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38 Cards in this Set
- Front
- Back
Define 5-meC and its role in the regulation of gene expression.
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cytosines in the CKG islands of DNA are methylated to form 5-methylcytosine. Proteins (MBPs) can bind to this and block gene expression.
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What is the class of antibiotics that inhibits DNA gyrase?
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AMINOCOUMARINs: (ex. nalidixic acid, novobiocin) bind to ATPase active site of DNA gyrase and block its energy source. QUINOLONES: (nalidixic acid) bind DNA gyrase and keeps it from decatenating DNA
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5'-mCpG mutation hot spots in DNA, fxn
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deamination of cytosine can be repaired, but deamination of 5-methylcytosine cannot be repaired. Therefore genetic disease often occurs at 5'-mCpG mutation "hot spots" in DNA.
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steps of synthesis and replacement of RNA primers?
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1 DNA primase synthesizes RNA primer, 2 primer extended, 3 DNA filled in after primer, 4 DNAp1 replaces RNA primer replaces RNA primer with DNA nucleotides, 5 DNA ligase closes gaps
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Name the enzyme that is responsible for each of the following: 1 synthesis of RNA primers,2 adding nucleotides to 3' end of DNA, 3 relieving supercoiling, 4 proofreading, 5 connecting Okazaki fragments
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1 DNA primase synthesizes RNA primers, 2 DNA polymerase (usually DNApIII) adds nucleotides to 3' end of DNA, 3 DNA gyrase (or topoisomerase) relieves supercoiling of DNA, 4 DNA polymerase I proofreads, 5 DNA ligase forms phosphoanhydride bonds (?) between Okazaki fragments
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nick vs. gap, def
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A nick is a interruption in the phosphoanhydride bonds, a gap is a place where whole nucleotides are missing
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Name the enzyme that is responsible for each of the following: 1 removing the RNA primer from the lagging strand close to the replication fork, 2 adding nucleotides to the place where the primer used to be
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1 RNAase removes primer from lagging strand, 2 telomerase lengthens newly synthesized lagging strand on 5' end
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What do DNA polymerases require in order to work?
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a primer with a free 3' OH group
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DNA gyrase, fxn
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alleviates supercoiling created by DNA helicase
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Define the following: transition mutation, transversion mutation, nonsense mutation, silent mutation, missense mutation
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transition mutation: pur for pur, pyr for pyr. Transversion mutation: pyr for pur, pur for pyr. Nonsense: forms a stop codon. Silient mutation: no change in aa. Missense mutation: base substitution changes resulting aa.
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Define the following: genome mutation, chromosome mutation, gene mutation. Give the rates that each occurs.
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GENOME MUTATION: chromosome missegregation (ex. aneuploidy) occurs 10^(-2) per division. CHROMOSOME MUTATION: (ex. translocation) occurs 6x10^(-4) per division. GENE MUTATION: base pair mutation (ex. point mutation) occurs 10^(-10) per base pair per division or 10^(-6) per locus per generation
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Give the effect on DNA for reach of the following mutagenic processes or chemicals: acid and heat depurination, ionizing radiation, alkylating agents, spontaneous deaminations
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acid and heat depurination (missing base), ionizing radiation (altered base), alkylating agents (altered base), spontaneous deaminations (incorrect base)
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Give the effect on DNA for reach of the following mutagenic processes or chemicals: intercalating reagents (acridines), UV irradiation, ionizing radiation, psoralen derivatives, mitomycin C
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intercalating reagents (deletion-insertion), UV irradiation (dimer formation), ionizing radiation (strand breaks), psoralen derivatives (interstrand cross-links), mitomycin C (interstrand cross-links)
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Describe the basic types of DNA repair. (3)
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1 PROOFREADING by DNA polymerases for mutations that occur during DNA replication, 2 MISMATCH for mutations that pass proofreading, 3 EXCISION REPAIR for mutations that occur spontaneously
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What is the significance of high fidelity DNA replication?
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Correlates with increased life span. People have greater DNA repair activity than shrews and we live longer.
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How are defects in DNA repair mechanisms related to cellular function and human disease?
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result in a high frequency of chromosome and gene (base pair) mutations, predisposing affected individuals to cancer (ex. leukemia)
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What is the orientation of the template strand, 3'->5' or 5'->3'
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5'->3' (nucleotides are added to the 3' end)
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Give a general description of bacterial DNA replication
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bidirectional or θ replication
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oriC: acronym, def, components (2)
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origin of Chromosomal replication; signal for the start of replication; contains 1 AT-rich region, 2 DnaA boxes
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What initiates replication of DNA? Describe the mechanism.
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binding of DnaA proteins to the DnaA box sequence; causes region to wrap around DnaA proteins and separates AT-rich region
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DNA helicase, fxn
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separates DNA strands
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SSB: acronym, fxn
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single-strand binding proteins; bind to separated DNA strands to hold them apart
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What is the eukaryotic equivalent of DNA gyrase?
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topoisomerase
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RNA primers: name of enz that synthesizes, average length of sequence
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synthesized by DNA primase; average length is 10-12 nucleotides
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telomerase: composition, fxn
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composed of protein and RNA, binds to 3' overhang of DNA and adds a repeating sequence. DNA primase later adds a primer and allows synthesis to occur as normal on the strand with a 5' end.
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most common types of polymerase errors? (2)
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frameshift, base substitution
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Substituting A for G would be an example of what kind of base substitution?
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transition
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Substituting T for G would be an example of what kind of base substitution?
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transversion
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Describe the functions of DNA polymerases I, II, and III.
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III: main replicating enz. I: fills in gaps, excises primers on lagging strand.
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DNA polymerases only read in the 5' to 3' direction, unless they are doing what?
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proofreading 3' to 5'
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polymorphism, def
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the presence of two or more distinct phenotypes in a population due to the expression of different alleles of a given gene (ex. blood types)
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SNP, acronym
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single nucleotide polymorphism
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What is the tautomeric form of adenine and cytosine vs. guanine and thymine
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adenine and cytosine form amino->imino tautomers, while guanine and thymine form keto->enol isomers
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C normally pairs with G. What does the tautomeric form pair with?
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A
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What will spontaneous deamination convert each of the following to? cytosine, adenine
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cytosine to uracil, adenine to hypoxanthine
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Describe the mechanism of mismatch repair
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some adenines of parental DNA strands are methylated, child DNA strands are reviewed for mismatches before methylation
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MBP, acronym
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5-meC binding protein, blocks gene expression on methylated strands of DNA
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"catenate", def
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arrange in a series of chains (ex. spores)
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