Term
| Mismatch Repair (enzymes needed) E.Coli |
|
Definition
MutH MutL (key protein) MutS (key protein) DAM Exonucleases Corrects spontaneous replication errors, mistmatches and 1 to 3 base insertions and deletions. It also deals with some bases mispaired due to the presence of lesions in DNA |
|
|
Term
|
Definition
| Endonuclease that specifically recognizes GATC sequences cutting only the strand containing the unmethylated A (INITIATES REMOVAL OF CUTTING OF THE BASE) |
|
|
Term
|
Definition
| Function unclear, interacts with MutS and is required for mismatch repair |
|
|
Term
|
Definition
| recognition of mismatches in DNA (triggers MutL and MutH) |
|
|
Term
|
Definition
| DNA adenine mehtylase, methylates A to produce N6-methyl-A which directs mismatch repair to the newly synthesized DNA strand |
|
|
Term
|
Definition
between the G and A of teh GATC sequence and ONLY if A is unmethylated It cuts nearest GATC on either side of mismatch |
|
|
Term
|
Definition
| cuts in the 5'--> 3' direction |
|
|
Term
|
Definition
| cuts in the 3'--5' direction |
|
|
Term
|
Definition
| requences cut and seals up the nick |
|
|
Term
|
Definition
| Chemical change that occurs in DNA resulting in a chemically modified base, sugar, or phosphate |
|
|
Term
|
Definition
| change in DNA sequence (bases are chemically normal, but 1 or more bases are different sequence from that of wild type). Single base change, deletion, insertion, etc. |
|
|
Term
|
Definition
| intact backbone, deoxyribose is present, but base is missing |
|
|
Term
|
Definition
| Break in DNA backbone, no missing base or sugar |
|
|
Term
|
Definition
| break in DNA backbone, one or more missing bases |
|
|
Term
|
Definition
Error prone DNA polymerases are recruited to DNA damage sites and complete replication at the expense of increased mutageneis. (read with lower fidelity and have a higher frequency of making a mutation) prokaryotes-SOS system Eukaryotes-14 polymerases |
|
|
Term
|
Definition
| photolyase activated by blue light (300-500nm) fixes the double bond that was created between bases |
|
|
Term
|
Definition
graph 1- shows that uvrA and recA are doing two separate thigns to repair UV repair graph 2- recA seems to be responsible in tolerance of dimers uvrA is used to remove the dimers |
|
|
Term
Nucleotide Excision Repair (e.coli) |
|
Definition
- uvrA recognizes BEND in DNA (not just islolated to dimerization)
- uvrB and uvrC are recuruited and then uvrA leaves
- uvrB and uvrC cleaves 7bp upstream and 4bp downstream from damaged site
- uvrB and C recruit uvrD
- uvrD(helicase) unwinds DNA
- pol I will resynthesize DNA (only pol I works with this system)
- DNA ligase seals this up
|
|
|
Term
Nucleotide Excision Repair (eukaryotic system) |
|
Definition
- XPC/hHR23B binds to lesion
- DDB1 and DDB2 bind to XPC
- XPA comes in and fits itself into unpaired region
- XPA recruits TFIIH (a 10 protein transcription factor complex) recruits XPB and XPD
- RPA is a single DNA binding protein that binds to one side
- XPB and XPD (helicases) open up region for polymerase
- XPG gets recruited. This is the key scaffolding onto which other proteins are built upon.
- XPG recruits XPF(uvrC equivalent).Then XPG makes a cut on 3' site and XPF makes a cut on 5' site
- All of the complex workers together and is replaced by the polarization of pol gamma/epsilon, RFC, and PCNA which work toegether to replace the piece of DNA
- Ligase I lagates the nick at the end
- Ligase I leaves
|
|
|
Term
Pulse labeling experiment (how does it work) [image] [image] |
|
Definition
- The alkaline sucrose separates the strands
- 3-thymidine is inserted into DNA
- in the wns graph of fig 1, the DNA that is synthesized after UV damage is synthesized in short pieces
- in the second graph of fig 2, the recA has ligated all the strands therefore you see a longer piece of labeled DNA strands
|
|
|
Term
Recombinational Repair (correction of the dimerization of two base pairs) |
|
Definition
[image] afterwards there is translesion synthesis |
|
|
Term
|
Definition
replication occurs over area which has damaged DNA by POL V pol V is known to cause mutations due to its inability to read the proper DNA sequences and insert random DNA bases to fill in the gap; therefore, the repair mechanism is mutagenic |
|
|
Term
|
Definition
- Glycosolase is used to clase base ou, leaving sugar, phosphate and ribose intact
- AP endonuclease cuts backbone of 3' site
- Polymerase and ligase repair and seal strand
|
|
|
Term
| Features of DNA Glycosylase |
|
Definition
low MW proteins no co-factor hydrolyze glycoslyic bond flip base our of helix and into active site there are two types - monofunctional glycosylase
- bifunctional glycosylase, which is able to do:
- beta elimination-cleaves backbone onone site and AP endonuclease cleaves other site
- beta delta elimination-cleaves off both ends
|
|
|
Term
|
Definition
- Can do glycosylas, AP endonuclease, pol and ligase OR
- XRC, PCNA, pol δ/ε, etc.
|
|
|
Term
|
Definition
Ada is a protein which is thought to act by flipping out the base, THEN removing the methyl group ADA transfers OH to methyl group which is then too unstable to be on the base and comes off thereby repairing the methylated DNA.
[image] |
|
|
Term
| Transcription Coupled Repair |
|
Definition
RNAP, when stalled at a lesion, recruits repair enzymes in the case of NER, - Mfd stalls RNA pol
- then kicks off hte RNA pol
- uvrA is recruited and this process occurs
|
|
|
Term
Transcription Repair (NER) in Eukaryotes |
|
Definition
- RNAP is stalled by CSB
- all the NER proteins are recruited EXCEPT recognition protein
|
|
|
