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74 Cards in this Set
- Front
- Back
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During which phase of the cell cycle does DNA replicate?
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S
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Old duplex is conserved and new duplex composed of two completely new strands.
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conservative replication
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Sections of the old duplex scattered somewhat randomly to the two daughter duplexes.
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dispersive replication
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Two daughter duplexes with one each of the old and new strands. |
semiconservative replication
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True or false: N15 is the naturally occurring isotope of nitrogen.
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false, N14
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What part of DNA contains nitrogen?
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bases
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method to separate molecules based on density |
ultracentrifugation
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What two opposing forces is the density gradient generated by?
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diffusion centrifugal |
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What is the DNA composition of the first generation after pulse?
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50% N15 and 50% N14
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What is often used in isopycnic centrifugation? |
caesium chloride
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What does isopycnic mean? |
equal density
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What are the three distinct stages of DNA replication? |
initiation elongation termination |
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How many base pairs per second does DNA replication occur?
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1000
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What polymerases play key roles in DNA replication? |
III and I
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catalyzes phosphodiester bond formation |
DNA polymerase
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What are required for DNA synthesis? (4)
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deoxynucleoside triphosphates Mg2+ template strand primer |
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In what direction does DNA polymerase move? |
3' to 5' end of template strand
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How is a new phosphodiester linkage formed? |
terminal 3' OH attacks alpha-phosphorous of incoming deoxynucleotide 5' triphosphate |
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What does DNA chain elongation require? (2) |
template and 3' end of a chain
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Why is DNA chain elongation essentially irreversible? |
ATP cleaved to pyrophosphate
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How does "proofreading" occur?
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DNA polymerase I possess 5' to 3' exonuclease activity
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What can catalyze both chain elongation and degradation?
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DNA polymerase I
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What recognizes distortion in DNA caused by incorrectly paired bases? |
DNA polymerase I
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What removes mispaired nucleotide before continuing? |
exonuclease activity of DNA polymerase I
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What is the error rate in the human genome and what does it mean? |
10^-9 1 error/daughter cell |
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Where does replication begin in E. coli?
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origin oriC
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When does replication stop in E. coli? |
two replication complexes meet at termination site
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protein machinery for replication
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replisome
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How long does it take the E. coli genome to be replicated and why?
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less than 40 minutes bidirectional |
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How is the much larger human genome replicated at the same rate as the genome of E. coli? |
multiple replisomes at the same time
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True or false: the leading strand moves in the same direction as the opening of the replication fork. |
true
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What unwinds superhelical structure? |
gyrase
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What breaks hydrogen bonding? |
helicase
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What keeps hydrogen bonds from rebinding? |
SSBP
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What is SSBP? |
single-stranded binding protein
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What does DNAa do?
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binds to the oriC and recruits DNAb
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What does DNAb do? |
helicase activity
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What bind to prevent reannealing of the helix? |
SSBP
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What make up the prepriming complex? |
DNAa, DNAb, and SSBP
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What are DNAa and DNAb? |
hexamers
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What is gyrase?
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form of topoisomerase that uncoils supercoil
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molecular zipper |
helicase
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motor proteins that move with directionality and processivity and utilize ATP to separate annealed DNA strands
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helicases
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bind ssDNA and prevent annealing |
SSBP
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True or false: SSBP are hexamers. |
false, tetramers
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What does SSBP bind to? |
AT rich sites
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True or false: SSBP binding is cooperative. |
true
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True or false: ssDNA with SSBP is flexible. |
false, inflexible
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What does it mean to be cooperative? |
once one binds it makes it easier for the rest to bind
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What does processive mean?
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grabs a hold and doesn't let go
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True or false: DNA polymerase can initiate new strands. |
false, cannot
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What can DNA polymerase covalently link a nucleotide to?
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primer
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What introduces primers?
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DNA primase
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What protein needs to act first for efficient DNA replication? |
gyrase
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synthesizes short RNA (about 10 nucleotides) complementary to a DNA strand |
an RNA polymerase called primase
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What is the site of replication called? |
replication fork
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True or false: both DNA strands are copied simultaneously. |
true
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Which strand only has one RNA primer?
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leading
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Which strand utilizes many RNA primers? |
lagging
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DNA synthesized between primers |
Okazaki fragments
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Explain discontinuous replication. |
done backwards; downstream formed first then more opens and more is able to be replicated upstream
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Approximately how long are Okazaki fragments? |
1000 nucleotides
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holoenzyme responsible for the majority of DNA synthesis in E. coli; a dimeric, multi-protein complex |
DNA polymerase III
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True or false: DNA polymerase III is highly processive. |
true
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What subunit of DNA polymerase III does DNA run through?
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Beta
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What join Okazaki fragments?
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DNA polymerase I and DNA ligase
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What are the three steps of joining Okazaki fragments to produce a continuous strand of DNA? |
removal of the RNA primer synthesis of replacement DNA sealing of adjacent DNA fragments |
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What removes RNA primer? |
DNA polymerase I
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What synthesizes replacement DNA? |
DNA polymerase I
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What seals adjacent DNA fragments?
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DNA ligase
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DNA polymerase I extends the Okazaki fragment while its 5' to 3' exonuclease activity removes the RNA primer |
nick translation
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sticks DNA within nick together by phosphodiester bonds |
DNA ligase
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True or false: nick translation occurs on the leading strand. |
false, lagging
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What is the correct order of events during DNA chain elongation? 1- Hydrolysis of pyrophosphate & phosphodiester bond formation 2- Base pairing & hydrogen bonding 3- 3'-hydroxyl group attacks the alpha-phosphorous atom |
2, 3, 1
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