Section 2: DNA replication Flashcards
What is DNA replciation?
DNA rep is the synthesis of 2 daughter DNA molecules identical to the parental DNA.
What must happen during DNA rep?
During division the cell must completely duplicate the genetic material so that each daughter cell has a copy of the cellular genome. The process of DNA rep is how the stored genomic info is passed down generations.
How many base pairs are in a cell?
The cell has around 6 billion base pairs in its diploid genome so it requires extensive monitoring and coordination.
What are the 6 key components to DNA rep?
1) Replication is semiconservative
2) Initiated at specific sites
3) Typically bidirectional
4) Semi discontinuous ie. Lagging Discontinuous, Leading continuous
5) RNA primers are needed to start it
6) Nucleases, polymerases, and ligases replace the RNA primers with DNA and seal the nicks
What is one way that DNA makes sure it is synthesized efficiently?
DNA rep is highly regulated and only starts if there are enough resources to form both cells
Who hypothesized DNA rep was semiconservative and why?
Watson and Crick, they though this because of their discovery of DNA structure
What were the 3 competing theories at the time?
Conservative-Both parental strands stay together and copy without unwinding to form identical daughter strands
Dispersive-The parental strand and new daughter strand were randomly mixed to create a patchwork of old and new
Semiconservative-Due to the DS-helical nature discovered by Watson and Crick, they thought that it must be unwound and that each parental strand was used as a template for the daughter strand
What is an origin of replication?
The specific sequence where DNA synthesis starts, always happened at a defined origin with the help of origin recognition system
What is the difference between bacterial and eukaryotic origins?
Circular bacterial chromosomes only have one origin, long linear eukaryotes have numerous
What is a replication bubble?
Open DNA that is being replicated ie. Large circle
What is a replication fork?
The point where the parental duplex separates and the daughter strands form ie. Opening into bubble
What does it mean that replication is typically bidirectional?
The replication fork is typically bidirectional ie. synthesis is moving in both directions from the origin of replication
What differs between leading and lagging with regards to direction and the fork?
Leading goes into the fork
Lagging goes away from the fork
Why is replication continuous on the leading strand and discontinuous on the lagging strand?
DNA being antiparallel means both strands can’t be synthesized into the replication fork so one is synthesized into the fork continuously and one away from the fork discontinuously.
What directions are each strand synthesized, including relative to the fork?
Leading-Into fork 5’ to 3’
Lagging-Out of fork 5’ to 3’
THE REPLICATION FORK MOVES BIDIRECTIONALLY
What does the lagging strand mean for extra replication work?
The lagging strand is synthesized away from the replication fork 5 to 3. Strand synthesis must be reinitiated at intervals and synthesized by a series of Okazaki fragments
Why is DNA replication semi-discontinuous?
This is because of the leading and lagging strand because only one daughter strand is made continuously while the other is made in discontinuous fragments
What is linked when nucleotides are added?
The 5’ alpha phosphate of the new dNTP is linked to the 3’OH group of the primer strand or residue
What linkage binds nucleotides on the same strand
Covalent
What direction do polymerases work?
5’ to 3’ only
What does primase do?
Synthesize RNA primers
How long are primers?
10-13 BP long
What are the 2 requirements of a primer?
1) Complementary to the template
2) Contain a free 3’OH group
What does ligase do?
Joins Okazaki fragments once the replication fork has passed
What does nuclease do and how?
Removes primers by hydrolyzing internucleotide phosphodiester linkages in amino acids
What must happen after replication and which enzyme does what?
RNA primers must be removed-Nuclease
Nicks and Gaps must be sealed-Ligase
What is a nuclease?
An enzyme that hydrolyzed the internucleotide phosphodiester linkages of nucleic acids
What is a polymerase?
An enzyme that catalyzes DNA synthesis from its deoxynucleoside 5’-triphosphate precursor
What is a ligase?
Enzymes that create a phosphodiester bond between the 3’ end of one DNA segment and the 5’ end of another
What 3 enzymes replace RNA primers with DNA and seal the nicks?
Ligase, Polymerase 1, and Nuclease
What are the 3 major domains of DNA Pol 1?
DNA polymerase
3’–> 5’ proofreading exonuclease
5’ –> 3’ exonuclease
List the steps of DNA pol 1 sealing nicks
Pol 1 degrades RNA primers in the 5’–> 3’ direction releasing dNMPs while simultaneously extending the 3’ terminus with dNTPs in the same direction.
What is the result of DNA pol 1 on the nick movement?
The nick moves in 5’ to 3’ along DNA until all RNA is removed
Does DNA ligase work before or after POL 1?
After, Ligase seals the fragments that Pol 1 has just edited (switched dNMPs for dNTPs).
What are the 3 domains on Pol 1?
Fingers, Thumb and Palm of right-hand pronated
The 3’ to 5’ proofreading exonuclease is the wrist
What is the fingers, thumb and palm domain?
Fingers-Where dNTPs enter
Thumb-Holds the template DNA strand in place so that nucleotides can be added
Palm-Template stand lays on the palm domain which has an active site of the enzyme. The template threads through the polymerase which attaches dNTPs to the growing strand
