Term
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Definition
unwinds strands in double stranded DNA
ATP dependent
E. Coli |
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Term
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Definition
23 chromosomes
6 x 10^9 base pairs
1 error per billion base pairs |
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Term
| Single stranded binding protein |
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Definition
binds DNA with low affinity
prevents DNA strands from re-annealing
E. Coli |
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Term
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Definition
synthesis of RNA primer on leading and lagging strand, uses single stranded DNA as template
E. Coli |
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Term
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Definition
holds DNA polymerase tightly on DNA, increasing processivity of DNA replication
catalyzed by clamp loading complex
E. Coli |
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Term
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Definition
primary replicative DNA polymerase
synthesizes DNA on leading and lagging strands
extends from RNA primer
E. Coli |
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Term
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Definition
uses previous okazaki fragment as primer and degrades RNA primer ahead
fills in the gap by extending the okazaki fragment
Does not catalyze the phosphodiester bond
E. Coli |
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Term
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Definition
seals the nick between 2 Okazaki fragments
E. Coli |
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Term
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Definition
| catalyzes the unwinding of DNA and forms what is the replication fork |
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Term
| single strand binding proteins |
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Definition
| attach to each single stranded molecule to stabilize replication fork and prevent reannealing |
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Term
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Definition
| relax the supercoil of the double stranded DNA |
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Term
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Definition
end of chromosomes, a certain sequence (TTAGGG) that shortens with every replication
lagging end is lost every time because no primer on very end |
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Term
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Definition
RNA dependend DNA polymerase that adds TTAGGG to the 3' end of telomeres
prevents gene loss |
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Term
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Definition
external DNA fragment homologous to a damaged sequence in cell is incorporated
Invasion, branch migration, formation and resolution of Holiday Junction intermediate |
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Term
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Definition
Part of Homologous recombination
Rec A binds to singel stranded DNA, coating DNA to form protein DNA filament |
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Term
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Definition
Part of Homologous recombination
catalyzed by RuvA and RuvB (2 enzymes with helicase)
the cross strand moves across and adds to old DNA |
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Term
| formation and resolution of Holliday Junction |
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Definition
Part of Homologous recombination
enzymes called resolvases cleave crossing strands and are joined by ligase |
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Term
| Non homologous recombination |
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Definition
| site specific recombination where break ends are directly ligated without homologous template. There is a complete excision and replacement |
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Term
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Definition
spontaneous deamination
spontaneous depurination
oxidation by O2 species
methylation or alkylation
UV radiation crosslinks pyrimidines forms dimers |
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Term
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Definition
repair enzyme detects damaged base
base is removed by cleavage of glycosyl bond
sugar phosphate backbone is removed
repair enzyme inserts base using template
DNA ligase connects phosphodiester bond |
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Term
| nucleotide excision repair |
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Definition
repair enzyme detects damaged sequence of bases
entire nucleotide sequence is removed
sugar phosphate backbone is removed
repair enzyme inserts bases using bottoms strand template
DNA ligase connects phosphodiester bond |
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Term
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Definition
incorrect bond prevents WC bond from forming
methylation of DNA allows for determination of original base
MutS, MutH, and MutL repair |
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Term
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Definition
| protein that finds damaged site for mismatch repair |
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Term
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Definition
| protein that recognizes methylated strand and protects |
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Term
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Definition
| degrades non-methylated strand |
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Term
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Definition
| synthesis of RNA molecule involving copying of 1 strand of DNA template using WC bond |
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Term
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Definition
Eukaryotic
transcribes ribosomal RNA genes and Class I transcription factors |
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Term
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Definition
| synthesizes mRNA in nucleus |
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Term
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Definition
| transcribes for small stable RNA and tRNA |
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Term
| Prokaryotic transcription-Initiation |
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Definition
RNA polymerase binds to promoter forming closed complex
RNA polymerase holoenzyme binds tighter forming open complex. DNA is opened forming transcription bubble
promoter clearance and movement of transcription bubble |
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Term
| Prokaryotic transcription-elongation |
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Definition
RNA polymerase moves along double helix, separating strands
RNA polymerase moves 3' to 5' along template strand
5' end of transcript emerges from polymerase first |
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Term
| Prokaryotic transcription-termination |
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Definition
GC rich palindrome sequence followed by 6-7 U's
palindrome forms a hairpin that triggers termination
3' end of transcript is pulled out of RNA polymerase active site |
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Term
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Definition
| sequences of nucleotides that ell RNA polymerase where to begin |
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Term
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Definition
TATAA- located 10 base pairs upstream from transcription beginning
TTGACA 35 bp upstream from start point |
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Term
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Definition
| interact with RNA polymerase and other elements of transcription |
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Term
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Definition
can synthesize RNA but cannot recognize promoters
2 α subunits
1 β subunit
1 β’ subunit |
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Term
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Definition
contains sigma subunit
recognizes promoter
different sigmas transcribe different genes |
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Term
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Definition
| class of DNA binding protein in Euk |
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Term
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Definition
| anti TB drug that inhibits RNA polymerase |
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Term
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Definition
| poison that inhibits euk polymerase II, causes liver failure in 3-4 hours |
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Term
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Definition
| determines where on DNA a protein binds |
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Term
| DNA footprinting procedure |
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Definition
1. end label DNA with radioactive/fluorescent tag at 5' terminus
2. digest mixture with DNAase and analyze product by denaturing through degrading electrophoresis |
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Term
| Footprinting interpretation |
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Definition
one well has DNA and nuclease only, shows typical breaking bands of DNA
one well has Protein and DNA and nuclease, will show a blank spot where protein binds |
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Term
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Definition
| genes who when mutated or overexpressed cause cause carcinogenesis |
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Term
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Definition
gene that encodes small DNA binding protein
king of tumor supressors
affects cell cycle
inhibits transcription of ceratin genes
50% of cancer patients have p53 mutation |
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Term
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Definition
single copy of p53 mutant gene
predisposition to carcinoma, sarcoma, leukemia, brain tumor |
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