Lecture 9 Flashcards
What three things does DNA replication requires?
- something to copy (parental DNA molecule)
- Something to do the copying (enzymes)
- Building blocks to make copy (nucleotide triphosphates)
What are the three stages of DNA replication?
- Initiation- replication begins
- Elongation- new strands of DNA are synthesized by DNA polymerase
- Termination-replication is terminated
DNA polymerases match existing DNA bases with______ ________ and links them, that is build new DNA strands
complementary nucleotides
What are three features of DNA polymerase?
- add new bases to 3’ end of existing strands
- synthesize in 5’ to 3’ direction
- require a primer of RNA
______ is used as model system for understanding universal attributes of replication
E.coli
What are four characteristics of E.Coli in correlation with Prokaryotic replication?
1.singular circular molecule of DNA
2.Replication begins at the origin of replication
3.Proceeds in both directions around the chromosome
4. replicon-DNA controlled by an origin
In prokaryotes, replication is _______ from a unique origin
bidirectional
What are the three DNA polymerases in E.coli?
- DNA polymerase I (Pol I)
- DNA polymerase II (Pol II)
- DNA polymerase III (Pol III)
What pol is the main replication enzyme?
Pol III
What pol is involved in DNA repair processes?
Pol II
What Pol acts on lagging strand to remove primers and replace them with DNA?
pol I
All three of the polymerase have 3’ to 5’ _____ activity
exonuclease
What does exonuclease activity serve as?
proofreading
What pol has 5’ to 3’ exonuclease activity when removing RNA primers?
Pol I
T or F: some polymerase molecules can remove nucleotides, acting as nucleases
True
What does it mean to be endonuclease?
cut DNA internally
What does it mean if polymerases are exonucleases?
it removes nucleotides from end of DNA
What enzyme unwinds DNA by using energy from ATP?
Helicase
What protein coats strands to keep them apart?
Single-strand-binding proteins
Unwinding of DNA introduces _____ ____ in the molecule that can lead to additional twisting of the helix
torsional strain
What is additional twisting of the helix called?
supercoiling
What enzymes prevent supercoiling?
topoisomerases
What is the topoisomerase involved in DNA replication that relieves the torsional strain?
DNA gyrase
T or F: Replication is semi discontinuous
True
T or F: DNA polymerase can only synthesize in the 5’ to 3 direction
True
Antiparallel nature of DNA means new DNA strands must be synthesized in ____ directions
opposite
What strand is synthesized continuously from an initial primer?
Leading strand
What strand is synthesized discontinuously with multiple priming events?
lagging strand
DNA fragments on the lagging strand are called _____ _____
Okazaki fragments
T or F: synthesis occurs at the replication fork?
True
What is the partial opening of helix formed where double stranded DNA is being unwound called?
RepliCatIon fork
___ will be removed and replaced with DNA later
RNA
Does the leading-strand synthesis have multiple priming events?
No
The leading strand is extended by what Pol?
Pol III
What is processivity?
the ability of a polymerase to stay attached to
What subunits form the sliding clamp to keep DNA Pol III attached to DNA?
beta
T or F: Lagging-strand synthesis does not require additional enzymes
False
What type of synthesis is the lagging-strand?
discontinuous
What enzymes are involved in lagging-strand synthesis?
- DNA Pol III
- Primase
3.DNA Pol I - DNA ligase
What does primase do?
makes RNA primer for each Okazaki fragment
What does DNA Pol I do?
removes all RNA primers and replaces with DNA primers
What does DNA ligase do?
joins Okazaki fragments to form complete strands
What occurs at specific site: DNA gyrase unlinks two copies
Termination
What is a macromolecular assembly of enzymes involved in DNA replication called?
replisome
What are the main components of a replisome?
- primosome
- complesxof two DNA Pol III
What does the primosome consist of?
primase, helicase, accessory
Why are there two DNA Pol III complexes in the replisome?
So there is one for each strand`
T or F: Eukaryotic replication and prokaryotic replication have the same complexity
False: Eukaryotic replication is more complex
Why is eukaryotic replication more complex than prokaryotic replication?
- larger amount of DNA in multiple chromosomes
2.Linear structure
T or F: Eukaryotic replication uses multiple origins
True
Why does Eukaryotic replication require new enzymatic activity?
Because of dealing with the ends
What does it mean if, in replication, there are multiple replicons?
There are multiple origins of replications for each chromosome
Before _ phase, helicases are loaded onto possible replication origins, but not activated.
S
During S phase, what is assembled?
the replisome
What polymerase synthesizes the leading strand?
DNA polymerase epsilon
What polymerase synthesizes the lagging strand?
DNA polymerase delta
_______ and eukaryotic replication proteins are evolutionary related
Archaeal
What enzymes are similar between eukaryotes and archaea but different from those in prokaryotes?
DNA polymerase
Replicative helicases
Primases
________ chromosomes have specialized ends
linear
What are Telomeres?
- specialized structures found on the ends of eukaryotic chromosomes
-composed of repeat sequences
What is the role of Telomeres?
- protect ends of chromosomes from nucleases
- maintain the integrity of linear chromosomes
The last primer removed from what of the lagging strand cannot be replaced?
lagging
What is the enzyme that synthesizes the telomere repeat sequences at the ends of stands?
Telomerase
What does Telomerase use as a template?
internal RNA
How is telomerase activity regulated?
developmentally
T or F: DNA damage constantly occurs
True
What are agents that increase the number of mutations above background level called?
mutagens
How is the importance of DNA repair indicated?
By the multiplicity of repair systems that have been discovered
What are the two categories of DNA repair?
- Specific repair
- Nonspecific repair
What DNA repair targets a single kind of lesion in DNA and repairs only that damage?
specific
Which DNA repair uses a single mechanism to repair multiple kinds of lesions in DNA?
nonspecific
What does the mismatch repair (mmr) do?
removes incorrect bases incorporated during DNA replication, by replacing them with the correct base by copying the template strand
What strand will be unmethylated for a brief window during which MMR can identify strands?
the newly synthesized strand
What type of repair mechanism is photorepair?
specific
What enzyme absorbs light in visible range and uses that energy to cleave thymine dimer?
photolyase enzyme
What type of repair mechanism is Excision repair?
nonspecific
What does excision repair do?
- recognizes the damage
- removes the damage region
- resynthesis using the information on the undamaged strand as a template
T or F: All DNA repair mechanisms are error-free
False, some are actually error-prone
