Chapter 6 Flashcards
Describe the three possible models of DNA replication
Semiconservative (1 old 1 new strand)
Dispersive (mix of old and new)
Conservative (1 old DNA, 1 new DNA)
What model of DNA replication did Watson and Crick like?
Semiconservative
Describe the experiment used to determine the basic model of DNA replication
Grow bacteria in 15N medium, then grow for 1 generation in 14N medium
Centrifuge to produce bands based on density (light higher in tube)
One generation of growth → One intermediate band → Ruled out conservative
2+ generations → One intermediate and one light strand → Ruled out dispersive
What would the results of the experiment to determine the basic model of DNA replication be if the other models were correct?
Conservative would have produced one light and one heavy band for both
Dispersive would have produced an intermediate band for both
What are the four enzymes required for the synthesis of lagging strands? What do they each do?
DNA primase, DNA polymerase, nuclease, and ligase
Primase to provide 3* OH
DNA polymerase to add new nucleotides
Nuclease to remove the RNA primer
Ligase to seal nicks by forming phosphodiester bonds via ATP hydrolysis
What are RNA primers for? How are they made? How many does each strand type need?
RNA primers are synthesized by primase, a type of DNA polymerase
One primer is required for the leading strand, and one primer is needed for each lagging strand
The primers provide a starting place (3* Hydroxyl) for DNA replication to begin
What is the role of the sliding clamp in DNA replication?
Hold RNA polymerases onto DNA
What is the role of the DNA helicase in DNA replication?
Unwinds double-stranded DNA with energy from ATP hydrolysis
What is the role of the single-stranded binding proteins in DNA replication?
Maintain strand separation
Prevents refolding and regenerating of H-bonds
What is the role of topoisomerases in DNA replication?
Relieve tension in front of the replication fork by breaking phosphodiester bonds (also catalyze reformation of that bond)
Why are linear chromosomes problematic?
Replication of linear chromosomes would shorten the DNA strands because the final RNA primer in lagging strands cannot be replaced with DNA (no starting point)
What are telomeres? What is their purpose?
Telomeres are repetitive G-rich sequences at the end of linear DNA that are heterochromatic and non-coding. They also prevent the ends of the chromosomes from fusing together
What does telomerase do?
Telomerase is a protein active in germline and cancer cells that prevents shortening of the telomeres and loss of genetic information by adding an RNA template to the template strand, allowing DNA polymerase to finish the lagging strand
Which direction relative to the origin do the leading and lagging strands go? What direction relative to 5/3?
Leading strand goes towards replication fork, lagging strand goes away from replication fork, towards origin (first one is next to the origin, pointing towards it)
Both synthesized 5-3
Describe the area where DNA replication begins
DNA replication begins at AT rich replication origins
Contain sequences recognized by initiator/helicase proteins that bind and open up DNA
Describe how the number of replication origins affects replication (include prokaryotic, eukaryotic
Bacterial chromosomes only have 1 origin, Eukaryotes have many
more origins, faster replication
Describe the two catalytic sites of DNA polymerase and their direction (5/3)
Synthesis goes 5* to 3* (new strand)
Nuclease/Proofreading goes 3* to 5* (compare with template strand)
How is DNA proofread?
Recognize mismatched bases by bond angles and repairs by removing newly synthesized DNA strand (identified by nicks), which is replaced by DNA polymerase and ligase.
What is correct repair so important?
Unrepaired DNA will produce 50% mutant/nonmutant, repair of template strand will produce 100% mutant
Describe the chemical mechanism of DNA synthesis
Polymerase must undergo condensation reactions and add to 3*, where there is no phosphate and the incoming deoxyribonucleoside triphosphate can hydrolyze (cleave phosphoanhydride bond, release pyrophosphate group) to provide energy for polymerization.
Give an overview of the direction of DNA synthesis and its effects on evolution
Synthesis must go 5→3 or replication would stop during proofreading when removal of an incorrect base would produce a phosphate on 5* end.
