MOLECULAR GENETICS PCB 4522
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This 8 page Class Notes was uploaded by Cameron Koss I on Friday September 18, 2015. The Class Notes belongs to PCB 4522 at University of Florida taught by William Gurley in Fall. Since its upload, it has received 11 views. For similar materials see /class/206948/pcb-4522-university-of-florida in Biology at University of Florida.
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Date Created: 09/18/15
Clamp A protein complex that forms a circle around the DNA by connecting to DNA polymerase it ensures that the enzyme action is processive Clamp loader A 5subunit protein complex that is responsible for loading the B clamp on to DNA at the replication fork Conditional letha l A mutation that is lethal under one set of conditions but not lethal under a second set of conditions such as temperature DNA ligase The enzyme that makes a bond between an adjacent 3OH and 5phosphate end where there is a nick in one strand ofduplex DNA Dna mutants T r sunit rquot 39 mutants in E coli that identifies a set of loci called the dna genes DNA polymerase An enzyme that synthesizes a daughter strands of DNA under direction from a DNA template Any particular enzyme may be involved in repair or replication or both DNA repair The removal and replacement of damaged DNA by the correct sequence DNA replicase See DNA polymerase Errorprone polymerase A DNA polymerase that incorporates noncomplementary bases into the daughter strand Gyrase An enzyme that changes the number of times the two strands in a closed DNA molecule cross each other It does this by cutting the DNA passing DNA through the break and resealing the DNA Helicase An enzyme that uses energy provided by ATP hydrolysis to separate the strands of a nucleic acid duplex Holoenzyme The DNA polymerase complex that is competent to initiate replication In vitro complementation A functional assay used to identify components of a process The reaction is reconstructed using extracts from a mutant cell Fractions from wildtype cells are then tested for restoration of activity Lagging strand The strand of DNA that must grow overall in the 3 to 5 direction and is synthesized discontinuously in the form of short fragments 53 that are later connected covalently Leading strand The strand of DNA that is synthesized continuously in the 5to 3 direction Lesion bypass Replication by an errorprone DNA polymerase on a template that contains a damaged base The polymerase can incorporate a noncomplementary base into the daughter strand Licensing factor A factor located in the nucleus and necessary for replication it is inactivated or destroyed after one round of replication New factors must be provided for further rounds of replication to occur Mutation hotspot A site in the genome at which the frequency of mutation or recombination is very much increased usually by at least an order of magnitude relative to neighboring sites Nick translation The ability of E coli DNA polymerase I to use a nick as a starting point from which one strand of a duplex DNA can be degraded and replaced by resynthesis of new material is used to introduce radioactively labeled nucleotides into DNA in Vitro Okazaki fragment Short stretches of 1000 to 2000 bases produced during discontinuous replication they are later joined into a covalently intact strand Primase A type of RNA polymerase that synthesizes short segments of RNA that will be used as primers for DNA replication Primer A short sequence often of RNA that is paired with one strand of DNA and provides a free 3 OH end at which a DNA polymerase starts synthesis of a deoxyribonucleotide chain Processivity The ability of an enzyme to perform multiple catalytic cycles with a single template instead of dissociating after each cycle Proofreading A mechanism for correcting errors in DNA synthesis that involves scrutiny of individual units after they have been added to the chain Quick stop mutant Temperature sensitive replication mutants that are defective in replication elongation during synthesis of DNA Replisome The multiprotein structure that assembles at the bacterial replication fork to undertake synthesis of DNA It contains DNA polymerase and other enzymes Semiconservative replication Replication that is accomplished by separation of the strands of a parental duplex each strand then acting as a template for synthesis of a complementary strand Semidiscontinuous replication The mode of replication in which one new strand is synthesized continuously while the other is synthesized discontinuously Singlestrand binding protein SSB The protein that attaches to singlestranded DNA thereby preventing the DNA from forming a duplex Slow stop mutant Temperature sensitive replication mutants that are defective in initiation of replication Topoisomerase An enzyme that changes the number of times the two strands in a closed DNA molecule cross each other It does this by cutting the DNA passing DNA through the break and resealing the DNA 539 end resection The generation of 339 overhanging singlestranded regions that occurs via exonucleolytic digestion of the 539 ends at a doublestrand break att sites The loci on a lambda phage and the bacterial chromosome at which recombination integrates the phage into or excises it from the bacterial chromosome Axial element A proteinaceous structure around which the chromosomes condense at the start of synapsis Bivalent The structure 39 39 U all four two r 39 g each homologue at the start of meiosis Branch migration The ability of a DNA strand partially paired with its complement in a duplex to extend its pairing by displacing the resident strand with which it is homologous Breakage and reunion The mode of genetic recombination in which two DNA duplex molecules are broken at corresponding points and then rejoined crosswise involving formation of a length of heteroduplex DNA around the site of joining Catenate To link together two circular molecules as in a chain Central element A structure that lies in the middle of the synaptonemal complex along which the lateral elements of homologous chromosomes align It is formed from Zip proteins Chiasma pl chiasmata A site at which two homologous chromosomes appear to have exchanged material during meiosis Chromosome pairing The coupling of the homologous chromosomes at the start of meiosis Core seguence The segment of DNA that is common to the attachment sites on both the phage lambda and bacterial genomes It is the location of the recombination event that allows phage lambda to integrate D loop displacement loop The loop ofdisplaced DNA generated by strand invasion and extension during homologous recombination Doublestrand breaks DSB Breaks that occur when both strands ofa DNA duplex are cleaved at the same site Genetic recombination is initiated by such breaks The cell also has repair systems that act on breaks that are created at other times Excision Release of phage or episome or other sequence from the host chromosome as an autonomous DNA molecule Gap repair A type of DNA repair in which one DNA duplex may act as a donor of genetic information that directly replaces the corresponding sequences in the recipient duplex by a process of gap generation strand exchange and gap filling Gene conversion The alteration of one strand of a heteroduplex DNA to make it complementary with the other strand at any positions where there were mispaired bases or the complete replacement of genetic material at one locus by a homologous sequence Gyrase Enzymes that introduce negative supercoils into DNA Heteroduplex DNA DNA that is generated by base pairing between complementary single strands derived from the different parental duplex molecules it occurs during genetic recombination Holliday 39unction A intermediate structure in homologous recombination for which the two duplexes of DNA are connected by the genetic material exchanged between two of the four strands one from each duplex A joint molecule is said to be resolved when nicks in the structure restore two separate DNA duplexes Homologous recombination Recombination involving a reciprocal exchange of sequences of DNA eg between two chromosomes that carry the same genetic loci Hotspot A site in the genome at which the frequency of mutation or recombination is very much increased usually by at least an order of magnitude relative to neighboring sites Integration Insertion of a viral or another DNA sequence into a host genome as a region covalently linked on either side to the host sequences Joint molecule A pair of DNA duplexes that are connected together through a reciprocal exchange of genetic material Lateral element A structure in the synaptonemal complex that forms when a pair of sister chromatids condenses on to an axial element Mating type cassette Yeast mating type is determined by a single active locus the active cassette and two inactive copies of the locus the silent cassettes Mating type is changed when an active cassette of one type is replaced by a silent cassette of the other type Mismatch repair Repair that corrects recently inserted bases that do not pair properly The process preferentially corrects the sequence of the daughter strand by distinguishing the daughter strand and parental strand sometimes on the basis of their states of methylation Nonhomologous end39oining NHEJ The process that ligates blunt ends It is common to many repair pathways and to certain recombination pathways such as immunoglobulin recombination Patch recombinant DNA that results from a Holliday junction being resolved by cutting the exchanged strands The duplex is largely unchanged except for a DNA sequence on one strand that came from the homologous chromosome Presynaptic filaments Singlestranded DNA bound in a helical nucleoprotein filament with a strand transfer protein such as Rad51 or RecA Prophage A phage genome covalently integrated as a linear part of the bacterial chromosome Recombinant 39oint The point at which two recombining molecules of duplex DNA are connected the edge of the heteroduplex region Recombinase Enzyme that catalyzes sitespecific recombination Recombination nodules nodes Dense objects present on the synaptonemal complex they may represent protein complexes involved in crossingover Resolution Resolution occurs by a homologous recombination reaction between the two copies of the transposon in a cointegrate The reaction generates the donor and target replicons each with a copy of the transposon Reverse gyrase Enzyme that introduces positive supercoils into DNA Singlestrand invasion or singlestrand The process in which a single strand of DNA displaces its homologous strand in a duplex Sister chromatid Each of two identical copies of a replicated chromosome this term is used as long as the two copies remain linked at the centromere Sister chromatids separate during anaphase in mitosis or anaphase II in meiosis Sitespecific recombination Recombination that occurs between two specific sequences as in phage integrationexcision or resolution of cointegrate structures during transposition Somatic recombination Recombination that occurs in nongerm cells ie it does not occur during meiosis most commonly used to refer to recombination in the immune system Splice recombinant DNA that results from a Holliday junction being resolved by cutting the nonexchanged strands Both strands of DNA before the exchange point come from one chromosome the DNA after the exchange point come from the homologous chromosome Supercoiling The coiling of a closed duplex DNA in space so that it crosses over its own axis I 39II I I I Synapsis The association of the two pairs of sister r D U that occurs at the start of meiosis the resulting structure is called a bivalent Synaptonemal complex The morphological structure of synapsed chromosomes Ac element Activator element an autonomous transposable element in maize Acentric fragment A fragment of a chromosome generated by breakage that lacks a centromere and is lost at cell division Alu element One ofa set ofdispersed related sequences each 300 bp long in the human genome members of the SINE family The individual members have Alu cleavage sites at each end Autonomous controlling element An active transposon in maize with the ability to transpose Cointegrate A structure that is produced by fusion of two replicons one originally possessing a transposon and the other lacking it the cointegrate has copies of the transposon present at both junctions of the replicons oriented as direct repeats Composite elements Transposable elements consisting of two IS elements can be the same or different and the DNA sequences between the IS elements the nonIS sequences often include genes conferring antibiotic resistance Conservative transposition The movement of large elements that were originally classified as transposons but now are considered to be episomes The mechanism of movement resembles that of phage excision and integration Controlling elements Transposable units in maize originally identified solely by their genetic properties They may be autonomous able to transpose independently or nonautonomous able to transpose only in the presence of an autonomous element Cytotype A cytoplasmic condition that affects P element activity The effect of cytotype is due to the presence or absence of a repressor of transposition which is provided by the mother to the egg Direct repeats Identical or closely related sequences present in two or more copies in the same orientation in the same molecule of DNA Ds element Dissociation element a nonautonomous transposable element in maize related to the autonomous Activator Ac element Helper virus A virus that provides functions absent from a defective virus enabling the latter to complete the infective cycle during a mixed infection with the helper virus Hybrid dysgenesis The inability of certain strains of D melanogaster to interbreed because the hybrids are sterile although otherwise they may be phenotypically normal Imprecise excision It occurs when the transposon removes itself from the original insertion site but leaves behind some of its sequence Insertion sequences IS A small bacterial transposon that carries only the genes needed for its own transposition Integrase An enzyme that is responsible for a sitespecific recombination that inserts one molecule of DNA into another Inverted terminal repeats The short related or identical sequences present in reverse orientation at the ends of some transposons Long interspersed elements LlNEs Long interspersed nuclear elements a major class of retrotransposons that occupy 21 of the human genome see retrotransposon Long terminal repeat LTR The sequence that is repeated at each end of the provirus integrated retroviral sequence Minus strand DNA The singlestranded DNA sequence that is complementary to the viral RNA genome of a plus strand virus lling element A r in maize that encodes a nonfunctional transposase it can transpose only in the presence of a transacting autonomous member of the same family Nonreplicative transposition The movement of a transposon that leaves a donor site usually generating a doublestrand break and moves to a new site Nonviral superfamily Transposons originated independently of retroviruses P element A type of transposon in D melanogaster Plus strand DNA The strand of the duplex sequence representing a retrovirus that has the same sequence as that of the RNA Plus strand virus A virus with a singlestranded nucleic acid genome whose sequence directly codes for the protein products Precise excision The removal of a transposon plus one of the duplicated target sequences from the chromosome Such an event can restore function at the site where the transposon inserted Provirus A duplex sequence of DNA integrated into a eukaryotic genome that represents the sequence of the RNA genome of a retrovirus R segments The sequences that are repeated at the ends of a retroviral RNA They are called RU5 and U3R Replicationdefective virus A virus that cannot perpetuate an infective cycle because some of the necessary genes are absent replaced by host DNA in a transducing virus or mutated Replicative transposition The of a r by a in which first it is replicated and then one copy is transferred to a new site Resolution It occurs by a homologous recombination reaction between the two copies of the transposon in a cointegrate The reaction generates the donor and target replicons each with a copy of the transposon Resolvase The enzyme activity involved in sitespecific recombination between two copies of a transposon that has been duplicated Retrotransposon retroposon A transposon that mobilizes via an RNA form the DNA element is transcribed into RNA and then reversetranscribed into DNA which is inserted ata new site in the genome It does not have an infective viral form Retrovirus An RNA virus with the ability to convert its sequence into DNA by reverse transcription Reverse transcriptase An enzyme that uses single stranded RNA as a template to synthesize a complementary DNA strand Short interspersed elements SINEs Short interspersed nuclear elements a major class of short lt500 bp nonautonomous retrotransposons that occupy 13 of the human genome see retrotransposon E Followed by a number it denotes bacterial transposons carrying markers that are not related to their function eg drug resistance Transducing virus A virus that carries part of the host genome in place of part of its own sequence The best known examples are retroviruses in eukaryotes and DNA phages in E coli Transposase The enzyme activity involved in insertion of transposon at a new site Transposon transposable element A DNA sequence able to insert itself or a copy of itself at a new location in the genome without having any sequence relationship with the target locus Q The repeated sequence at the 339 end of a retroviral RNA Q The repeated sequence at the 539 end of a retroviral RNA
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