Unit 3 weeks 1 and 2 flashcards
Unit 3 weeks 1 and 2 flashcards BI381
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This 18 page Study Guide was uploaded by Jessica Niswonger on Friday October 16, 2015. The Study Guide belongs to BI381 at Southeast Missouri State University taught by Dr. Rebeccah Kurzhals in Summer 2015. Since its upload, it has received 373 views. For similar materials see Molecular Genetics in Biology at Southeast Missouri State University.
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Date Created: 10/16/15
Phosphate group Nitrogenous Base Purine Adenine A Deoxyribose sugar Nitrogenous base Pyrimidine Cytosine C Nitrogenous Base Nitrogenous Base Purine Pyrimidine Guanine G Thymine T Purine N bases have A and T equal what G C Describe the difference between Purine and Pyrimidine double rings Purine pairs with pyrimidine If you know the structure you can nd what The sequence Meselson and Stahl came out with a paper on what DNA structure Semi conservative replication What kind of media was the Eco grown in Minimal media They gave the bacteria a heavier source of what A heavier nitrogen source N15 N15 was used as the nitrogen source for how many generations At least 14 DNA doesn39t grow it its Replicated They used what to measure the density of the DNA Density gradient centrifugation When centrifuging the bacteria they added Cesium chloride What type of detergent did they add to the DNA SDS What did the detergent added to the bacteria what did it cause it to do Causes the bacteria to lyse brings the DNA to outside of the bacteria Bringing the DNA to the outside of the bacteria allows for what You to distinguish the size of the molecules Why does a density gradient work in separating out N15 and N14 They have varying densities The semi conservative model of replication shows what in regard to the strands The one new strand is completely made up of new DNA the other new strand is completely made up of old DNA There are two complete DNA strands replicated this way The conservative model of replication shows what in regard to the strands One new double strand of DNA is entirely made up of new DNA one new double strand of DNA is entirely made up of old DNA How did they see the DNA They used Xray lm and shone UV light in it Absorbed light at different frequencies They though the DNA would break every 5 bonds to replace because They didn39t know about topoisomerase Explain how the 1St and 2nCI generation of DNA replicated in the conservative model would look when centrifuged 1 1 strand of heavy DNA one strand of light DNA 2 1 strand of heavy DNA that is thicker 1 strand of light DNA that is thicker Explain how the 1St and 2nCI generation of DNA replicated in the semiconservative model would look when centrifuged 1 1 band of DNA slightly lighter than the original 2 two bands of DNA one slightly lighter than the original and one much lighter than the original DNA DNA always replicates 51 to 31 What end of DNA is 31 in what direction always usable DNA Replication starts Nucleotide DNA polymerase does Catalyzes reaction with what triphosphate what The energy used comes from what Breaking the phosphate bonds DNA polymerase always catalyzes reaction in what direction 51to 31 DNA polymerase needs what to start Deoxyribose nucleotide triphosphate dGTP Deoxyribose nucleic triphosphate dGTP is added to what The 31 hydroxyl OH of another nucleotide The leading strand synthesizes in which direction Towards the template strand The lagging strand synthesizes in which direction Away from the template strand unwinds DNA each strand serves as a Helicase Template Leading strand replication is what ConUnuous Lagging strand is done how ln fragments Fragments in the lagging strand are called Okazaki fragments Helicase What is the rst enzyme needed in replication Helicase How does helicase work Enzyme that disrupts hydrogen bonds that are holding together the two DNA strands ssDNA Helicase breaks what kind of bonds Hydrogen bonds What is the consequence of heHcase Overwinding DNA further upstream What does single stranded binding protein SSB do Binds ssDNA prevents helix from reforming DNA Gyrase does what Removes extra twists What does topoisomerase do Removes supercoiling 1St step topoisomerase does Breaks one or both strands What bond does topoisomerase break when breaking the strands Phosphate bond Topoisomerase breaks what kind of bond Covalent bond 2nCI step topoisomerase does Rotates the DNA so it s relaxes 3rCI step topoisomerase does Rejoins the strands Origin of replication is speci c to what Proka ryotes Ecoi has what oriC The origin of replication is made of what AT rich sequence What does DNA A do Binds AT rich sequence at origin Explain the process DNA A uses seperates strands unwind recruits proteins for DNA replication The box in the diagrams refer to what A speci c region DNA A is needed for what To bring in DNA Primase is a RNA What does primase Synthesizes a short polymerase of what do segment of RNA that is complimentary to DNA Primase provides what A 31 OH Primase forms a DNA pol III for DNA pol lll starting point for what DNA pol III is the main DNA polymerase for strands Both Holoenzyme is what Multiprotein complex DNA pol lll does what Catalyze synthesis of DNA pol III as what 31 to 51 leading and lagging kind of exonuclease strands activity Adds nucleotides 51 to 31 What does 31 to 51 Removes mismatched The beta clamp is Prokaryote exonuclease activity do base pairs after checking width speci c to what Beta clamp is shaped like what A donut Beta clamp does what Keeps DNA pol attached to DNA by encircling the DNA Beta clamp posesses what kind of factorenzyme Processivity Procesive Explain how beta clamp works DNA pol lll can only add 10 nucleotides before it falls of B clamp allows it to stay on so it can synthesize for thousands of nucleotides DNA pol l is what kind of enzyme Polymerase enzyme DNA pol l synthesizes what strand Lagging strand How does DNA pol l Removes RNA on DNA pol lls in gap DNA nucleotides dNTP work lagging strands adds with what DNA and seals it up removes RNA primes dNTP stands for what Deoxyribonucleic acid What kind of 51 to 31 Nitrogenous base exonuclease activity 31 to 55 TP triphosphate DNA polymerase activity does DNA pol l have Study Guide Questions 1 Describe the types of chemical bonds in the DNA double helix There are covalent and hydrogen bonds in the DNA double helix The covalent bonds are strong and bind together the bases sugars and phosphate groups in a single strand The hydrogen bonds are generally weak but when combined become strong The hydrogen bonds bind together the nitrogenous bases of one strand to the nitrogenous bases of the second strand 2 Why is DNA synthesis continuous on one strand and discontinuous on the opposite strand On the lagging strand the template strand is oriented 51 to 31 at the replication fork Therefore the copying will result in a 31 to 51 direction relative to the fork movement Synthesis on the lagging strand is discontinuous due to the orientation of the template strand since RNA primers must be added as the opening of the replication fork continues to expose new template On the leading strand the template strand is oriented 31 to 51 at the replication fork This allows for extension of the RNA primer to occur continuously into the replication fork as it continues to open to the right 3 If cytosine makes up 15 of the bases in a speci c DNA molecule what percentage of bases are thymine AT and GC Cytosine15 Guanine15 CG30 loo 3070 70235 Therefore thymine makes up 35 of the bases in a speci c DNA molecule 4 If adenine makes up 37 of the bases in a speci c DNA molecule what percentage of bases is cytosine AT and GC Adenine 37 Thymine37 AT74 1007426213 Therefore cytosine makes up 13 of the bases in a speci c DNA molecule 5 At each origin of replication DNA synthesis proceeds bidirectionally from two replication forks What would be the effect on DNA replication if a mutant arose having only one functional fork per replication bubble Replication would take twice as long since only one of the two forks is funcUonaL 6 What are helicases and topoisomerases What types of bonds do they break Helicase is an enzyme that disrupts hydrogen bonds holding together the two DNA strands creating ssDNA The consequence of helicase is over winding DNA further upstream Topoisomerase breaks the covalent bonds in the phosphate backbone of one or both of the strands of DNA After breaking the covalent bonds topoisomerase rotates the DNA so it s relaxed and then rejoins the strands 7 Explain how each of the following problems is solved in E coli replication In each case specify the enzyme involved and explain what they do to solve the problem39 a Pol III needs a primer with a 339 end to start replication Primase is an RNA polymerase that synthesizes a short segment of RNA that is complimentary to the DNA Primase provides a 31 OH as a starting point for DNA pol lll b As the strands of template DNA molecule are separated other parts of the molecule become supercoiled Topoisomerase DNA Gyrase breaks the covalent bonds in one or more of the phosphate backbones of DNA It then rotates the DNA so it s relaxed and rejoins the strands This corrects the supercoiling that occurs when the strands of template DNA molecules are separated c There is RNA in the newly synthesized polynucleotide strands DNA pol 1 removes the RNA on lagging strands adds DNA and seals it up d The lagging strand is in sort segments rather than a continuous polynucleotide strand DNA ligase takes the 31 end of the gap lling DNA and connects it to the 51 end of okazaki fragments joining the segments together 8 Assume that a certain bacterial chromosome has one origin of replication Under some conditions of rapid cell division replication could start from the origin before the preceding replication cycle is complete How many replication forks would be present under these conditions There would be 6 replication forks 9 Would the Meselson and Stahl experiment have worked if diploid eukaryotic cells were used instead of haploid E coli Explain your reasoning Yes because DNA replication is semiconservative in diploid eukaryotes 10 What would be the effect of a mutation in the enzyme telomerase What would happen to the DNA A mutation in telomerase could have several results There could be a loss in telomere length regulation mislocalization of chromosomes within the nucleus telomeretelomer fusions and chromosome instability 11 What would be the consequence if during DNA replication the topoisomerases were unable to reattach the DNA fragments of each strand after unwinding the DNA molecule The DNA strands would never be rejoined causing the DNA to become fragmented 12 What is meant by a quotprimerquot and why are primers necessary for DNA replication A primer is a short chain of nucleotides It provides a 31 OH for DNA pol III to bind to Without a primer there would be no place for DNA pol III to bind 13 What would be the consequence if during DNA replication the topoisomerases were unable to reattach the DNA fragments of each strand after unwinding the DNA molecule The DNA strands would never be rejoined causing the DNA to become fragmented 14 An asteroid probe brings back a bacterial species that has DNA as its genetic material You perform a MeselsonStahl experiment and show that after one round of replication in 14N medium half of the daughter DNA duplexes have 15N in both strands whereas the other half have 14N in both strands Interpret these data ie what type of replication model is this consistent with This data would be consistent with the replication model of Conservative DNA The conservative model shows that the new DNA would make up one of the DNA double helices while the Template DNA strands would make up the other DNA double helices entirely 15 Explain how RNA participates in DNA replication 16 How are DNA polymerase I and DNA polymerase III different 17 If a mutation inactivated DNA polymerase I in a strain of E coli what kind of abnormalities would you expect to nd in the cell 18 Describe how DNA replication is initiated in eukaryotes 19 Describe how DNA replication is initiated in prokaryotes 20 Why did Meselson and Stahl let the E coli go through 2 generation times instead of just one in their experiment 21 How are betaclamp and PCNA similar How are they different 22 List some proteins required for DNA replication but not directly involved in synthesizing a new strand and describe their functions 23 What would be the affect on DNA replication if the incoming nucleotide lacked a 339 OH Be speci c in our answer 24 How do eukaryotes ensure that an origin of replication res only once during 5 phase Primase synthesizes what Short RNA oligonucleotides primers copied from DNA DNA pol lll does what Elongates RNA primers with new DNA DNA pol I does what Removes RNA at 51 DNA ligase does what Connects adjacent end of neighboring fragments fragments and lls gap Explain the steps in 1 primase synthesizes RNA primase lays Primer synthesizing the lagging strand short RNA primers copied from DNA 2 DNA pol lll elongates RNA primers with new DNA 3 DNA pol I removes RNA at 51 end of neighboring fragment and lls gap 4 DNa ligase connects adjacent fragments down what Explain why RNA Pays down primer The 31 OH is necessary lts needed for the DNA primase is necessary provides for 31 OH because pol III to add nucleotide DNA pol 1 comes in 51 to 31exonuclease What connects Okazaki DNA pol 1 Uses what type of exonuclease activity Needs what DNA pol needs 31 OH fragments How 51 to 31 exonuclease DNA ligase does what Joins short DNA fragments in lagging strand together Takes 31 end of gap lling DNA with 51 end of okazaki fragments 51 monophosphate and 31 OH What are the prokaryotic speci c mechanisms oriC dnaA Beta clamp What are the eukaryotic speci c mechanisms Origin of replication ORC PCNA CAFl What type of sequence does yeast have for the origin of replication well de ned Eukaryotes have well de ned not well de ned sequence for origin of replication Not well de ned What makes origin of replication not well de ned Gene rich DNA replicates before gene poor DNA Many origins per chromosome Compare prokaryote origin of replication to eukaryote Prokaryotes have one origin oriC eukaryotes have many different What structure is analogous to prokaryotic dnaA ORC origin of replication Complex What does ORC do Recruites Cdc6 and Cdtl What do Cdc6 and Cdtl do Recruit heicase and DNA replication proteins When does ORC re During 5 phase What is necessary to make sure that DNA replication origins only re once Csc6 and Cdtl get degraded during 5 phase What does pcna stand for Proliferating cell nuclear an gen What is pcna analogous to Beta clamp in Ecoli Describe PCNA and what is does Donut shaped molecule Processivity factor Holds the dna polymerase on DNA What does CAFl stand for Chromatin assembly factor 1 What does CAF1 do Brings new histone proteins to replicating DNA and assembles DNA into chromatin 1 CAFl 2 PCNA
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