DNA Replication Flashcards
DNA replication is ____ & ______.
Bidirectional and semiconservative
Semiconservative: each copy of the DNA molecule, after replication, contains one strand from the __________ and one from the ________
Original template, newly synthesized
Prokaryotes have ______ origin of replication and _____ DNA
1, circular
Origins of replication sequences are almost exclusively ____ and _____ bases.
A-T bases
These proteins bind to single strands to prevent reannealing and protect DNA from nuclease degradation.
SSBs: Single-Stranded binding proteins
This enzyme unwinds the DNA helix.
DNA Helicase
DNA is a helix, so when helicases separate the strands of DNA, _________ ahead of the replication fork will occur.
Supercoiling
________ alleviate supercoiling ahead of the replication fork.
Topoisomerases
____________ creates a nick in one strand which allows the DNA to swivel around the intact strand, then seals the nicked strand.
Type I topoisomerase
__________ cut both strands to relieve the supercoiling then re-ligates the two strands
Type II topoisomerase
A special Type II topoisomerase (found in bacteria), __________ - introduces (-) supercoils - inhibited by ________
**Also important for the separation of circular chromosomes after replication.
DNA Gyrase, quinolones
All polymerases that synthesize nucleic acids only catalyze synthesis in the ____ to _____ direction.
5’ to 3’
Since DNA is antiparallel, the template must be read in the ____ to _____ direction.
3’ to 5’
Nucleic Acid Synthesis direction: _______
Template Reading Direction: _______
5’ to 3’
3’ to 5’
During DNA replication, this strand is synthesized continuously.
Leading Strand
During DNA replication, this strand is synthesized discontinuously away from the replication fork.
Lagging Strand
In DNA replication, the discontinuously synthesized fragments are called _____ fragments and are later joined to become a continuous segment of DNA
Okazaki
DNA polymerases require a free _________group to begin synthesis.
During DNA replication, this problem is solved by the action of ________.
3’ hydroxyl, Primase
Primase is an ____________ and does not require a free 3’ OH group to begin synthesis. It copies the first ~10 nucleotides to prime synthesis.
DNA polymerases then begin synthesis from the free 3’OH group from the RNA primer.
RNA polymerase
Each new DNA fragment on the lagging strand begins with the action of ________ laying down an _______
Primase, RNA primer
________ recognizes the RNA primer and begins to synthesize the DNA
DNA polymerase III
___________ catalyze a reaction between the 3’OH group of the strand being synthesized and the ______________ of an incoming nucleotide specified by the template being copied.
DNA polymerases, 5’ triphosphate
Net reaction of DNA Polymerase = addition of a ______ to a growing DNA strand and the release of __________.
_________ is further cleaved to _____________ to make the reaction irreversible and drive the reaction in the forward direction.
Nucleotide, pyrophosphate, Pyrophosphate, inorganic phosphate (Pi)
_______ - a common theme in many condensation reactions in biochemistry
A coupled irreversible reaction -
_______ high energy bonds are cleaved for each added nucleotide in a growing DNA chain.
2
________ is the enzyme in prokaryotes that elongates both the leading and lagging strands
DNA polymerase III
pol III
DNA polymerase III (pol III) is the enzyme in _________ that elongates both the leading and lagging strands.
Prokaryotes
DNA replication needs to be as accurate as possible - a single nucleotide mutation can have devastating consequences. Pol III, as well as many other DNA polymerases, have ______ _____
Proofreading Activity
If DNA polymerase mispairs a nucleotide with the template, it uses its ________ to excise the mismatched nucleotide.
3’ to 5’ exonuclease activity
________ checks each added nucleotide to make sure it is correctly base-paired with the template strand.
Pol III
When pol III detects a mistake, it __________ one nucleotide and she’s the misincorporated nucleotide.
This is called ________
Shifts backward
3’ to 5’ exonuclease activity
This enzyme has 5’ to 3’ polymerase activity, and exonuclease activity in BOTH the 3’ to 5’ and 5’ to 3’ directions
DNA polymerase I (pol I)
RNA primer is elongated by ______ until another stretch of RNA is encountered.
RNA primer is excised by ______, one ribonucleotide at a time.
Gap is filled by _____.
Remaining nick is sealed by ______.
DNA polymerase III
DNA polymerase I
DNA polymerase I
DNA-ligase
_______ lays down an RNA primer to begin each new strand.
Primase
______ extends the leading and lagging strands.
Pol III
________ removes RNA primers and replaces them with DNA.
Pol I
In Eukaryotic Cell Cycle, this phase is the most variable in terms of time, growth, and metabolism
G1 Phase (G stands for gap)
This phase occurs when DNA is replicated.
S Phase (S stands for synthesis)
This phase has a second “gap” phase where the cell prepares to divide.
G2 Phase
This phase is the phase of Cell Division.
M phase (M for Mitosis)
Eukaryotic DNA Polymerases:
Pol (alpha) - contains ______ + ______ (begins strand synthesis)
Pol (delta) - _______ + _______ (extends strands)
Primase + DNA polymerase
DNA polymerase + proofreading
(Know that alpha and delta cooperate)
Eukaryotic chromosomes are _______. At the end of the DNA molecule, the _______ strand will have a gap once the ________ is removed.
Eukaryotes solve this problem by the action of enzymes called _______.
Linear
Lagging
RNA Primer
telomerases
The ends of eukaryotic chromosomes contain repeated sequences called ______.
Telomeres.
___________ extends the ends of linear chromosomes.
Telomerase
Telomerase also contains a _________ - it copies its own template (RNA) into DNA extending the 3’ overhang on the chromosome. This process is repeated many times.
Reverse transcriptase
Cells that do not express _______ have their chromosomes shortened after every cellular division (cellular equivalent of aging)
Telomerase
A defect in mismatch repair is responsible for ____________, one of the most common inherited cancers.
HNPCC
Hereditary nonpolyposis colorectal cancer
UV light usually causes pyrimidine dimers - usually _____ dimers.
Thymine
In humans, a rare genetic disorder called ____ _____ most often results from a deficiency in excision endonuclease.
Xeroderma pigmentosum
In humans, a rare genetic disorder called xeroderma pigmentosum most often results from a deficiency in ______ ______.
Excision endonuclease.
