DNA Metabolism Flashcards
What did the Meselson Stahl Experiement prove?
The semiconservative model of DNA replication
- The first division ruled out conservative because all DNA was of intermediate density
- The second division ruled out dispersive model because DNA was either of intermediate or light density
What is DNA polymerase?
Synthesize a complementary DNA strand in the 5’ to 3’ direction
It reads a DNA in the 3’ to 5’
DNA-dependent DNA polymerase
What is the leading strand in a replication fork?
The strand synthesized in the same direction as fork movement in the 5’ to 3’ direction
What is the Lagging strand in the replication fork?
The strand synthesized in the 5’ to 3’ in the opposite direction as fork movement
What are some characteristics of the lagging strand?
Can’t be synthesized continuously
Synthesized as small fragments called Okazaki fragments which are later ligated
What are Okazaki fragments?
Small fragments of newly synthesized DNA in the lagging strand of a replication fork
DNA synthesis is semi-continuous, what does this mean?
Leading strand synthesis is continuous
Lagging strand synthesis is discountinuous
Where are the only spots that replication can begin?
At the “origins of replication”
From every origin of replication, how many replication forks are formed?
Two replication forks begin, migrating in opposite directions
What doe DNA polymerase require in order to start DNA synthesis?
Require an existing 3’-OH to add nucleotides to provided by a primer
When two replication forks open, where are the leading strands?
One strand will be the leading strand for one fork but the lagging strand for the other fork
(Leading strands are on opposite sides replicating away from each other)
12
34
E.g 1 and 4, 2 and 3 if 1,3 is a replication fork and vice versa
What reaction causes DNA chain elongation?
Transesterification
An irreversible reaction due to how much energy was used. Hydrolysis contributes to the energétics
What substrate adds the base to the elongating DNA chain?
Deoxynucleotidetriphosphates (dNTPS)
What is the reaction mechanism on dNTP for DNA chain elongation? (Simple)
Nucleophilic attack by 3’ -OH of primer on first phosphate (alpha) of the incoming dNTP
The 2nd and 3rd phosphates (beta and gamma) are release as inorganic pyrophosphate (PPi)
What is processivity?
The ability of an enzyme to catalyze multiple reaction without releasing its substrate
What is an example of a processivity enzyme?
DNA polymerase
-This process is faster than distributive enzymes
What are distributive enzymes?
Enzymes that disassociate from substrate and product after catalyzing their reaction
DNA polymerase have varying processivity, Which are high and low?
DNA polymerase III has high processivity
DNA polymerase I has low processivity
What are sliding clamps (associated with polymerase)
Highly processive DNA polymerase use sliding clamps to remain associated with their templates
Loading of sliding clamps require ATP hydrolysis
How often do DNA polymerase make mistake?
Every 10k to 100k bp
How are the mistakes of DNA polymerase removed?
Proofreading
(Separate activity from DNA polymerase)
A 3’-5’ exonuclease activity
What are the 2 mechanisms to detect incorrect nucleotides?
- Mispairing results in weaker H-bonding and brings new strands to exonuclease site of polymerase
- Mispairing inhibits translocation of DNA through polymerase. The pause allows the new strand to enter the exonuclease site
(Shifts backwards a little bit)
By how much does proofreading improve DNA synthesis?
Improves fidelity of replication by 100-1000 fold
How many origins do bacteria have?
One replication origin: oriC
This site is highly conserved across bacteria species
What is the bacteria replication origin rich in?
High in GATC-methylated adenosines
2 regions with repeats
-9 by repeats, 12bp AT rich repeats
What initiates strand separation in bacteria at the AT-rich repeats?
DnaA (initiator protein)
Where does DnaA bind to?
The 9bp repeats
What is DnaC?
Helicase loading protein
Associates with DnaA and helps recruit DnaB
What is DnaB and what’s it do?
Helicase enzyme
It further separates the strands and 2 replication forks begin? (DnaA initiates the separation)
When does initiation not occur at replication origins?
When the strands are hemimethylated origins
-it takes around 20 minutes to full methylate
When can DNA replication occur after the strands are open in bacteria?
When DNA becomes fully methylated
Hemi looks like an eye with eyelashes and fully has strands on both side going up and down
What is DNA helicase?
Enzymes that separate (unwind) the strands of dsDNA
They bind one strand, translocate along it and displace the other strand
What does DNA helicase induce?
Induces positive supercoils
This is resolved by topoisomerase
What does DNA helicase require in order to work?
Requires energy to break the H-bonds
ATP hydrolysis: ATP -> ADP + Pi
Wha do single-stranded DNA binding proteins do?
- Protect single-stranded DNA from nuclease attack
- Prevent reannealing
- Aid helicase by destabilizing the double helix
What does primase do? Bacteria
Generates 8-10bp of RNA to as a primer
Associates transiently with the helicase to form a primosome
Generates primers periodically on the lagging strand as the replication fork moves
What is the primary DNA polymerase in bacteria?
DNA polymerase III
What is the difference of okazaki fragments in bacteria vs eukaryotes?
Bacteria 1k-2k bases
Eukaryote are 100-200
What is the activity of DNA polymerase III?
Synthesize the leading and lagging strands
- 5’-3’ DNA polymerase (DNA synthesis)
- 3’-5’ exonuclease (proofreading)
What is the replisome? (Bacteria)
A complex made by the 2 DNA polymerase (for the leading and lagging strands)
What is the trombone model?
The lagging strand loops out as it is replicated so the polymerase can follow the replication fork
What periodically creates new RNA primers on the lagging strand? (Bacteria)
Primase in the primosome
After a primase adds a new RNA primer to the DNA template, what is loaded to the end of the new primer?
A new sliding clamp is loaded at the end of the new primer
What happens when DNA polymerase III on the lagging strand hits the preceding RNA primer? (Bacteria)
It releases the DNA strand
What is a nick?
An adjacent nucleotide not connected by a phosphodiester bond
What does DNA polymerase I do? (Bacteria)
Bind to the nick and removes the RNA
-It has a 5’-3’ exonuclease activity for the nick
Synthesis DNA in the space (5’ to 3’)
Then proofreads (3’to5’)