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50 Cards in this Set

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What are the characteristics of prokaryote replication?
1. Prokaryotes lack nucleus, 2. circular chromosome, 3. Origin of replication, 4. strands separated at origin -> synthesis begins in both directions -> creates a replication bubble -> proceeds till two separate circles are made
Function of topoisomerase?
Relieves supercoiling
Function of helicase?
Unwinds helix to separate pairs
Function of single stranded binding protein
Maintains strands to be single
What is the function of DNA polymerase?
Synthesizes new strand; works in 5'-> 3' direction(adds dNTP to 3' OH group of chain); PYROPHOSPHATE degraded to keep equilibrium conditions favoring synthesis of DNA
What strand has continuous synthesis?
Leading strand; replication fork opens up ahead of polymerase in RIGHT direction
What strand is synthesized in opposite directions(away from fork)?
Lagging strand; replication fork uncovers DNA behind polymerase-> thus has to start many times
What are the error prevention mechanisms?
DNA polymerase can correct errors -> contains 3' -> 5' exonuclease activity (aka digest DNA from 3' end); activated by mis-match Base pairing -> cuts off incorrect base -> moves back along strand -> inserts new nucleotide
What enzyme makes RNA primers needed for replication?
Primase
What strand requires and RNA primer in multiple locations?
Lagging strand
Which strand undergoes discontinuous synthesis?
Okazaki fragments (1k-2k bp) requires RNA primers to start the polymerization; RNA primers need to b converted back to DNA -> RNAase H digests RNA hybridized DNA -> DNA polymerase enters -> lays down DNA -> DNA ligase seals the nick between the 2 new DNA fragments made
Function of DNA ligase?
Closes nicks in DNA backbone at 3' end
During the eukaryotic cell cycle: what phase duplicates chromosomes?
S phase only
How does a eukaryotic cell ↑ the speed of replication?
1. multiple origins of replication thus forming multiple bubbles, 2. forks are bi-directional
Function: Polymerase I
• Replication, Repair, Primer excision
Function: Polymerase II
• DNA Repair
Function: Polymerase III
• Major replication polymerase, 3’-5’ exonuclease for proofreading activity
Function: Polymerase a
• Associated with primase
Function: Polymerase g
• Mitochondrial DNA synthesis
Function: Polymerase b
• DNA repair, primer excision
Function: Polymerase d
• Replication, 3’-5’ exonuclease for proofreading
Function: Polymerase e
• DNA repair
Topoisomerase vs DNA gyrase
Topoisomerase = eukaryote enzyme that relieves supercoiling of DNA, DNA gyrase = prokaryotic enzyme that relieves supercoiling
What drug targets NDA gyrase?
Quinolone anti-biotics
What are the 2 types of eukaryotic topoisomerase?
Type 1 = 1 cuts one strand, Type 2 = 2 cuts both strands
Function of helicase
Opens double helix -> separates strands by breaking hydrogen bonding between strands
What happens to linear chromosomes lagging strand?
It contains a 3' overhand -> single stranded DNA can be degraded and lost; How to prevent this? Use telomerase
Function of telomerase?
Lengthens telomeres (repetitive DNA sequences at the end of a chromosome) contains RNA complementary sequence -> uses reverse transcriptase to elongate; important in senescence (in ability for cell to continue to divide)
What enzyme is used in cancer cells to enable them to keep dividing?
telomerase
What is the procedure for DNA repair?
1. Identify damage, 2. remove damage(endo/exonuclease), 3. repair polymerase fills in gap, 4. DNA ligase seals nick
What is the chemical in tobacco that attacks cellular DNA?
Benz[a]pyrene -> oxidized in body -> reacts w/guanine -> distorts helix
How does UV damage DNA?
UV creates thymine dimer (T-T)(two pyrimidines covalently linked) -> distorts double helix
What does cytosine deaminate into?
Cytosine -> uracil
What does 5-methylcytosine deaminate into?
5-methylcytosine (aka cytosine)-> thymine
Function of nucleotide excision repair?
Cuts out damaged nucleotides
Function of base excision repair?
Removes abnormal base, leaves backbone intact
Function of mismatch repair?
Cuts out incorrect base, depends on methylation to identify strands
Function of transcription coupled repair?
Repairs transcribed genes preferentially
Function of glycosylase?
Removes only one base
Function of endonuclease
Removes damaged nucleotides(groups of DNA) + cuts backbone w/missing bases
Function of exonucleases
Removes adjacent bases -> creates a gap
Which DNA strand is the original strand? Newly synthesized strand?
Original strand has methylated bases (Ch3); newly synthesized strand = no methylation
Pt w/ UV exposure -> skin lesion -> NUCLEOTIDE EXCISION REPAIR DEFECT -> accumulation of DNA defect in skin -> tumors
Xeroderma pigmentosum
Pt w/ DEFECT IN MISMATCH REPAIR GENES -> accumulation of mutations over time -> cancer
Hereditary non-polyposis colorectal cancer
What are the mechanisms used for DNA rearrangements?
1. Recombination, 2. translocation, 3. transposable element, 4. retroviral insertion
What is the holiday structure?
The combination of parental chromosomes during meiosis
Define: translocation
Genetic material exchanged between non-homologous chromosomes -> happens in cancer
Define: transposable elements
Jumping genes - mobile genetic elements -> cuts out of old position -> finds new site
Define: retroviral insertion
RNA Viruses -> reverse transcriptase -> cDNA copy of RNA genome ->RNA degraded-> makes ds cDNA -> DNA is incorporated into cell DNA
What are the drugs that are chain terminators?
1. AZT (zidovudine, retrovir), 2. dideoxycytidine (zalcitabine, DDC); MOA = incorporated into growing chain and since DNA polymerase lacks proofreading it cant remove the base and it stops synthesis of DNA)