Ch 12 DNA Replication & Recombination Flashcards
model of replication:
- two nucleotide strands separate and each serves as a template for synthesis of a new strand
- original strands stays intact but does not combine into same molecule
semiconservative replication
model of replication:
- entire dsDNA serves as template for new DNA molecule
conservative replication
model of replication:
- both nucleotide strands broken into fragments and reassemble into new DNA molecules
- each DNA molecule has interspersed original and new DNA
dispersive replication
what did Meselson and Stahl’s experiment determine was the correct mode of replication?
their experiment determined semiconservative replication was the right model
characteristics of theta replication model (DNA template, breakage of nucleotide strand, origin of replications, directions, products)
- circular DNA
- no breakage
- one origin of replication
- unidirectional or bidirectional
- two circular DNA products
characteristics of rolling circle model (DNA template, breakage of nucleotide strand, origin of replications, directions, products)
- circular DNA
- breakage in single strand
- one origin of replication
- unidirectional
- one circular and one linear DNA product (that can circulize to produce more)
characteristics of linear eukaryotic model (DNA template, breakage of nucleotide strand, origin of replications, directions, products)
- linear DNA
- no breakage
- multiple origins of replications
- bidirectional
- two linear DNA products
Requirements for DNA replication
- single-stranded DNA template
- raw materials (substrates) to be assembled into new nucleotide strand (dNTPs)
- enzymes & proteins that read the template and assemble the new strand
what are the substrates that are assembled into a new nucleotide strand during DNA replication?
deoxyribonucleoside triphosphates (dNTPs)
how are the substrates assembled into a new nucleotide strand during DNA replication?
dNTPs bonds with the 3-OH of previous nucleotide, cleaving off two phosphates, and a phosphodiester bond forms between the two nucleotides
in what direction is DNA replication?
5’ –> 3’
nucleotides added only to 3’ end of growing strand
enzymes that synthesize DNA
DNA polymerases
strand synthesized during replication that is continuous
leading strand
what strand does the template strand exposed in the 3’ –> 5’ direction synthesize?
it synthesizes the leading strand
strand synthesized during replication that is discontinuous
lagging strand
what strand does the template strand exposed in the 5’ –> 3’ direction synthesize?
it synthesizes the lagging strand
fragments of lagging strand that are linked together to create a continuous new DNA molecule
Okazaki fragments
does synthesis of leading strand go towards or opposite of replication fork unwinding?
synthesis of leading strand goes towards replication fork unwinding
does synthesis of lagging strand go towards or opposite of replication fork unwinding?
synthesis of leading strand goes opposite of replication fork unwinding
four stages of bacterial DNA replication:
initiation, unwinding, elongation, termination
binds to origin of replication (oriC) and separates DNA strands to initiate replication
initiator protein
explain process of bacterial initiation
initiator proteins bind to origin of replication (oriC), causing short section of DNA to unwind
explain process of bacterial unwinding
unwinding proteins (DNA helicase, single-strand-binding proteins, and DNA gyrase) bind to DNA to assist in unwinding
breaks hydrogen bonds between nucleotide bases and unwinds DNA at replication fork
DNA helicase
attach to unwound DNA and stabilize the strands in place to prevent secondary structures from forming
single-strand-binding proteins
moves ahead of replication fork and reduces torsional strain that builds due to unwinding of DNA
DNA gyrase
DNA gyrase is what type of topoisomerase? What does it do?
type II topoisomerase
- makes double-strand break in segment of DNA helix
- passes one segment through the break
- reseals broken ends of DNA back together
explain process of bacterial elongation
- primase synthesizes RNA primers for DNA polymerase to add DNA molecules onto
- DNA polymerase III synthesizes DNA on leading and lagging strand
- DNA polymerase I removes and replaces primers
- DNA ligase seals breaks of Okazaki fragments
RNA polymerase that synthesizes primers on template DNA strand to provide a 3’-OH group for attachment of DNA nucleotides
DNA primase
short stretches of RNA nucleotides synthesized on template DNA strand
primers
why are primers required for DNA replication?
for DNA synthesis, all DNA polymerases require a 3’-OH group in order to add a nucleotide. DNA doesn’t have 3’-OH group, so primase synthesizes primers, which provide a 3’-OH group for DNA polymerases to add DNA nucleotides on
what do all DNA polymerases require in order to add nucleotides?
a 3’-OH group
describe DNA polymerase III
elongates new nucleotide strand from 3’-OH group provided by
- 5’ –> 3’ polymerase activity (DNA synthesis)
- 3’ –> 5’ exonuclease activity (proofreading)
high processivity
describe DNA polymerase I
removes and replaces RNA primers with DNA
- 5’ –> 3’ polymerase activity (DNA synthesis)
- 3’ –> 5’ exonuclease activity (proofreading)
- 5’ –> 3’ exonuclease activity (remove primers)
catalyzes formation of phosphodiester bonds between Okazaki fragments and seals breaks
DNA ligase
describe process of bacterial termination
terminus utilization substance (Tus) binds to termination sequences and blocks helicase movement, preventing replication
what are processes that lead to the high accuracy of DNA replication
- nucleotide selection
- proofreading
- mismatch repair
process of DNA polymerase particular pairing nucleotides with complements on template
nucleotide selection
process of proofreading
DNA polymerase removes incorrect paired nucleotide and replaces it
process of mismatch repair
enzymes excise incorrectly paired nucleotides and replace with correct ones AFTER replication
binds to defined origins or replication and initiates replication
origin-recognition complex (orC)
how do the origins or replication differ in eukaryotes than prokaryotes
eukaryotes have many, prokaryotes usually have one
explain process of eukaryotic initiation
- replication licensing factors attach to origins to license and approve them for replication
- initiator proteins bind
explain process of eukaryotic unwinding
unwinding proteins (DNA helicase, single-strand-binding proteins, and topoisomerases) bind to DNA to assist in unwinding
describe DNA polymerase α
has primase activity and synthesizes RNA primers
describe DNA polymerase δ
synthesizes lagging strand
describe DNA polymerase ε
synthesizes leading strand
explain nucleosome assembly in eukaryotic replication
- original nucleosomes disrupted
- old histones redistributed onto new DNA
- new histones synthesized and added to form new nucleosomes
what organisms face end-replication problem and why?
eukaryotes face end-replication problems because they have linear DNA
describe the end replication problem
DNA replication leaves gaps at end of chromosomes due to removal of terminal primers
sequences at the end of chromosomes that have many copies of short repeated sequences (G-rich overhang TTAGGG)
telomeres
enzyme that prevents shortening of chromosomes by extending sequence
telomerase
what cells would telomerase most likely be found in?
stem cells and germ cells
single-stranded protruding end of telomere
G-rich overhang
describe how telomerase extends DNA to fill in gaps at ends of chromosomes
- telomerase base pairs with G-rich strand, and provides template for nucleotide synthesis
- nucleotides are added to 3’ end of G-rich strand
- telomerase moves along DNA so more nucleotides could be added
what types of problems could lack of telomerase in a cell cause?
progressive shortening of chromosomes and premature aging
what types of problems could overabundance of telomerase in a cell cause?
promotion of cancer
homologous combination
exchange of genetic information between homologous chromosomes
summary of the Holliday model of homologous recombination
- single-strand breaks occur in homologous chromosomes
- strand invasion to broken end of other DNA
- Holliday junction formation
- branch migration
