Chapter 15

24 July 2022
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Short segments of newly synthesized DNA are joined into a continuous strand by _____.
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ligase
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The first step in the replication of DNA is catalyzed by _____.
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helicase • The first step of DNA replication is unwinding the DNA double helix.
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The action of helicase creates _____.
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replication forks and replication bubbles • A replication fork is the transition region between paired and unpaired DNA strands.
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Why is the new DNA strand complementary to the 3' to 5' strands assembled in short segments?
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DNA polymerase can assemble DNA only in the 5' to 3' direction • Since DNA polymerase can assemble DNA only in the 5' to 3' direction, the new strand complementary to the 3' to 5' strand must be assembled either in short 5' to 3' segments, which are later joined together by ligase, or be assembled continuously.
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The synthesis of a new strand begins with the synthesis of a(n) _____.
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RNA primer complementary to a preexisting DNA strand • The synthesis of a DNA strand begins with the formation of an RNA primer.
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What catalyzes DNA synthesis?
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DNA polymerase
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Which of the following statements about DNA synthesis is true?
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Primers are short sequences that allow the initiation of DNA synthesis. • When a primer is added to a single strand of DNA, DNA polymerase can start adding nucleotides to synthesize a complementary strand.
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Which part of a deoxynucleoside triphosphate (dNTP) molecule provides the energy for DNA synthesis?
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phosphate groups • The potential energy stored in the bonds of the phosphates provides the energy for DNA synthesis.
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Which of the following enzymes is important for relieving the tension in a helix as it unwinds during DNA synthesis?
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Topoisomerase • This enzyme untwists the coils that occur in the DNA as it is being unwound into a single-stranded template.
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What would be the consequence(s) for DNA synthesis if DNA ligase were defective?
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Lagging strand synthesis would be incomplete; leading strand synthesis would be largely unaffected. • Without DNA ligase activity, Okazaki fragments on the lagging strand would not be joined together; leading strand synthesis would be largely unaffected.
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What would be the consequence(s) for DNA synthesis if primase were defective?
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Both leading and lagging strand synthesis would be incomplete. • Primase is required to synthesize the RNA primers on both the leading and lagging strands (all DNA polymerases require a primer).
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Put the steps of DNA replication in chronological order.
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1. Hydrogen bonds between base pairs of antiparallel strands are broken. 2. Single-stranded binding proteins attach to DNA strands. 3. Primase binds to the site of origin. 4. An RNA primer is created. 5. DNA polymerase binds to the template strand.
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What is the role of DNA ligase in the elongation of the lagging strand during DNA replication?
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It joins Okazaki fragments together.
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Which of the following help(s) to hold the DNA strands apart while they are being replicated?
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single-strand DNA binding proteins
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A DNA replication bubble forms at a specific sequence of bases called the ___________.
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origin of replication
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primase
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An enzyme that joins RNA nucleotides to make the primer using the parental DNA strand as a template.
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helicase
helicase
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An enzyme that unzips the double helix of DNA at the replication forks. • breaks hydrogen bonds
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DNA polymerase III
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synthesizes new DNA only in the 5' to 3' direction • starts DNA synthesis at the 3' end of a primer. • "start here" signal for DNA replication • has ability to act as exonuclease to proofread and correct complementary base pairing mistakes
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exonuclease
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an enzyme that removes successive nucleotides from the end of a polynucleotide molecule
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DNA ligase
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enzyme that chemically links DNA fragments together • catalyzes the formation of phosphodiester bonds between DNA fragments.
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Topoisomerase
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corrects "supercoiling" ahead of replication forks by breaking, swiveling, and rejoining DNA strands • relaxes supercoiled DNA by catalyzing the controlled cleavage and rejoining of DNA. • like a comb that prevents tangling
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DNA polymerase I
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removes the RNA primer and replaces it with DNA nucleotides
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sliding clamp
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holds DNA polymerase in place during single strand extension
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primease
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enzyme that builds short complementary RNA primer on each strand of DNA
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Eukaryotic telomeres replicate differently than the rest of the chromosome. This is a consequence of which of the following?
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gaps left at the 5' end of the lagging strand
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single strand binding proteins
single strand binding proteins
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bind to and stabilize single-stranded DNA • prevents rejoining due to hydrogen bonds
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Hershey and Chase (1952)
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• is genetic material protein or DNA ? • Used a bacteriophage (virus that attacks bacteria) to provide evidence that DNA was a molecule of heredity
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Watson and Crick (1953)
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• Discovered double helix structure of DNA • Bases can pair to replicate
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Meselson and Stahl (1958)
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• Determined method of DNA replication • DNA replication is semiconservative (half old DNA and half new)
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which direction does does DNA replicate
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5' --> 3'
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telomere
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region at either end of a eukaryotic chromosome; consisting of noncoding sequences • involved in aging as they get shorter and shorter over time
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Telomerase
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enzyme that REPLICATES TELOMERES but its only active in meiotic cells forming gametes • Its important that you pass on all the genetic material you can to offspring otherwise they would be born old if they were passed down DNA with degraded telomeres
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what are the causes of DNA damage?
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• Spontaneous breakage (nobody knows why) • Radiation • Free radicals • Chemicals
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Excision repair systems
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groups of enzymes that recognize damage in DNA, excise surrounding nucleotides and repair using template strand
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Gene expression
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process of converting archived info into molecules that actually do things
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Central dogma of molecular biology (Crick)
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DNA—> RNA—> protein • DNA = hereditary material • Gene = specific stretch of DNA • DNA transcribed into mRNA since it cant leave nucleus • mRNA is translated to protein
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RNA polymerase
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enzyme that builds mRNA single strand complementary to DNA sequence
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Genetic code
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rules that specify relationship between sequence of nucleotides in DNA or RNA and sequence of amino acids in protein
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what are the characteristics of the genetic code?
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• Redundant (amino acid —> codon) • Unambiguous (single codon = 1 amino acid) • Non overlapping • Nearly universal (with few exceptions) • Conservative (codons differ in 3rd base when coding for amino acids)
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Triplet
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3 letter code in DNA
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Codon
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three-nucleotide sequence on mRNA that codes for a single amino acid
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anticodons
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a sequence of three nucleotides forming a unit of genetic code in a tRNA molecule, corresponding to a complementary codon in messenger RNA.
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Nirenberg and Mattaei (1961)
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deciphered genetic code
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phenylalanine
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UUU
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Start codon
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AUG (codes for methionine)
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Stop codon
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UAA, UAG, UGA, (dont code for amino acids; just signals to stop production)
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Beadle and Tatum (1941)
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1st to use "knock out" genes (if you want to know how a gene works, you mutate it and see what happens when it doesn't work) • Used metabolic pathway using bread mold • Proposed "one gene, one enzyme" hypothesis