Dna Flashcards
(31 cards)
What are the three types of topoisomerases and what do they do?
Type 1- relieves torsional stress caused by negative supercoiling
Type 2- introduces negative super coils
Type 3- introduces positive super coils, mostly in Archaea
Archaea and bacteria have what kind of DNA ?
Circular
What benefit does positive supercoiling have in hyper thermophilic Archaea?
It helps prevent denaturing of DNA in extreme environments
What do type 1 topoisomerases do?
Enzyme attaches to DNA and causes a single strand break during replication
What does type 2 topoisomerases do?
GyrB and GyrA
Creates negative supercoils, causes a double stranded break, costs ATP
Occurs after replication when packing up the DNA
Can also fix positive supercoiling
How’s is eukaryotic DNA organized?
In chromatin where it is wrapped in histones
DNA + histones=nucleosome
Archaea DNA is similar
What are the basic steps of DNA replication?
- Binding of DNA-A, costs ATP
- Formation of open complex
- DNA-C is the loader that binds DNA-B
- DNA-B unwinds helix
- Primase (DNA-G) adds RNA primer
- DNA polymerase 3 binds and creates new strand
What is oriC?
Where DNA replication begins. DNA-A binds and melts DNA at the oriC
What does opening the DNA during replication do?
Allows recruitment of helicase enzymes
What are helicase s ?
DNA-G
Protein that opens up the 2 strands and two forks
One helicase per each fork
One helicase moves in each direction in front of polymerase
Recruits primase
What is primase?
DNA g
Inserts RNA primer into genome so polymerase can start on the 3’ end
What direction does replication go?
5’-3’
Polymerase can only attach to the 3’ OH
What end does polymerase add to?
To the 3’
What help repair lagging strand gaps?
RNase removes the primer
DNA polymerase 1 fills in gaps
Ligase seals nicks left in lagging strand
What are catenanes?
2 circular daughter cells bound together after replication
What happens at the Ter site?
It’s the termination site that causes polymerase and proteins to fall off
What are the major characteristics of an eukaryotic genome?
Linear
Has multiple origins of replication
Only occurs during S- phase
Once replication begins it must finish or die
What are the major characteristics of the prokaryotic genome?
No S-phase
Can have multiple strands of replication happening at the same time
Replication machinery stays stationary while chromosomes move around cell
Is bidirectional- 2 lagging strands and 2 leading strands
What does DNA polymerase 3 do?
Proof reading
Removes mismatched base from 3’ end by exonuclease activity of enzyme
How does mismatch repair work?
When a wrong base is put down, it results in a bulge
Mut S detects bulge and recruits Mut H to bind to base
Mut L binds Mut H and S together to fix bulge by methylating strand, marking it for destruction
Mut H nicks the DNA and exonucleases degrade bad strand
How does base or nucleotide excision repair work?
Is when it’s bad nucleotide, not wrong base
Enzymes bind it, clean it up, then DNA polymerase comes back to fix it
What is SOS repair?
When all else fails…DNA polymerase 3 finds damaged DNA, stalls and partially detaches to allow rec A to
Rec A- protein that binds and removes damaged sequences
Not always fixed correctly but allows replication to continue
What is the holiday junction?
A 4 way intersection after the catanase starts to separate
What is the shine dalgarno sequence?
The site where ribosomes clamp on to mRNA to initiate protein synthesis and proper alignment with the start codon
