|
|
Term
| what is the appx thermal energy at biological conditions? |
|
Definition
|
|
Term
| What is the distance between C's in a C-C single bond? |
|
Definition
|
|
Term
| How is an angstrom defined? |
|
Definition
| 10^-10 meters or 1/10th of a nm |
|
|
Term
| What is the equation for coulombs law? |
|
Definition
|
|
Term
| What is solved for in coulombs law? |
|
Definition
| Force between two electrical charges |
|
|
Term
| What is k in coulombs law? |
|
Definition
| proportionality constant (8.99*10^9 J*m*C^-2) |
|
|
Term
| What is D in coulombs law? |
|
Definition
|
|
Term
| What is the dielectric constant of water? |
|
Definition
|
|
Term
| What is happening in a H-bond? |
|
Definition
| A H is being shared by two electronegative atoms |
|
|
Term
| What are the EN atoms that participate in H bonding (for our purposes) |
|
Definition
|
|
Term
| What does water behave like in terms of its structure? |
|
Definition
| It behaves like an octomere |
|
|
Term
| what are typical H-bond distances? |
|
Definition
|
|
Term
| What directionality leads to the strongest H-bonding? |
|
Definition
|
|
Term
| What is the typical Energy of H-bonds (in ice for example)? |
|
Definition
|
|
Term
| H-bonds in macromolecules have definite ____________ |
|
Definition
|
|
Term
| when water solvates H-bonding groups in macromolecules you keep the same # of ____________ but lose ____________ |
|
Definition
|
|
Term
| What is the driving force between the non-interference w/ water structure aspect of hydrophobic bonds? |
|
Definition
| Entropy.. mixing w/ H2o decreases entropy.. segregating increases entropy |
|
|
Term
| What are van der waals interactions? |
|
Definition
| Induced dipoles, weak electrostatic interactions |
|
|
Term
| Draw and explain the graph of the VDW interaction between two atoms or molecules |
|
Definition
|
|
Term
|
Definition
|
|
Term
| What is the VDW radius of CH3? |
|
Definition
|
|
Term
| what is the VDW radius of 1/2 thickness aromatic ring? |
|
Definition
|
|
Term
| what is the VDW radius of N? |
|
Definition
|
|
Term
| What is the VDW radius of P? |
|
Definition
|
|
Term
| What is the VDW radius of O? |
|
Definition
|
|
Term
VDW interactions have _____ directionality
However when macromolecular surfaces are complementary the VDW interactions are _______ directional |
|
Definition
|
|
Term
| What are the three pKas of the O atoms on P? |
|
Definition
|
|
Term
| What bases have phenolic pKas? |
|
Definition
| Guanine thymine and uracil |
|
|
Term
| H-bonding is driven by _________ effects |
|
Definition
|
|
Term
| Who ran the lab Crick and Watson where working in when they discoverd the DNA double helix |
|
Definition
|
|
Term
| Who in Braggs lab was working on the structure of hemoglobin? |
|
Definition
|
|
Term
| Who in Braggs lab was working on the structure of myoglobin? |
|
Definition
|
|
Term
| J. watson was a __________ student in Braggs lab |
|
Definition
|
|
Term
| F. Crick was a _______ student in Braggs lab |
|
Definition
|
|
Term
| What two structures had linus pauling discovered? |
|
Definition
|
|
Term
| Who saw diffraction of DNA ~10yrs previous to Watson and Crick? |
|
Definition
|
|
Term
| what is purified DNA like? |
|
Definition
|
|
Term
| DNA diffraction suggests what kind of a structure? |
|
Definition
|
|
Term
| In X-ray diffraction one only sees results when the X-rays are ________ |
|
Definition
|
|
Term
| Crystals are oriented in 3D in a ______ way |
|
Definition
|
|
Term
| who wrote the Helical Transform in 1952? |
|
Definition
|
|
Term
| What did Cochran, Crick and Vand write in 1952 |
|
Definition
|
|
Term
|
Definition
|
|
Term
| What is the n in braggs law representing? |
|
Definition
|
|
Term
| what does the lambda denote in braggs law? |
|
Definition
| the wavelength of the x-ray |
|
|
Term
| What does the d in braggs law represent? |
|
Definition
| spacing of atoms and molecules (regular spacing) |
|
|
Term
| What does theta represent in braggs law? |
|
Definition
|
|
Term
| A large bragg angle indicates... |
|
Definition
|
|
Term
| a small bragg angle indicates a |
|
Definition
|
|
Term
| what is used to move from reciprocal space to real space and vice versa? |
|
Definition
|
|
Term
| What are three major features of the X-ray diffraction picture from DNA? |
|
Definition
1. Strong meridianal reflections
2. regular layer lines of spots
3. cross pattern or "helical cross" |
|
|
Term
| What about the x-ray diffraction picture generated by DNA suggests that it is a helix? |
|
Definition
| the cross pattern or "helical cross" |
|
|
Term
| If there is a helical repeat every n spacings there will be a ______ _________ _______ on the nth layer line |
|
Definition
| strong meridianal reflection |
|
|
Term
| DNA diffraction picture has a Strong Meridianal reflection on the ____ layer line indicating... |
|
Definition
| 10th, a helical repeat every 10 "spacings" |
|
|
Term
| The equitorial reflection measurement of ___Å indicated... |
|
Definition
| 22Å, it is likely that the diameter of the helix is 22Å |
|
|
Term
| Using the fact that DNA helix repeats(at least in terms of structure) every 10 spacings and that the unit spacings are 3.4Å how long is a single helical repeat? |
|
Definition
|
|
Term
| What are 5 pieces of information Watson and Crick had to work with in determining the structure of DNA? |
|
Definition
1. Chemical structure of the nucleotides
2. X-ray data
3. Chargaffs rules
4. densities of A and B forms of DNA
5. chain polarity |
|
|
Term
| The A form of DNA is ________ and the B form is __________ |
|
Definition
| crystaline, paracrystaline |
|
|
Term
| There is a ___ _________ of the dna as it moves from b form to a form |
|
Definition
|
|
Term
| what process leads to the conversion of b form dna to a form? |
|
Definition
|
|
Term
| Because A form DNA forms crustals one can calculate the _____ _____ _____________ of the crystal |
|
Definition
|
|
Term
| How does one calculate the length of spacingings in the A form of DNA? and what is the length of spacing in A form? |
|
Definition
| 3.4Å(length of spacing in B form)*.70(A form is 70% the length of B form)= 2.4Å |
|
|
Term
| What three facts can be used to calculate the number of nucleotides in a unit cell? |
|
Definition
1. the density of A form DNA
2. The chemical structure of nucleotides
3. the dimensions of the unit cell |
|
|
Term
| what is the length of the unit cell in A form DNA? |
|
Definition
|
|
Term
| It can be calculated that there are ____ nucleotides per unit cell |
|
Definition
|
|
Term
| Dividing the length of the unit cell by the length of the spacings in A form DNA it is determined that..? |
|
Definition
| there are 12 spacings per unit cell |
|
|
Term
| Dividing the number of nucleotides in the unit cell by the number of spacings per unit cell tells us..? |
|
Definition
| How many nucleotides are involved in each spacing... this is 2 |
|
|
Term
| Because of his previous studies of x-ray crystallography Crick recognized a ____ _____ ____ in the diffraction pattern of DNA which indicated? |
|
Definition
| C2 spacing group, a two-fold axis of symmetry |
|
|
Term
| It was determined that the two strands involved in DNA must be ___________ because parallel starnds do not have a ___________ ______ __ ________ |
|
Definition
| antiparallel, two-fold axis of symmetry |
|
|
Term
| the ratio of (A+T)/(C+G) can be anywhere from ___ to ___ |
|
Definition
|
|
Term
| the minor groove is formed by the side of the nucleotide pairs where... |
|
Definition
|
|
Term
| The major groove is formed by the side of the nucleotide pairs opposite.. |
|
Definition
|
|
Term
| the distance between C1s of A-T and G-C are.. |
|
Definition
|
|
Term
| A ___ handed helix seemed much more plausable than a _____ handed helix |
|
Definition
|
|
Term
| The method used most heavily by Watson and Crick to determine the structure of DNA was..? |
|
Definition
|
|
Term
|
Definition
| When the two bases involved in pairing are not coplanar |
|
|
Term
| Three weak interactions in DNA? |
|
Definition
1.H-Bonding between base pairs
2.Electrostatic PO4- repulsion
3.Hydrophobic, base stacking, dipole-dipole interactions |
|
|
Term
| The sugar are almost __________ along the axis while the bases are _________ |
|
Definition
|
|
Term
| In the A form of DNA there is a helical repead every ____ and the diameter of the helix is ____ |
|
Definition
|
|
Term
| The diameter of the B form of DNA is ____ |
|
Definition
|
|
Term
| In the A form of DNA the major groove is ______ while the minor groove is _________ |
|
Definition
|
|
Term
| In soln DNA is predominantly found in the ___ form while RNA is found in the ___ form |
|
Definition
|
|
Term
| At what wavelength of UV light does DNA have its max absorbance, which is in the ______ of the UV range |
|
Definition
|
|
Term
| What is Hypochromiciy and what is it caused by? |
|
Definition
| Decreased absorbance of UV light ds DNA compared to random coil DNA and individual mononucleotides, caused by the electronic interactions between stacked bases |
|
|
Term
| As the temp of a soln containing DNA rises the UV absorbance _________ |
|
Definition
|
|
Term
| Why is the denaturation DNA described as a cooperative process? |
|
Definition
| the collapse of one part of the duplex structure destabilizes the remainder |
|
|
Term
What is another term for the denaturation of ds dna? |
|
Definition
|
|
Term
| What are the symmetry operations to generate the DNA helix? |
|
Definition
1. Rotation about the axis (36 degrees per base)
2. Translation along the axis(rise) of 3.4A per base |
|
|
Term
| _____ base stacking is stronger than ___ stacking.. so helicies with higher _____ content have a higher melting temp |
|
Definition
|
|
Term
How does a higher salt conc. lead to increased stability in DNA? |
|
Definition
| The ions diffuse the negative charges on the phosphate groups lowering ther repulsion |
|
|
Term
| while reading a spectrophotomer a drop in volts indicates a ________ in absorbance |
|
Definition
|
|
Term
| In DNA hybridization a stable __________ duplex can be formed if the strands are complementary |
|
Definition
|
|
Term
| What two groups experiments showed that DNA was the genetic material? |
|
Definition
-Avery et. al.(1940s)
-Hershey and Chase(1950s) |
|
|
Term
| How did Avery show DNA to be the genetic material? |
|
Definition
Putting DNA from smooth pneumoccous collonies placed in rough cells spawned smooth colonies |
|
|
Term
| What arguments where used against Averys results? |
|
Definition
| His DNA was not 100% pure.. could be caused by protein impurities |
|
|
Term
| What vehicle did hershey and chase use to study DNA? |
|
Definition
| A T2 bacteriophage which infected e.coli |
|
|
Term
| how is a Phage organized.. what is it made up of? |
|
Definition
| A head or capsid which is full of DNA followed by a tail and tail fibers |
|
|
Term
| How does a phage infect a cell? |
|
Definition
| It attaches to the cell membrane and injects DNA |
|
|
Term
| What did hershey and chase label in their Phages? |
|
Definition
Labeled Protein w/ 35^S( no S in DNA)
Labeled DNA w/ 32^P (No P in protein) |
|
|
Term
| After infecting e.coli w/ their labeled phage how did Hershey and Chase seperate the cells from the phages protein coats? |
|
Definition
They put the cells in a blender, shearing forces knocked the protein coats off.
Then the solution was put in a centerfuge and the cells precipitated while the coats remained in the supernatant |
|
|
Term
| what machine did Hershey and Chase use to look for their radioactive markers after infection took place? Why? |
|
Definition
| A liquid Scintillation counter, it can record the presence of 35^S and 32^P and tell them apart. |
|
|
Term
| How does a liquid scintillation counter work? How does this help identify 35^S and 32^P |
|
Definition
| measures the emmission of ß-particles, both radioactive elements emmit a maximum ammount of ß-particles at characteristic energies |
|
|
Term
| Where did hershey and chase find their radioactive atoms? |
|
Definition
| 32^P was found in the pellet(in the cells) and 35^S was found in the supernatant(protein coats) |
|
|
Term
| How did hershey and chase conclude that DNA was the genetic material? |
|
Definition
| Cells containing only DNA from the Phage spawn more phages, so the phages must be coming from the DNA not the protein |
|
|
Term
| Who developed the technique of seperating 14^N and 15^N using the ultracentrifuge? how did this work? |
|
Definition
| S. Vinograd, he generated a cscl gradient the heavy isotope sinks lower, the light isotope rises higher |
|
|
Term
| What where bacteria grown in to incorperate 15^N into their DNA? for how long? |
|
Definition
| 15^NH4Cl, many generations |
|
|
Term
| In a density gradient DNA will settle at its _______ ______ |
|
Definition
|
|
Term
| After one division of heavy e. coli in light media what did messelsen and stahl observe in the ultracentrifuge? |
|
Definition
| One band of moderate density |
|
|
Term
| After two generations what did messelsen and stahl observe in their density gradient? as generations progressed which band grew in size(or became darker.. whatever) |
|
Definition
| Two bands one moderate one light, the light band incresed w/ successive generations |
|
|
Term
| What are the precursors of DNA? |
|
Definition
|
|
Term
| Who discovered PolI? and what else did he discover? |
|
Definition
| A. Kornberg, that 5'NTPs are the precursors of DNA |
|
|
Term
|
Definition
| A protein which catalyzes biochemical Rxns |
|
|
Term
|
Definition
| An RNA that catalyzes biochemical Rxns |
|
|
Term
| What is a cell free extract? |
|
Definition
| A cellular extract which no longer retains the shape and organization of the cell, produced by opening up the cells |
|
|
Term
| What did A. Kornberg discover about cell free extract from e.coli? |
|
Definition
| it could still replicate DNA |
|
|
Term
| How did A. kornberg further isolate the protein he was looking for from the cell free extract? |
|
Definition
| he centrifuged the cell free extract, the proteins remained in the supernatant. |
|
|
Term
| How did A. kornberg further seperate the proteins in his cell free extract supernatant? |
|
Definition
| He "salted out" proteins, by adding salt (NH4)2SO4 slowly you can crudely fraction out differnt proteins. |
|
|
Term
| How Does Salting out work? |
|
Definition
| As the salt conc. increases the activity of water decreases and solute-solute interactions become stronger than solute-solvent interactions. At high salt concentrations so many ions are solvated that the ammount of bulk solvent available becomes insufficient to dissolve other solutes. |
|
|
Term
| How did A. Kornberg further seperate the enzyme he was looking for from the salted out fractions? |
|
Definition
|
|
Term
| What are two different types of column chromatography? |
|
Definition
1.Columns that fractionate according to size
2.Columns that fractionate due to ion exchange |
|
|
Term
| How do Columns that fractionate according to size work? |
|
Definition
| they contain a matrix whixh ties up small proteins and does not allow large proteins to enter, so the large exit first (move arounsd the entire matrix) and the small proteins exit last (have to move through matrix) |
|
|
Term
| What kind of a charge does a cation exchange column have? |
|
Definition
|
|
Term
| What kind of charge does an anion exchange column have? |
|
Definition
|
|
Term
| How does an ion exchange column work? |
|
Definition
| The protein associates with the column based on charge, you start by pouring soln through the column with a low ionic strength and gradually increase to a high ionic strength. Different proteins will elute at different ionic strengths giving fractions with differnt proteins. |
|
|
Term
| What does TCA stand for and what does it do? |
|
Definition
| Trichloroacetic acid, will cause macromolecules to precipitate, while monomers remain in solution |
|
|
Term
| How did Kornbergs assay work? |
|
Definition
"fraction" + pppN(a-labeled(32^P) or pppT(3H labeled T))---->incubate at 37?-----> +5% TCA to ppt macromolecule------> count macromolecules (measure radioactivity.
if precipitated DNA contains radioactive atoms enzyme is working |
|
|
Term
| Why did the fraction kornberg obtained after salting out not work? how was this confirmed? |
|
Definition
| The pure enzyme and 5'NTPs will not work, the DNA template is needed this was confirmed by adding DNA macromolecules back in and observing synthesis |
|
|
Term
| It was observed that very pure and intact DNA will not work as a template for polymerization but messy broken up DNA works great why is this? |
|
Definition
| The messy DNA has nicks and breaks which afford a 3' OH for the polymerase to work on while the intact DNA had no 3' end free to act as a primer for the DNA Polymerase to work on |
|
|
Term
| What where 5 properties of the DNA polymerase isolated by A. Kornberg? |
|
Definition
1. Needs a primer and a template
2. Needs all four pppNs
3. 5' exonuclease activity
4. 3' exonuclease activity
5. synthesizes exclusivly in the 5'-->3' direction |
|
|
Term
| By what mechanism does DNA synthesis occur? |
|
Definition
| By nucleophilic attack of the 3' OH on the phosphate connected to the 5' carbon in the dNTPs |
|
|
Term
| What properties of the DNA polymerase isolated by Kornberg led J.Cairns to believe it was not the correct DNA polymerase? |
|
Definition
1. 3' exonuclease activity 2. 5' exonuclease activity 3. synthesis exclusivle in the 3'---> 5' direction |
|
|
Term
| Who doubted A. Kornbergs Polymerase and spent a year trying to find a mutant w/o the kornberg polymerase? |
|
Definition
|
|
Term
| What was cairns trying to do and did he succeed? |
|
Definition
| He was trying to find a mutant lacking the Kornberg polymerase, yes he finally succeeded after a year of tedious work |
|
|
Term
| What where some puzzling aspects of cairns Pol II? and what did this lead cairns to do? |
|
Definition
| had 3' exonuclease activity and only synthesized in the 3'-->5' direction, was also very sensitive to UV light. Cairns began searching for a mutant lacking Pol II |
|
|
Term
| Who finally found the main DNA polymerase for e. coli? what was it called? what where some of its properties? |
|
Definition
| J. cairns, Pol III, 3' exonuclease activity and synthesis exclusivly in the 5'--->3' direction |
|
|
Term
| How was it determined that Pol III was the main.. essential DNA polymerase in e. coli? |
|
Definition
| A heat sensitive mutant of pol III was found such that at certain temperatures it ceased to work. using this it was determined that e.coli w/ pol III grew happily but w/o Pol III the cells did not grow at all. Cells w/o Pol I and Pol II grew happily if they had Pol III |
|
|
Term
| What are Pol I and II good for in e.col and what hinted at this fact? |
|
Definition
| Pol I and Pol II are used in DNA repair and this was hinted at by the fact that mutants lacking Pol I where extremely sensitive to damage via UV radiation |
|
|
Term
| Besides discovering Pol III what other important experiment was conducted by J. Cairns? |
|
Definition
| He labeled e. coli genomes w/ tridium (3^H) and then exposed it to high levels of tridium during replication so he could visualize the DNA synthesis using a photographic emulsion. |
|
|
Term
| What did Cairns discover by labeling newly synthesized DNA in the e. coli genome w/ high levels of tridium mid-synthesis? |
|
Definition
1. DNA replication is bi-directional, synthesis occurs at both replication forks 2. replication occurs on both strands bidirectionally, synthess on both leading and lagging strands |
|
|
Term
| What did okazaki observe after exposing DNA to a short pulse of 3^H-TTP and seperating it via sedimentation velocity? |
|
Definition
| A distinct band of small pieces of DNA and a band of large pieces of DNA |
|
|
Term
| What did okazaki observe after chasing DNA exposed to a short pulse of 3^H-TTP with cold TTP and seperating it via sedimentation velocity? |
|
Definition
| All of the short pieces became long and only a band of long DNA was observed |
|
|
Term
| What was particularly confusing about the results okazaki observed in his sedimentation velocty pulse-chase experiment? |
|
Definition
| there where never any intermediate sized DNA bands, only short bands which became long in one discrete jump |
|
|
Term
What did Okazaki propose to explain the discrete jump he saw in DNA sizes in his sedimentation velocity pulse-chase experiment? |
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Definition
| on the lagging starnd of DNA small portions are synthesized and then ligated to the much larger DNA strand. When you pulse w/ 3^H and centrifuge you can see the small pieces of DNA before they are ligated.. but after a cold chase all your hot DNA has become incorperated into the new growing genome and shows up as large DNA. Liagtion turns small dna into large dna in one discrete step |
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Term
| what two molecules are needed to seal up a nick in DNA? |
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Definition
| The ligase enzyme and NAD (nicotinamid adenine dinucleotide) |
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Term
| How did okazaki set about answering the question of what is the primer used on the lagging strand? |
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Definition
| he used a pulse chase experiment again but this time utilizing a Cs2SO4 gradient in the ultracentrifuge. So he was sperating by density not size. |
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Term
| What did okazaki observe in his pulse-chase experiments in the ultracentrifuge? |
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Definition
| That the fragments of DNA on the lagging strand where more dense than the DNA incorperated into the genome.. this lead him to believe that these fragmets where DNA/ RNA intrastrand hybrids. |
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Term
| How did okazaki confirm that the more dense band DNA he was seeing in his pulse-chase density gradient experiment contained RNA? |
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Definition
| After adding ribonuclease (an enzyme which chews out RNA) the band disappeared, only the less dense DNA only band was visible |
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Term
| how many origins of replication does the e.coli genome have? |
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Definition
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Term
| what binds to the origin of replication to begin to seperate the genome in e. coli? |
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Definition
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Term
why does RNA polymerase bind at the origin? what is its purpose? |
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Definition
| there are several RNA promoters to attract it, it opens the helix and gets the "ball rolling" so to speak on replication |
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Term
| What does DNA B do? (Two Jobs) |
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Definition
1. Unwinds ds DNA
2. Directs binding of primase |
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Term
| What is SSB and what does it do? |
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Definition
| Single strand binding protein, it stabilizes single strands of DNA, prevents annealing |
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Term
| Where does SSB bind, what purpose does this serve? |
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Definition
| Binds to the backbone so DNA polymerase can "see" bases |
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Term
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Definition
| wherever you have ss dna you have SSB |
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Term
| After DNA B has bound the double helix and SSB has stabilized the single strands what protein comes in next? What does it do? |
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Definition
| Primase, an RNA polymerase, it lays down the primers for DNA synthesis |
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Term
| DNA polymerase always needs a ________, RNA Pols _______ |
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Definition
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Term
| What is responsible for the high processivity of Pol III? |
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Definition
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Term
| What is the structure of the ß-clamp? |
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Definition
| Shaped like a doughnut w/ two subunits each constituting half of the doughnut |
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Term
| What is the diameter of the hole in the ß-clamp? |
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Definition
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Term
| How does the ß-clamp get onto the DNA? |
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Definition
| It is loaded on by the "clamp loader", which is the gamma complex of DNA Pol III |
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Term
| Where is the ß-clamp located in terms of DNA pol III during replication? |
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Definition
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Term
| What is the alpha subunit of DNA Pol III? |
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Definition
|
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Term
| what is the function of the epsilon subunit of DNA Pol III? |
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Definition
| 3'-->5' exonuclease activty |
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Term
| what is the function of the theta subunit of DNA pol III? |
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Definition
| stimulates error correcting ability of the epsilon unit |
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Term
| What is another name for the ß2 subunit of DNA pol III? |
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Definition
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Term
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Definition
| Organized group of proteins which forms the replication complex |
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Term
| How is the lagging strand oriented in the replisome? |
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Definition
| It is looped inside the replisome |
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Term
| What is the function of Pol I? |
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Definition
| Chews out RNA primer replacing it with DNA |
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Term
| What is "nick translation" |
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Definition
| As DNA Pol I replaces the RNA primer w/ DNA it moves the existing nick at the back of the RNA primer to what was the front of the RNA primer |
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Term
| How long is a typical RNA primer? |
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Definition
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Term
| how fast does Pol III polymerize DNA? |
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Definition
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Term
| what is L and what does it equal? |
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Definition
| L is the linking number and it equals T+W |
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Term
| what is L in a closed circular loop of DNA? |
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Definition
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Term
| as you seperate DNA and lower T what happens to W? |
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Definition
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Term
| each turn of watson crick ds DNA T=? |
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Definition
| +1 (one right handed turn of the double helix) |
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Term
| by disrupting 1 T you create what..? |
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Definition
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Term
| what is positive supercoiling? |
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Definition
+1 left handed plectonemic turn or
+1 right handed solenoidal turn |
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Term
| what kind of a turn is T=+1 |
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Definition
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Term
| what is negative supercoiling? |
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Definition
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Term
| what is negative supercoiling? |
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Definition
+1 RH plectonemic turn
+1 LH solenoidal turn |
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Term
| how does the cell deal with supercoiling? |
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Definition
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Term
| what are the two classes of topoisomerases? |
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Definition
| Topoisomerase I and Topoisomerase II |
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Term
| To move from a negative supercoil to relaxed what kind of topoisomerase is used? does this require ATP? |
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Definition
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Term
| to move from relaxed DNA to - supercoiling what topoisomerase is used? does it require ATP? |
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Definition
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Term
| To move from + supercoiling to to relaxed DNA what topoisomerase is used? does it require ATP? |
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Definition
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Term
| Replication generates what kind of supercoiling? and what sort of topoisomerase does this require for relaxation? |
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Definition
| Positive, Topo II (uses ATP) |
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Term
| How does Topo II change W? does it use ATP? |
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Definition
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Term
| How does Topo I change W and does it require ATP? |
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Definition
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Term
| what is another name for topo II? |
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Definition
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Term
| what are three main steps in the mechanism of dna gyrase? |
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Definition
1. cuts DA
2. gyrase seperats in two
3. reattaches dna so as to introduce -2 W
(see overhead) |
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