14.1 The Nature of the Genetic Material
14.2 DNA Structure
14.3 Basic Characteristics of DNA Replication
14.4 Prokaryotic Replication
14.5 Eukaryotic Replication
14.6 DNA Repair
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| 327133224 | Griffith finds that bacterial cells can be transformed. | Nonvirulent S. pneumoniae could take up an unknown substance from a virulent strain and become virulent. | 1 | |
| 327133225 | Avery, MacLeod, and McCarty identify the transforming principle. | The transforming substance could be inactivated by DNA-digesting enzymes, but not by protein-digesting enzymes. | 2 | |
| 327133226 | Hershey and Chase demonstrate that phage genetic material is DNA. | Radioactive labeling showed that the infectious agent of phage is its DNA, and not its protein. | 3 | |
| 327133227 | DNA's components were known, but its three-dimensional structure was a mystery. | The nucleotide building blocks for DNA contain deoxyribose and the bases adenine (A), guanine (G), cytosine (C), and thymine (T). Phosphodiester bonds are formed between the 5' phosphate of one nucleotide and the 3' hydroxyl of another nucleotide (see figure 14.4). | 4 | |
| 327133228 | Chargaff, Franklin, and Wilkins obtained some structural evidence. | Chargaff found equal amounts of adenine and thymine, and of cytosine and guanine, in DNA. The bases exist primarily in keto and enol forms that exhibit hydrogen bonding. X-ray diffraction studies by Franklin and Wilkins indicated that DNA had a helical structure. | 5 | |
| 327133229 | The Watson-Crick model fits the available evidence. | DNA consists of two antiparallel polynucleotide strands wrapped about a common helical axis. These strands are held together by hydrogen bonds forming specific base pairs (A/T and G/C). The two strands are complementary; one strand can specify the other. | 6 | |
| 327133230 | Meselson and Stahl demonstrate the semiconservative mechanism. | Semiconservative replication uses each strand of a DNA molecule to specify the synthesis of a new strand. Meselson and Stahl showed this by using a heavy isotope of nitrogen and separating the replication products. Replication produces two new molecules each composed of one new strand and one old strand. | 7 | |
| 327133231 | DNA replication requires a template, nucleotides, and a polymerase enzyme. | All new DNA molecules are produced by DNA polymerase copying a template. All known polymerases synthesize new DNA in the 5'-to-3' direction. These enzymes also require a primer. The building blocks used in replication are deoxynucleotide triphosphates with high-energy bonds; they do not require any additional energy. | 8 | |
| 327133232 | Prokaryotic replication starts at a single origin. | The E. coli origin has AT-rich sequences that are easily opened. The chromosome and its origin form a replicon. | 9 | |
| 327133233 | E. coli has at least three different DNA polymerases. | Some DNA polymerases can also degrade DNA from one end, called exonuclease activity. Pol I, II, and III all have 3'-to-5' exonuclease activity that can remove mispaired bases. Pol I can remove bases in the 5'-to-3' direction, important to removing RNA primers. | 10 | |
| 327133234 | Unwinding DNA requires energy and causes torsional strain. | DNA helicase uses energy from ATP to unwind DNA. The torsional strain introduced is removed by the enzyme DNA gyrase. | 11 | |
| 327133235 | Replication is semidiscontinuous. | Replication is discontinuous on one strand. The continuous strand is called the leading strand, and the discontinuous strand is called the lagging strand. | 12 | |
| 327133236 | Synthesis occurs at the replication fork. | The partial opening of a DNA strand forms two single-stranded regions called the replication fork. At the fork, synthesis on the leading strand requires a single primer, and the polymerase stays attached to the template because of the β subunit that acts as a sliding clamp. On the lagging strand, DNA primase adds primers periodically, and DNA Pol III synthesizes the Okazaki fragments. DNA Pol I removes primer segments, and DNA ligase joins the fragments. | 13 | |
| 327133237 | The replisome contains all the necessary enzymes for replication. | The replisome consists of two copies of Pol III, DNA primase, DNA helicase, and a number of accessory proteins. It moves in one direction by creating a loop in the lagging strand, allowing the antiparallel template strands to be copied in the same direction. | 14 | |
| 327133238 | Eukaryotic replication requires multiple origins. | The sheer size and organization of eukaryotic chromosomes requires multiple origins of replication to be able to replicate DNA in the time available in S phase. | 15 | |
| 327133239 | The enzymology of eukaryotic replication is more complex. | The eukaryotic primase synthesizes a short stretch of RNA and then switches to making DNA. This primer is extended by the main replication polymerase, which is a complex of two enzymes. The sliding clamp subunit was originally identified as protein produced by proliferating cells and is called PCNA. | 16 | |
| 327133240 | Archaeal replication proteins are similar to eukaryotic proteins. | The replication proteins of archaea, including the sliding clamp, clamp loader, and DNA polymerases, are more similar to those of eukaryotes than to prokaryotes. | 17 | |
| 327133241 | Linear chromosomes have specialized ends. | The ends of linear chromosomes are called telomeres. They are made by telomerase, not by the replication complex. Telomerase contains an internal RNA that acts as a template to extend the DNA of the chromosome end. Adult cells lack telomerase activity, and telomere shortening correlates with senescence. | 18 | |
| 327133242 | Cells are constantly exposed to DNA-damaging agents. | Errors from replication and damage induced by agents such as UV light and chemical mutagens can lead to mutations. | 19 | |
| 327133243 | DNA repair restores damaged DNA. | Without repair mechanisms, cells would accumulate mutations until inviability occurred. | 20 | |
| 327133244 | Repair can be either specific or nonspecific. | The enzyme photolyase uses energy from visible light to cleave thymine dimers caused by UV light. Excision repair is nonspecific. In prokaryotes, the uvr system can remove a damaged region of DNA. | 21 | |
| 329453875 | Transformation | The transfer of virulence from one cell to another. Now known to be the transference of genetic material between cells. | 22 | |
| 329453876 | Bacteriophages Phages | Viruses that infect bacteria. Very simple; comprised of little but coat proteins and DNA. | 23 | |
| 329453877 | Proteins were initially thought to be the mode of passing on hereditary information | Due to there being more AAs than bases, meaning there could be more combinations, which was supposedly necessary to create the amount of genes we have. | 24 | |
| 329453878 | How did the responsible for transformation in Griffith's experiment resemble DNA? | - Elemental composition very similar - Centrifuge indicated same density - Extraction of proteins and lipids did not reduce transforming activity - Protein- and RNA-digesting enzymes had no effect - DNA-digesting enzymes destroyed all transforming activity | 25 | |
| 332014057 | How did Hershey and Chase establish that it was DNA and not proteins that were transferred? | They labeled phages with isotopes specific to DNA (³²P) or proteins (³⁵S) and it was found that in infected bacteria cultures there was not much coat isotope. Thus it must have been the DNA that was conserved. | 26 | |
| 332014058 | Components of a nucleotide | - a ribose sugar - a phosphate group - a nitrogenous base | 27 | |
| 332014059 | Phosphodiester Bond | A bond between two nucleic acid; called such because a phosphate is linked between two ribose sugars using ester bonds. | 28 | |
| 332014060 | What group is bound at the 5' end? The 3' end? | In a nucleic acid, the phosphate group is attached to the 5' carbon, and a hydroxyl group is added to the 3' carbon. | 29 | |
| 332014061 | Chargaff's Rules | - The proportion of A always equals that of T, and the proportion of G is always equals that of C - There are always equal proportions of purines (A+G) and pyrimidines (C+T) | 30 | |
| 332014062 | What Photo 51 revealed | - that DNA was helical - had a consistent diameter of 2 nm - had a complete helical turn ever 3.4 nm - had phosphates and sugars on the outsides, bases stacked on the inside | 31 | |
| 332014063 | Tautomers | Different structural forms; when DNA is in solution, bases exist as different tautomers, which initially threw off Watson and Crick in regards to finding DNA's true structure. | 32 | |
| 332014064 | Major Groove vs. Minor Groove | The different spacings in DNA due to its uneven twisting; there are larger gaps between phosphodiester backbones (major) and smaller ones (minor). |  | 33 |
| 332014065 | Which complementary base pair has three hydrogen bonds? Which has two? | G-C has three hydrogen bonds and is thus stronger than A-T, which only has 2. | 34 | |
| 332014066 | Antiparallel Construction | dsDNA is put together so that the 3' and 5' ends of each strand are opposite as such; this has important implications in DNA replication. |  | 35 |
| 332014067 | Conservative Model | A replicative model in which both strands of the parental duplex would remain intact and new DNA copies would be all-new. | 36 | |
| 332014068 | Semiconservative Model | A replicative model in which one strand of the parental duplex would remain intact in daughter strands while a new complementary strand was build alongside the parental strand. | 37 | |
| 332014069 | Dispersive Model | A replicative model in which each strand of DNA consisted of a mix of old parental DNA and newly synthesized DNA. | 38 | |
| 332014070 | The Meselson-Stahl Experiment | DNA was labeled with a heavy nitrogen isotope (¹⁵N), allowed to replicate twice, and was centrifuged after 1 round and then 2 rounds of replication - initially all DNA was heavy - after 1 round, there was one medium band present, ruling out a conservative model (which would've had a heavy and a light band) - after 2 rounds, there was a medium band and a lighter band, ruling out a dispersive model (which would've had one single med-light band) | 39 | |
| 332014071 | Why does DNA replicate semiconservatively? | The other two methods are too inefficient; conservative replication would require the two new strands to be separated from their templates and then stuck together, while dispersive is too messy. | 40 | |
| 332014072 | The three main things DNA replication requires | - a template - nucleotides - a polymerase enzyme (there's more to it, but these are the basics) | 41 | |
| 332014073 | The terms used to describe steps in a biochemical process | Initiation Elongation Termination | 42 | |
| 332014074 | DNA Polymerase | The enzyme responsible for assembling a new strand of DNA by matching existing bases with complementary nucleotides and then linking the nucleotides together. All DNA polymerases add new bases to the 3' end of an existing strand and synthesize in a 5'-to-3' direction. Thus, all DNA polymerases require primer to work. | 43 | |
| 332014075 | Why do DNA polymerases require primer? | DNA polymerases require a primer to synthesize a new strand of DNA because they can only add to an existing strand; RNA polymerases can begin a new strand without an existing strand, and so usually synthesize the primers. | 44 | |
| 332014076 | Prokaryotic replication starts at a single origin | - starts at a specific site called the origin [oriC] - ends at specific site called the terminus - oriC consists of repeated nucleotides that bind an initiator protein and a AT-rich area to unzip. | 45 | |
| 332014077 | Prokaryotic replication proceeds bidirectionally | - DNA is in a circle - two replisomes unzip and synthesize new strands, resulting in an awkward pretzel - termination site reached; the pretzel unwinds and the result is two circular chromosomes - the DNA controlled by an origin is a replicon; the chromosome plus the origin forms a single replicon | 46 | |
| 332014078 | DNA Polymerase I [Pol I] | - the first DNA polymerase isolated in E. coli - at first assumed to do the bulk of synthesis (wrong) - has 3'-to-5' exonuclease activity (can proofread) - has 5'-to-3' exonuclease activity - acts on the lagging strand to remove primers, replace them with DNA | 47 | |
| 332014079 | DNA Polymerase II [Pol II] | - the second DNA polymerase found in E. coli - has 3'-to-5' exonuclease activity (can proofread) - not involved with replication; involved in DNA repair processes | 48 | |
| 332014080 | DNA Polymerase III [Pol III] | - the third DNA polymerase found in E. coli - has 3'-to-5' exonuclease activity (can proofread) - the main synthesis enzyme | 49 | |
| 332014081 | Endonucleases Exonucleases | Nucleases that either cut DNA internally (endo) or at the end (exo). | 50 | |
| 332014082 | Helicases | A class of enzymes whose job it is to unwind DNA strands to prep them for replication; they use ATP as a power source. | 51 | |
| 332014083 | Unwinding DNA | - requires helicase to separate strands - requires SSBs to keep strands separate - needs topoisomerases to release tension | 52 | |
| 332014084 | SSBs | Single-strand-binding proteins; they coat single strands of DNA during replication to prevent them from coming back together. | 53 | |
| 332014085 | Supercoiling | Coiling caused by the uncoiling of some other region of a coiled substance. | 54 | |
| 332014086 | Topoisomerases | Enzymes that can alter the topological state of DNA. They act to relieve torsional strain caused by unwinding and to prevent supercoiling. | 55 | |
| 332014087 | DNA Gyrase | The topoisomerase involved in DNA replication. | 56 | |
| 332014088 | Leading Strand | The strand of DNA that is being replicated continuously, as one long strand. | 57 | |
| 332014089 | Lagging Strand | The strand of DNA that is being replicated dis continuously, as many short fragments. | 58 | |
| 332014090 | Okazaki Fragments | The DNA fragments synthesized on the lagging strand. | 59 | |
| 332014091 | Replication Fork | The point where a dsDNA is split open. Synthesis occurs at the replication fork. | 60 | |
| 332014092 | DNA Primase | - the enzyme that provides a starting point for Pol III to work off of - an RNA polymerase - produces 10-20 bp-long fragments | 61 | |
| 332014093 | Processivity | The ability of a polymerase to remain attached to the template. | 62 | |
| 332014094 | β Subunit | - a ring-like structure of two identical protein chains that come together to encircle DNA - what lets Pol III to have a high processivity - requires a multisubunit protein called the clamp loader to open and close it - found in both proks and euks | 63 | |
| 332014095 | How synthesis on the lagging strand is done | - DNA Pol I removes primers using its 5'-to-3' exonuclease activity - then it replaces the missing bases with its 5'-to-3' polymerase activity, primed by the previous Okazaki fragment's free 3' ⁵-OH group - Pol I leaves, and ligase comes in to seal the "nick" between fragments | 64 | |
| 332014096 | What occurs during termination? | - termination occurs at a specific site located roughly opposite of oriC - two daughter molecules intertwined like rings in a chain produced - unlinked by DNA gyrase | 65 | |
| 332014097 | Replisome | - a macromolecular assemble; the "replication organelle" - has two main components: the primosome, and a complex of two DNA Pol III enzymes, one for each strand - primosome comprised of primase and helicase as well as accessory proteins - two Pol III complexes contain 2 synthetic core units, each with its own β subunit - entire replisome complex held together by proteins including clamp loader - replisome stationary; pushes DNA through itself | 66 | |
| 332014098 | A replisome works on both strands simultaneously. How? | One Pol III complex is on the leading strand; the lagging-strand one makes the strand form a loop so that it's close enough to the replisome complex. | 67 | |
| 332014099 | Origin sites on proks vs. euks | Prokaryotes only have one origin site. Eukaryotes have multiple. This is because euks have longer genomes that would be too much for a single origin site to suffice. Replication must occur at multiple sites to be efficient. | 68 | |
| 332014100 | Archael replication characteristics | The archael replication process and proteins are more similar to those of eukaryotes than of prokaryotes. | 69 | |
| 332014101 | Eukaryotes' main replication complex is comprised of what? | Two enzymes, DNA polymerase epsilon (pol ε) and DNA polymerase delta (pol δ). | 70 | |
| 332014102 | Telomeres | - specialized structures found at the ends of euk chromosomes - protect the ends of chromosomes from nucleases, maintain integrity of linear chromosomes - compose of specific DNA sequences, but not made by replication complex | 71 | |
| 332014103 | Telomerase | - the enzyme that creates the short, repeated DNA sequences found in telomeres - uses internal RNA as a template, not DNA itself |  | 72 |
| 332014104 | How do telomeres protect the genome? | If a linear chromosome were to be replicated, then as Pol I removed primers, a gap would be left at the 5' end of the strands where primer used to be. Pol I would be unable to fill this gap (no OH to go off of) and so the template would be shortened. Telomeres keep the end of the chromosome thick with repeated sequences to stave off chromosome shortening. | 73 | |
| 332014105 | Telomerase, aging, and cancer | - a hallmark of aging is the erosion of telomeres due to the suppression of telomerase activity - cancers keep themselves young by keeping their telomeres long with lots of active telomerase | 74 | |
| 332014106 | Mutagen | Any agent that can increase the number of mutations above background levels. | 75 | |
| 332014107 | DNA repair can be specific or nonspecific | Specific: targets a single kind of lesion in DNA and repairs only that damage. Nonspecific: uses a single mechanism to repair multiple kinds of lesions in DNA. | 76 | |
| 332014108 | Photorepair | - a specific repair mechanism - fixes damage caused by UV light (thymine dimers) - photolyase absorbs light in the visible range and uses the energy to cleave the dimer, restoring the thymines to their original state - does not occur in cells deprived of visible light - photolyase found in many organisms - proks, euks | 77 | |
| 332014109 | Thymine Dimer | A covalent bond between two adjacent thymines, sp. in a dsDNA. | 78 | |
| 332014110 | Excision Repair | - a nonspecific repair mechanism - a damaged section is removed and replaced by DNA synthesis - in euks, uses proteins coded by uvr A, B, C genes - follows 3 steps: recognition of damage, removal of damaged region, resynthesis using undamaged strand as template - accomplished w/ UvrABC complex + Pol I or Pol II | 79 | |
| 332015046 | Other forms of nonspecific repair | - error-free - error-prone (last-ditch; "SOS response") - breaks in strands (uses enzymes involved in recombination in meiosis) | 80 |
