-
oriC
Bacterial origin of replication
-
DNA A
Melts bacterial DNA at Origin of replication
-
DNA B
bacterial DNA helicase, creates replication forks
-
DNA Pol III
Bacterial main DNA polymerase
-
DNA Pol I
Bacterial polymerase, 5-3 RNA exonuclease activity and 3-5 proofreading activity
-
ORC
6 protein complex, recognises eukaryotic origins of replication and recruits DNA helicase
-
MCM
eukaryotic helicase for replication, 6 subunits
-
Cdc6, Cdt1
Licensing factors for ORC to recruit MCM (2)
-
Dna C
Bacterial protein, helps load helicase to origin
-
RPA
Single stranded binding protein in eukaryotic cells
-
DNA Pol alpha, delta, epsilon
Eukaryotic DNA polymerases
-
PCNA
Sliding clamp in eukaryotic cells
-
RFC
Eukaryotic clamp loader
-
gamma-complex
bacterial clamp loader
-
ATP dependent DNA ligase
eukaryotic DNA ligase
-
NAD dependent DNA ligase
bacterial DNA ligase
-
RNaseH
eukaryotic: removes primer of RNA paired to DNA, leaving small flap
-
Fen1
Cuts off flap of primer in eukaryotic cells
-
Topoisomerase
Untangles DNA during replication. Type I cuts a single strand, Type II cuts a duplex, passing one under the other so positive supercoiling is reduced.
-
Etoposide, doxorubicin
Inhibit topoisomerase II (2)
-
camptothecin
inhibits toposomerase I
-
Heterochromatin
Densely packed DNA, not transcribed, replicated late is S phase, no meiotic recombination
-
Euchromatin
transcribed DNA - not as tightly packed
-
Barr bodies
Inactivated X chromosomes, seen at side of cell
-
Telomerase
self-templating reverse transcriptase (protein and RNA template components)
-
Hayflick's limit
the amount of times somatic cells (20-30), depending on the length of their telomeres
-
T loop
structure at end of telomere, protects from recombination/degradation/end-to-end fusion
-
TTAGGG
Repeating unit (About 1000 times) in telomeres
-
Retrotransposons
Transposition via RNA. Can be conserative of replicative
-
Transposase
Enzyme that moves transposons around the genome
-
RAG recombinases
recombination activation gene - mediate antibody diversity
-
4 types of mobile genetic elements
- - LINEs (long interspersed nuclear elements)
- - SINEs (short ...) (inc Alu!)
- - Retrovirus like elements
- - DNA transposon fossils
-
4 classes of repetitive sequences
- - 3% Simple sequence repeats, <100bp, CACACACACACA
- - 5% Segmental duplications, 10-300kb
- - 45% Transposon-derived repeats
- - Inactive copies of partially retrotransposed cellular genes
-
EcoRV
Restriction endonuclease, makes blunt ended DNA molecules
-
EcoRI
Restriction endonuclease, makes sticky ended DNA molecules (--TTAA)
-
Dye used in Southern Blotting, intercalates between DNA
ethidium bromide
-
PCR temperatures
- - >90 degrees: melting
- - 55-60 degrees: annealing primers
- -72 degrees: extending
-
FISH
fluorescent in situ hybridisation - can look for chromosomal rearrangements, gene copy number in cancer cells
-
Transition
Purine swapped for purine, or pyrimidine swapped for pyrimidine
-
Transversion
Purine swapped for pyrimidine or vice versa
-
5 types of DNA replication errors
- - Base mismatches
- - Deletions
- - Insertions
- - Incomplete replication
- - Breaks
-
3 types of single strand DNA break repair
- - Base excision repair
- - Nucleotide excision repair
- - Mismatch repair
-
3 examples of base excision repair
- Cyclobutyl ring: UV causes dimersation of two Ts, (obstructs replication/transcription) DNA photolyase photoreactivates it back
- Tautomeric shift cytosine -> uracil: via spontaneous deamination/nitrite treatment - Uracil DNA glycosylase (UDG) cleaves the U, nuclease (AP endonuclease (bac)/pol beta (humans)) cleaves backbone, DNA pol (1/beta) fills in gap
- 8-oxoG: flipped, and recognised as T (specific DNA glycosylase removes 8-oxoG)
-
Example of nucleotide excision repair
UV induced thymidine dimer (eukaryote): DNA unwound around lesion, strand cut up/down stream, gap filled by DNA pol and sealed by DNA ligase
-
2 types of nucleotide excision repair
- Global genomic NER
- Transcription coupled repair: RNA pol II holoenzyme (transcribed genes repaired faster)
-
Mismatch repair detection pro/eukaryotic
- Prokaryotic: hemimethylated strand
- Eukaryotic: use nicks
-
2 types of double strand repair
- NHEJ: direct rejoining of ends, low fidelity - can lose DNA. Important in resting, G1 and G0.
- Homologous recombination: uses sister chromatid to find matching sequences. Also used to restart stalled/broken DNA replication forks. Also for gene targeting in embryonic stem cells.
-
RecA (bacteria), RAD51 (eukaryotes)
Recognise single stranded 3' end in HR, scans genome for identical strands and directs strand invasion. Eukaryotic/prokaryotic forms.
-
RuvAB
Facilitates Holliday junction branch migration in bacteria
-
VDJ recombination
antibody diversity generation, using HR. diversity increased by enzymes eg terminal transderase (adds extra nucleotides at junction point... sloppily)
|
|