Chapter 6 Flashcards
when does DNA replication occur?
before a cell can produce two genetically identical daughter cells
what do replication initiator proteins do?
recognize sequences of DNA at replication origins and pry apart the two strand of double helix
the exposed single strand can serve as what for copying DNA?
templates
replication forks move in what direction?
move away in opposite directions from multiple replications origins in eukaryotic chromosome
what direction is DNA synthesized?
5’ to 3’
the addition of what to the 3’-hydroxyl end of a polynucleotide chain is the fundamental reaction by which DNA is synthesized?
deoxyribonucleotide
the nucleotides enter the reaction as ______
nucleoside triphosphates
what does DNA polymerase do?
catalyzes the addition of nucleotides to the free 3’ hydroxyl on the growing DNA strand
what does the breakage of a phosphoanhydride bond in the incoming nucleoside triphosphate do?
release a large amount of free energy and thus provides the energy for the polymerization reaction
at the replication fork, the two new synthesized DNA strands are of _____
opposite polarities
the lagging strand of DNA must be made initially as……
a series of short DNA strands called Okazaki fragments that are later joined together
the DNA strand that is synthesized discontinuously is called?
the lagging strand
the DNA strand that is synthesized continuously is called?
the leading strand
can DNA polymerase proofread its own work?
yes
if an incorrect nucleotide is added to a growing strand, the DNA polymerase will do what?
cleave it from the strand and replace it with the correct nucleotide before continuing
true or false? DNA polymerase contains separate sites for DNA synthesis and proofreading?
true
why does proofreading explain why DNAs are synthesized in 5’ to 3’ direction?
growth in 5’ to 3’ direction allows chain to continue to be elongated when incorrect nucleotide has been added then removed
how is RNA primers made?
at intervals of about 200 nucleotides on lagging strand by primase
how long are RNA primers
10 nucleotides long
how are primers removed?
by nucleases that recognize an RNA strand in and RNA/DNA helix and degrade it
removing a primer leaves a gap, how is it filled?
filled by a DNA repair polymerase that can proofread as it fills in the gaps
how are the completed fragments joined together?
by DNA ligase
what does DNA ligase do?
catalyze the formation of phosphodiester bond between 3’ OH end of fragment and 5’ phosphate end of the next-linking up sugar phosphate backbone
where are DNA polymerase located when DNA is replicating?
one on leading strand and other on lagging strand
how is DNA polymerase held on to DNA?
by a circular protein clamp that allow the polymerase to slide
what does DNA helicase do?
uses the energy from ATP hydrolysis to move forward and separate strands of the parental DNA double helix
what helps the two strands stay separated to provide access for primase and polymerase?
single-strand DNA-binding proteins
why is the DNA on the lagging strand folded?
to bring the lagging-strand DNA polymerase in contact with the leading strand DNA polymerase
the folding also does what?
brings the 3’ end of each completed O fragment close to the start side for next O fragments
the lagging strand DNA polymerase can be reused for what?
to synthesize successive O fragments
to synthesize the lagging strand at the end of a chromosome, the DNA replication machinery requires what?
requires the length of template DNA extending beyond the DNA that is to be copied
what does telomerase do?
adds a series of repeats of a DNA sequence to the 3’ end of the template strand, which allows lagging strand to be completed by DNA polymerase
what are mutations?
permanent changes of DNA caused by copying error and accidental damage
how is colon cancer caused?
accumulation of multiple mutations
what will happen if the mutation is uncorrected?
the mismatch will lead to permanent mutation in 1 of the 2 DNA molecules produced in next replication
what will happen is the mismatch is repaired using new DNA strand as template?
both DNA molecules produced in next replication will contain mutation
what will happen if the mismatch is correct using original template strand as the template?
the mutation is eliminated
why are newly replicated DNA strand preferentially nicked?
nicks provide signal that directs the mismatch repair machinery to appropriate strand
what does DNA mismatch do to the geometry of the DNA?
distorts it
the DNA mismatch repair protein recognizes the distortion and does what?
removes the newly synthesized DNA
the gap in the newly synthesized DNA is replaced by what?
by a DNA polymerase, which proofreads as it synthesize and sealed by DNA ligase
where are these nicks known to occur?
in the lagging strand, less observed in leading strand
what are the most frequent chemical reactions that cause serious DNA damage in cells?
depurination and deamination
what is depurination?
purine bases lost from DNA in cells
what is deamination?
loss of amino group from cytosine in DNA to produce uracil
what happens if deamination of cytosine is uncorrected?
results in the substitution of one base fro another when DNA is replicated
in deamination, what does uracil pair with?
adenine
what does UV radiation from sunlight cause?
DNA damage
What does UV radiation do to thymine bases?
2 adjacent thymine bases become covalently attached to one another to form thymine dimer
what is the 1st step of DNA repair?
excision- damage DNA cut out by nucleases
what is the 2nd step of DNA repair?
resynthesis- orig DNA sequence is restored by DNA polymerase, fills in the gap
what is the 3rd step of DNA repair?
ligation- DNA ligase seals the nick.
what energy does nick sealing require?
energy from ATP hydrolysis to remake broken phosphodiester bond
what can cells use to repair double-strand breaks?
nonhomologous end-joining “quick and dirty”
what allows for flawless repair of DNA double-strand breaks?
homologous recombination
when is homologous recombination initiated?
when a double strand break occurs shortly after a stretch of DNA has been replicated
