Term
| Miescher's Discovery of DNA |
|
Definition
| Cell Nuclei contain protein and nucleic acid |
|
|
Term
| What is Avery, Macleod, and McCarthy's Mouse Experient? |
|
Definition
| mention deoxyribonucleases, mouses (s & r strains), in-vitro, phage ghosts, phage progeny |
|
|
Term
| Which organism did the infecting? |
|
Definition
|
|
Term
| Describe the body of the phage |
|
Definition
| dna and protein in its capsule head, protein in legs, legs used as syringe |
|
|
Term
| Describe One gene - One enzyme Hypothesis |
|
Definition
| wrong belief that one gene is responsible for one gene |
|
|
Term
| Who is Garrod and what did he do? |
|
Definition
| discovered that alkaptonuria results from homozygous recessive gene which causes a defiency in the enzyme that usually converts homogentistic acid into a colorless acid |
|
|
Term
| What did Beadle and Tatum discover? |
|
Definition
| Neurospora Crassa auxotrophs are blocked at a specific step in the metabolic pathway and accumulate large queitites of the substance formed just prior to the blocked step |
|
|
Term
|
Definition
| a mutant that requires a specific supplement(aa and/or vitamin) that isn't required by the wild-type parent |
|
|
Term
|
Definition
Dna (transcription)--> RNA (transcription)--> protein
blueprint, working copy, product. |
|
|
Term
| How do nucleic acids differ and what's the significance? |
|
Definition
| Ribose sugars have a hydroxyl at their 2 prime whereas deoxyribose sugars have a hydrogen at their 2 prime |
|
|
Term
| What can a pentose chain do? |
|
Definition
| Each pentose chain can close to form a 5-carbon ring in which an oxygen bridge joins the C1 and C4 |
|
|
Term
|
Definition
| published in his observations of human, rat, chicken, and octopus that most organisms have an equal molar concentration of A-T and G-C |
|
|
Term
|
Definition
| has deep major groove and shallow minor groove |
|
|
Term
|
Definition
| they are more open. proteins can easily recognize the DNA in the outer groups. Compressors and activators and other components combine to initiate transcription. it has a lot of surface area and is much easier to recognize |
|
|
Term
|
Definition
| minor groups are stacked and squeezed within proteins. |
|
|
Term
| DNA conforms to which shape in water? How many base-pairs per turn |
|
Definition
|
|
Term
| In what forms and conditions does A-DNA apply? |
|
Definition
| dry forms, rna-dna hybrids, and transcripts |
|
|
Term
| Where does the TATA box binding protein bind? |
|
Definition
| In the minor groove of a protein at a specific sequence, TATAAA |
|
|
Term
| What is the effect of G-C content on DNA melting temperature? |
|
Definition
| Thermophilic organisms have a mugh higher GC - percent. Low GC levels correlate to melting at lower temperatures. GC data can give info about hydrogen bonds and melting and denaturing. |
|
|
Term
| How can I safely denature DNA? |
|
Definition
| Use high pH because DNA is very resistant to alkaline hydrolysis. DNA is preferably for scientific purposes denatured at high pH's. |
|
|
Term
| How many base pairs are there in a chromosome? |
|
Definition
|
|
Term
| Name the structures in a prokaryote. |
|
Definition
| Cell wall, membrane, cavity |
|
|
Term
| What are the different regions in chromatin? Is chromatin reserved? |
|
Definition
| Super coiled region, relaxed region. Conserved region |
|
|
Term
| What is the genome size(haploid) in bps |
|
Definition
|
|
Term
| What is the gene number in humans? |
|
Definition
|
|
Term
| What is the genome size(haploid) for E.Coli ? |
|
Definition
|
|
Term
| How many genes are there in E. Coli? |
|
Definition
|
|
Term
| How many chromosomes in E. Coli ? |
|
Definition
|
|
Term
| How much of the human genome is invasive non-host sequences?(junk dna) |
|
Definition
|
|
Term
| To what does the primer attach to and at which end? |
|
Definition
|
|
Term
| For how many base pairs does the primer need to attach? |
|
Definition
|
|
Term
| What is the molecular mechanism for nucleotide addition? |
|
Definition
| Hydroxyl group from 3' nucleotide attacks a-phosphate, and thus phophodiester bond is made |
|
|
Term
| What are the precursors for DNA Polymerase I? |
|
Definition
|
|
Term
| What does DNA Polymerase 1 require? |
|
Definition
| Mg ion, primer strand, and template strand |
|
|
Term
| What is the mistake proportion in DNA? |
|
Definition
| 1 mistake in every 1-10 million base pairs |
|
|
Term
| What is the size of E. Coli genome? |
|
Definition
|
|
Term
| What is the DNA polymerase error rate? |
|
Definition
|
|
Term
| How many meters of DNA are there in every cell? |
|
Definition
|
|
Term
| Describe DNA polymerase I's proofreading activity? |
|
Definition
| It has something called 3'-5' exonuclease activity which removes incorrect insertions and will hydrolyze a diphosphate which leaves a DNTPS |
|
|
Term
| Another type of exonuclease activity? |
|
Definition
| Periphery exonuclease activity |
|
|
Term
| By how much does the exonuclease activity help DNA polymerase I's error rate? |
|
Definition
|
|
Term
| What is the Klenow fragment? |
|
Definition
| It it a part of DNA polymerase I. It has an amino terminus, domain 1 (5-3 exonuclease, domain 2 (3-5 exonuclease), and domain 3, followed by a carboxy terminus. Domains 2 and 3, aka Klenow fragment are needed to replicate short stretches of DNA |
|
|
Term
| Describe Mg2+ and its roles in DNA replication |
|
Definition
| DNA polymerase has two catalytic Mg2+ ions. Mg2+ bonds at the active 3' OH site. it interacts with triphosphates, and is needed for catalysis. Ions are held in place by the side chains of aa's like aspartic acid and glutamate also stabilize it. The two Magnesium ions play a role in coordinating the new phosphates from the triphosphates. |
|
|
Term
| Is DNA semiconservative, conservation, or dispersive? |
|
Definition
| Semiconservative meaning in a double helix, one strand is parental and the other strand is completely daughter |
|
|
Term
| How long is prokaryote DNA molecule? |
|
Definition
|
|
Term
| Is prokaryotic DNA replication unidirectional or bidirectional? |
|
Definition
| bidirectional thus it has two forks but still one origin |
|
|
Term
| How was it realized that bacterial replication is bidirectional? |
|
Definition
| There was high specific activity of radioactively labelled 3H - thymidine at the ends of the replication forks. If unidirectional, it the labelled replication fork would only show up on one side. If it was bidirectional, the high specific activity 3H thymidine would show up on both sides. This was observed using a light microscope. |
|
|
Term
| What does topoisomerase I do? |
|
Definition
|
|
Term
| The bacterial chromosome has to broken 400,000x to separate the DNA for the daughter strands. How fast is this process and how long would it take? |
|
Definition
| Prokaryotes make 1000 bases/sec, thus 40 minutes |
|
|
Term
| Why is DNA replication discontinous? |
|
Definition
| Since DNA is made 5-3. The bottom template, where the okazaki fragments are being made in discontinous strands because the replication fork is moving the opposite way of the okazaki fragments. However since the top strand is moving in the same direction as the replication fork, it can be continuous. |
|
|
Term
| How would I quickly freeze Okazaki fragments? |
|
Definition
| To stop quickly, take DNA and cells and throw into boiling NaOH(or highly alkaline soln), this would freeze all metabolic activity. Shorter fragments are more stable. |
|
|
Term
| On average, how long are Okazaki fragments? |
|
Definition
|
|
Term
| How fast and how many base pairs are in Okazaki fragments? |
|
Definition
| works at 1000 bases / sec |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| What can RNA polymerase do that DNA polymerase cannot? |
|
Definition
| It can make new strands without requiring a primer |
|
|
Term
| What does RNA primer do and what fixes it? |
|
Definition
| RNA primer lays down RNA but DNA polymerase I comes in and fixes it by replacing RNAs with DNAs |
|
|
Term
| What active moving molecules are needed for replication? |
|
Definition
| primer, DNA/RNA polymerase, and ligase |
|
|
Term
| Does E.Coli require DNA polymerase I? |
|
Definition
| It is without it but needs the 5'-3' exonuclease activity |
|
|
Term
| What are the 3 stages of DNA replication? |
|
Definition
| initation, elongation, and termination |
|
|
Term
| Describe initation of DNA replication |
|
Definition
| it is the assembly of the replication apparatus at a unique site |
|
|
Term
| Describe elongation of DNA replication? |
|
Definition
| leading and lagging strand synthesis |
|
|
Term
| Describe termination in DNA replication? |
|
Definition
| begins when the two replication forks meet half way around the chromosome |
|
|
Term
|
Definition
| E. Coli origin of replication oriC. Cannot be deleted. it is 244 base pairs long. It is required for DNA synthesis. Required important binding site for proteins used for DNA synthesis |
|
|
Term
| How would you isolate E. Coli oriC? |
|
Definition
| Break it up into thousands of fragments. Make plasmids and put them back into the same solution and see if origin transforms into them. It will survive if you put an antibiotic in it. Only plasmids with origins will replicate and confer antibiotic resistance. Thus the cells that grow and survive and express antibiotic resistance will have it. |
|
|
Term
| What will happen if there are mutations in E.Coli oriC? |
|
Definition
| If you change a single nucleotide, it will not replicate |
|
|
Term
|
Definition
| DnaA boxes and 13-mer sites |
|
|
Term
|
Definition
| There are the R-sites where DNA initially binds. |
|
|
Term
|
Definition
| After R1-R5 DNA box binding sites, there are the next binding sits involved. |
|
|
Term
|
Definition
| IHF are proteins which are activators for DNA synthesis |
|
|
Term
|
Definition
| The 13 GATC Dam-methylation sites are where methylation occurs. Usually occurs once every 256 bases in E.Coli but there are 13 sites in oriC. oriC will only work if both strands are methylated |
|
|
Term
| What are the different elements of oriC? |
|
Definition
| DnaA boxes, I boxes, and 13-mers |
|
|
Term
|
Definition
| 9-mers with consensus sequence 5'TTAXCACA. DnaA boxes bind DnaA-ATP and Dna-ADP |
|
|
Term
|
Definition
| There are the DNA binding sites after R1-R5 box binding sites have been taken up. They only bind DnaA-ATP. DnaA-ATP binds I boxes only after DnaA boxes are occupied |
|
|
Term
|
Definition
| They are AT-rich regions that unwind (regions where DNA bubbles up at the origin). DnaA-ATP binds single stranded regions after unwinding (this stabilizes unwound form). Single-stranded DNA binding protein also binds single-stranded region |
|
|
Term
| What are the regulation features of replication initiation? |
|
Definition
| DnaA-ADP cannot bind to I boxes. DnaA has an ATPase activity that hydrolyzes DnaA-ATP to DnaA-ADP after replication starts. ADP must be replaced by ATP for replication to re-start. Only fully methylated DNA is replicated. So after replication starts, oriC becomes hemimethylated @ both GATC sites. oriC is sequestered by SeqA, which binds to hemimethylated GATC sites for 15-20 minutes. |
|
|
Term
| Describe E. Coli replication initiation cycle |
|
Definition
| DnaA-ATP protein has to recognize origin. DnaA-ATP unwinds DNA at AT-rich regions. DnaB and DnaC are both helicases and combine into DnaB(b)C(b) and open up the DNA further. Helicases attach onto both strands and while its translocating, primase is making primer and once it has, primase loads onto the helicase. they both stop at which point primase loads the primer, and then get backs on and translocation continues. once primer is attached, primer + helicase translocate again. DNA polymerase comes in as a sliding clamp. primase is a product of the DnaG gene. DnaB drives replication because its an ATPase. When sliding clamp is loaded on, it is also an ATPase. |
|
|
Term
| Describe Helicase/primase |
|
Definition
| It is a bacteriophage and is fast-growing. Helicase is a 6 membered ring, can translocate on DNA, unwinds DNA, has polypeptides in center of the ring that unwind and pull DNA thru the middle. works in 5-3. doesn't readily fall off. uses ATP and hydrolysis to drive power. Helicase is mostly on the lagging strand because thats where primers need to go and it does pause once in a while for the primase to load its primer on. |
|
|
Term
|
Definition
| DnaB is a helicase. also an ATPase. DnaB only gets onto DNA in oriC. Primase works 1000x better with helicase, and thus cannot really work alone. DnaB targets larger strands of DNA and will ONLY load on in the presence of ATP. If there is a tail, it'll stick to the inner strand(template strand) and will eventually peel off the tail. If there is no tail, helicase pulls both strands thru and thus no peeling. |
|
|
Term
| Explain replication fork elongation |
|
Definition
| Unwinding parent duplex by helicase. Elongation of leading strand by DNA polymerase III holoenzyme (and the helicase unwinding) expose the single-strand region on the lagging strand. Helicase is translocating and primase synthesizes an RNA primer at the replication fork because thats where the helicase is. DNA poly III comes in and finds primer end and adds DNA nucleotides up until the next okazaki fragment(to the next 3'). Once DNA poly III hits next okazaki fragment, that is its signal to come off. RNase H degrades the RNA bases( in the presence of hybrid transcriptis). DNA Poly I extends to the next fragment and ligase connects the two. Process goes at about 1000 bases/sec. |
|
|
Term
| What are the reactants and products of primer removal and gap filling by poly DNA I |
|
Definition
| template bonded to primer. dna poly I with dNTPS fills in gap at 3' OH. byproduct is pyrophosphate ion. |
|
|
Term
| What are the proteins involved in bacterial replication elongation? |
|
Definition
| DNA poly III, DnaB, DnA gyrase and topoisomerase I, and single-stranded binding protein, Primase(DnaG), Ribonuclease( RnaseH), DNA poly I, DNA ligase |
|
|
Term
|
Definition
| bacterical replicative DNA polymerase |
|
|
Term
|
Definition
| helicase, uses ATP to unwind dsDNA, moves 5-3 along lagging strand(think replication fork), activates primase |
|
|
Term
| Describe DNA gyrase and topoisomerase I |
|
Definition
| these two enzymes work together to act cooperatively to relieve torsional strain created by unwinding the double helix |
|
|
Term
| describe single-stranded binding protein |
|
Definition
| coats the lagging strand template as helix is unwound by helicase and removes small secondary structures |
|
|
Term
|
Definition
| product of DnaG, catalyzes the formation of RNA primers for okazaki fragment formation during lagging strand synthesis |
|
|
Term
|
Definition
| aka RNase H, removes RNA primers from the 5' of okazaki fragments |
|
|
Term
| Describe DNA Polymerase I |
|
Definition
| extends the 3' end of the okazaki fragment to the 5' end of the next fragment after primer removal |
|
|
Term
|
Definition
| joins adjacent okazaki dna fragments |
|
|
Term
| Describe process of DNA Poly III and how it is processive when on a circular single-stranded template. |
|
Definition
| If oyu have a single-stranded phage DNA template, with one RNA primer, and the template has tons of single-stranded DNA binding protein (SSB) to it which are tetramers(cover 65 nucleotides when bound), and the appropriate dNTPS are provided with the holoenzyme. (pyrophosphate will be a product), you can newly ds dna |
|
|
Term
| DNA Polymerase III has three subassemblies. What are they? |
|
Definition
| The core polymerase subassembly, the clamp loader assembly, and sliding clamp subassembly |
|
|
Term
| Core Polymerase has three subunits, what are they? |
|
Definition
| alpha subunit - catalyzes 5-3 growrth and is essential for DNA synthesis, E subunit, 3-5 exonuclease activity for proofreading(note cells with defective E subunits have high mutation rates (10^-3 -- 10^-4), and 0 subunit, may stimulate E subunit but isnt essential |
|
|
Term
| What is the product of the DnaN gene? |
|
Definition
| the sliding clamp which is a dimer |
|
|
Term
| Describe the sliding clamp |
|
Definition
| it is a homodimer with semicircular subunits, forms a ring with a big inner diameter big enough to fit ds DNA, sufficient space between ring n DNA for one or two water layers(allows for clamp sliding), carboxyl ends of subunits associate with remainder of DNA poly III holoenzyme |
|
|
Term
| Describe clamp loader and what it does and what it needs? |
|
Definition
| clamp loader and sliding clamp bind in presence of ATP, complex binds to DNA, once sliding clamp is on, it comes off ATP is hydrolyzed to ADP + Pi + unbound clamp loader. compound of DnaX/ATPase. it has helper proteins that form a ring with dnaX |
|
|
Term
| Describe the trombone model of replication |
|
Definition
| DnaB is on the lagging strand and interacts with primase occasionally. Clamp loader is intact directly with DNA poly III and helicase. loader has activity in organizing replication fork. clamp loader works with 2 different polymerases. there are 2 copies of core which a linked to the clamp loading complex. CLC stimulates the helicase to go faster. 3 polymerases are involved. clamps increase processivity |
|
|
Term
| Describe primase and helicase interactions |
|
Definition
| primase interacts with helicase at start of primer synthesis but they pull apart and move in opposite directions along the lagging strand |
|
|
Term
| What influences the activities of both helicase and primase? |
|
Definition
| clamp loader. its association with helicase increases its activity 25 fold. displaces primase from ssb and RNA primer site. clamp loader can then load sliding clamp onto primed template. |
|
|
Term
| What are the analogous versions of helicase in E. Coli, humans, and yeast? |
|
Definition
| DnaB, T antigen, MCM proteins |
|
|
Term
| What are the analogous versions of primase in E.Coli, humans, and yeast? |
|
Definition
| DnaG primase, Primase subunit of polymerase a-primase, and primase subunit of polymerase a-primase |
|
|
Term
| Whats the major problem with replication forks in bacterial chromosomes? |
|
Definition
| You want the forks moving the same way |
|
|
Term
|
Definition
| Tus is a protein that binds at Ter sites to arrest progress of the replication fork, that allows a one-way gatel rejects one of the helicases; first interacts with dnaB on lagging strand; Tus keeps fork at certain region and forces it to stop there. it has two sides, B sheets and alpha-helices. main active side is b-sheets. |
|
|
Term
| Is eukaryotic replication faster or slower and by how much? and why? |
|
Definition
| 20x slower because of the condensed chromatin |
|
|
Term
| What does the ORC do in the assembly complex at the origin? |
|
Definition
| it binds to the origin, binds ARS elements, and recruits other proteins to the complex like cdc6 and Cdt1. cdc6 is a cell division cycle protein, it helps to recruit cdt1, and is degraded once initiation is complete. MCM is an atp-dependent helicase that unwinds DNA and surrounds ds-DNA |
|
|
Term
| What are proto-oncogenes? |
|
Definition
| genes that promote cell growth, highly self-regulated, always in active state |
|
|
Term
| What are tumor suppressor genes? |
|
Definition
| genes that slow cell growth and regulate cell growth |
|
|
Term
| What are the two types of DNA repair? |
|
Definition
| direct reversal of DNA binding and excise defective elements and replace with normal nucleotides |
|
|
Term
| Describe UV-A, UV-B, and UV-C |
|
Definition
| UV-A: 320-400nm, majority of UV light reaching heart, does little damage. UV-B: 295-320nm; ~10% reaches earth, responsible for most of DNA damage in skin. most varying range. UV-C - includes wavelength maximum of DNA, little reaches earth's surface due to ozone layer. |
|
|
Term
| What happens during UV-induced DNA damage? |
|
Definition
| dimer formation between adjacent pyrimidine rings on same strand |
|
|
Term
| What's one of the dimers produced from UV-induced DNA damage? |
|
Definition
| cyclobutane pyrimidine dimer (CPD); accounts for 75% of UV induced damage. thymine-thymine dimers are most common. C-C bond is made between adjacent bases which forms a cyclobutane ring |
|
|
Term
| Ionizing radiation directly and indirectly generations DNA lesions, explain how. |
|
Definition
| For direct, the DNA or water bound tightly to it absorbs the radiation. water molecules that absorb radiation can turn into hydroxyl radicals. indirect damage is done by water or other molecules surrounding the DNA absorbing the radiation and/or reactive species that damage the DNA are formed. Think gamma rays. |
|
|
Term
| What are some various chromosomal aberrations gamma ray ionizing radiation can cause to DNA? |
|
Definition
| deletions, duplications, inversion, translocations, ie fusion promoter for oncogenes or removes promoter for tumor suppressor genes |
|
|
Term
| What are the three types of bonds that are susceptible to hydrolytic cleavage in DNA? |
|
Definition
| phosphodiester bonds, N-glycosyl bonds, and bonds linking exocyclic amine groups to bases(cytosine) |
|
|
Term
| What does N-glycosyl bond cleavage do? |
|
Definition
| It cleaves off the purine base from a NTP and so the sugar waits for instructions which it would usually get from the base |
|
|
Term
| What is one example of water-mediated deamination? |
|
Definition
| Cytosine to Uracil(amide to carbonyl) |
|
|
Term
| What is a transition mutation? and what is it caused by? |
|
Definition
| Deamination causes a transition mutation which switches a pyrimidine for a pyrimidine or a purine for a purine |
|
|
Term
| What other mutation does deamination cause? |
|
Definition
| A transversion which switches a pyrimidine for a purine or a purine for a pyrimidine |
|
|
Term
| Alkylating agents damage DNA - explain! |
|
Definition
| transfer of lesser damage groups like methyl and ethyls or more damaging groups like larger alkyl groups to DNA |
|
|
Term
| Alkylation takes place where? |
|
Definition
| nitrogen and oxygen atoms external to the base ring systems, non-bridging oxygen atoms in phosphate groups, and nitrogen atoms in base-ring systems except those linked to deoxyribose |
|
|
Term
| When happens when MMS-methymethane sulfonate reacts with guanine? |
|
Definition
| Decreases stabilization of glycosidic bond by 83% |
|
|
Term
| What forms base mispairs? |
|
Definition
| O6-methylguanine and O4-mthylthymine |
|
|
Term
| Know 2 structures of polycyclic aromatic hydrocarbons, as they are environmental agents |
|
Definition
| 3-zigzag benzenes...3benzenes in a row with one going to the diagonal outter side |
|
|
Term
| What needs to happen to Aflatoxins in order for them to damage DNA? |
|
Definition
| they need to be activated by cytochrome P450 --> causes liver cancer, toxic molds, high humidity, don't eat black peanuts |
|
|
Term
| What do you know about N38? |
|
Definition
| Involved in remaining alkylation damage in the backbone |
|
|
Term
| What's one of the targets in alkylation damage? |
|
Definition
|
|
Term
| For normal DNA, should there or should there not be a methyl group @ #38 |
|
Definition
|
|
Term
| Which enzymes remove alkyl groups? |
|
Definition
| O6-alkylguanine DNA alkyltransferases 1 and 2...it can transfer off 2 alkyl groups n once its doubly methylated, it has done its job |
|
|
Term
| Which enzyme excises a damaged base? |
|
Definition
|
|
Term
| What does DNA glycosylase/lyase do? |
|
Definition
| cleaves base and cleaves at 3' site |
|
|
Term
| Describe where and why AP endonuclease cleaves |
|
Definition
| It cleaves at the 3' leaving you with a 3' OH so you can have addition thereee |
|
|
Term
| Steps in nucleotide excision repair |
|
Definition
1. damage recognition
2. incision on each side, 4 bases in 1 direction and 7 bases on other direction(AP glycolyase/lyase)
3. excision(AP endonuclease)
4. synthesis of new DNA(Poly-B)
5. ligation(ligase) |
|
|
Term
| Cyclobutane pyrimidine dimers do what to DNA? |
|
Definition
| they make a kink in the DNA! |
|
|
Term
| What fixes thymine dimers and bulky dimers? |
|
Definition
| UvrABC endonucleases repair thymine and bulky dimers, works with naked DNA |
|
|
Term
| UvrA endonuclease does what? |
|
Definition
| has ATPase activity that influences binding to damaged DNA; influences UvrB |
|
|
Term
|
Definition
| it's an ATPase, plays a central role in nucleotide excision repair, interacts with UvrA to locate the lesion, helps UvrC bind to DNA |
|
|
Term
|
Definition
| binds to Uvr-DNA complex and makes incisiosns of both sides of the lesion |
|
|
Term
| Explain the formation of a stable UvrB-DNA complex |
|
Definition
| UvrA+ATP= dimer -> interacts with UvrB = complex -> attaches to DNA and finds damage --> helicase activity of UvrB translocates to damaged site. UvrB induces conformational changes and UvrA is released. DNA is bent sharply and unwound so that damaged site can be accessed. UvrC comes and makes nicks, it has two nucleases. UvrD(helicase)+ Dna Poly I help replace DNA |
|
|
Term
| How much of the genome do transposons cover? |
|
Definition
|
|
Term
| What are the three mechanisms for movement of mobile genetic elements? |
|
Definition
| transposition and retroviral integration, conservative site-specific recombination(lambda phage thatll relocate a whole sequence), and target-primed reverse transcription |
|
|
Term
|
Definition
| an element moves between dna sites that lack homology using a self-encoded transposase |
|
|
Term
| define conservative site-specific recombination |
|
Definition
| a segment of dna moves between specific recombination sites as a DNA element with the aid of a cognate recombinase |
|
|
Term
| define target primed reverse transcription |
|
Definition
| a free 3' end of a broken target DNA is used to prime a replication process that allows a DNA copy to be made of al element that moves a a segment of RNA |
|
|
Term
| Do DNA transposons translocate with or without RNA intermediate? |
|
Definition
|
|
Term
| Do retrotransposons travel via an RNA intermediate ? |
|
Definition
|
|
Term
|
Definition
| two residues of aspartic acid and one of glutamic acid in the active site of the transposase, involves binding of Mg ions |
|
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Term
| Explain the transposase insertion sequences |
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Definition
| the flanking DNA sequences include one or more binding sites for the transposase, the inverted repeated sequences identify the place where the transposase breakage events will occur |
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Term
| composite transposons have.. |
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Definition
| two insertion elements that can surround a gene, thus if a transposase recognizes both ends, it can move the whole piece. this is how antibiotic resistance moves in bacteria |
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Term
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Definition
| a big and important class of transposons and it makes copies of itself |
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Term
| What are the 5 reaction mix components for assaying RNA polymerase activity? |
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Definition
| RNA polymerase, DNA, Mg2+ cofactor, three nonradioactive NTPs and one radioactive NTP |
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Term
| What are the five subunits of E.Coli RNA polymerase? |
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Definition
| alpha(2 in holoenzyme-required for enzyme assembly), beta, beta prime, omega, sigma(directs enzyme to promoters) |
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Term
| How would you find the promoter region? |
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Definition
| Just add the RNA polymerase holoenzyme which would find it and bind to it, then add DNase which would degrade everything that isnt bound to the RNA polymerase holoenzyme |
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Term
| What is the -35 consensus sequence? |
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Definition
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Term
| What is the -10 consensus sequence? |
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Definition
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Term
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Definition
| It helps identify protein binding sites on DNA. two sets of gels, 32P label one end, add specific binding protein |
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Term
| All of the sigmas compete with which sigma when it comes to E.Coli? |
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Definition
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Term
| What are the steps of transcription initiation? |
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Definition
| closed complex formation, dna segment bends at active site channel-dna begins to melt, dna fully melts, transcription bubble is open and sigma 1.1 has to open to let RNA out, RNA elongates to 12 nt's, movement of RNA polymerase away from promoter |
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Term
| From which range does the transcription bubble open up? |
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Definition
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Term
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Definition
| it is a 6 subunit hexamer, it is in ring formation, its a motor protein thus its an ATPase, and is required for termination on many chromosomes. there is a primary binding site on each surface subunit, pinches off once rna is bound to 2ndary binding site |
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