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Biochem Test 2
replication, recombination, repair, and transcription
46
Biochemistry
Undergraduate 3
11/13/2013

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Term
DNA B Helicase
Definition
unwinds strands in double stranded DNA
ATP dependent
E. Coli
Term
Human Genome
Definition
23 chromosomes
6 x 10^9 base pairs
1 error per billion base pairs
Term
Single stranded binding protein
Definition
binds DNA with low affinity
prevents DNA strands from re-annealing
E. Coli
Term
DNA G primase
Definition
synthesis of RNA primer on leading and lagging strand, uses single stranded DNA as template
E. Coli
Term
sliding clamp
Definition
holds DNA polymerase tightly on DNA, increasing processivity of DNA replication
catalyzed by clamp loading complex
E. Coli
Term
pol III
Definition
primary replicative DNA polymerase
synthesizes DNA on leading and lagging strands
extends from RNA primer
E. Coli
Term
Pol I
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
Term
DNA ligase
Definition
seals the nick between 2 Okazaki fragments
E. Coli
Term
DNA B helicase
Definition
catalyzes the unwinding of DNA and forms what is the replication fork
Term
single strand binding proteins
Definition
attach to each single stranded molecule to stabilize replication fork and prevent reannealing
Term
topoisomerases
Definition
relax the supercoil of the double stranded DNA
Term
Telomere
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
Term
telomerase
Definition
RNA dependend DNA polymerase that adds TTAGGG to the 3' end of telomeres
prevents gene loss
Term
Homologous recombination
Definition
external DNA fragment homologous to a damaged sequence in cell is incorporated
Invasion, branch migration, formation and resolution of Holiday Junction intermediate
Term
Strand Invasion
Definition
Part of Homologous recombination
Rec A binds to singel stranded DNA, coating DNA to form protein DNA filament
Term
Branch Migration
Definition
Part of Homologous recombination
catalyzed by RuvA and RuvB (2 enzymes with helicase)
the cross strand moves across and adds to old DNA
Term
formation and resolution of Holliday Junction
Definition
Part of Homologous recombination
enzymes called resolvases cleave crossing strands and are joined by ligase
Term
Non homologous recombination
Definition
site specific recombination where break ends are directly ligated without homologous template. There is a complete excision and replacement
Term
types of damage to DNA
Definition
spontaneous deamination
spontaneous depurination
oxidation by O2 species
methylation or alkylation
UV radiation crosslinks pyrimidines forms dimers
Term
base excision repair
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
Term
nucleotide excision repair
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
Term
Mismatch Repair
Definition
incorrect bond prevents WC bond from forming
methylation of DNA allows for determination of original base
MutS, MutH, and MutL repair
Term
MutS
Definition
protein that finds damaged site for mismatch repair
Term
MutH
Definition
protein that recognizes methylated strand and protects
Term
MutL
Definition
degrades non-methylated strand
Term
Transcription
Definition
synthesis of RNA molecule involving copying of 1 strand of DNA template using WC bond
Term
RNA polymerase I
Definition
Eukaryotic
transcribes ribosomal RNA genes and Class I transcription factors
Term
RNA Polymerase II
Definition
synthesizes mRNA in nucleus
Term
RNA polymerase III
Definition
transcribes for small stable RNA and tRNA
Term
Prokaryotic transcription-Initiation
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
Term
Prokaryotic transcription-elongation
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
Term
Prokaryotic transcription-termination
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
Term
Promoters
Definition
sequences of nucleotides that ell RNA polymerase where to begin
Term
consensus sequences
Definition
TATAA- located 10 base pairs upstream from transcription beginning
TTGACA 35 bp upstream from start point
Term
enhancers
Definition
interact with RNA polymerase and other elements of transcription
Term
Core RNA polymerase
Definition
can synthesize RNA but cannot recognize promoters
 2 α subunits
 1 β subunit
 1 β’ subunit
Term
Holoenzyme
Definition
contains sigma subunit
recognizes promoter
different sigmas transcribe different genes
Term
histones
Definition
class of DNA binding protein in Euk
Term
Rifampicin
Definition
anti TB drug that inhibits RNA polymerase
Term
alpha-amantin
Definition
poison that inhibits euk polymerase II, causes liver failure in 3-4 hours
Term
DNA footprinting
Definition
determines where on DNA a protein binds
Term
DNA footprinting procedure
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
Term
Footprinting interpretation
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
Term
oncogenes
Definition
genes who when mutated or overexpressed cause cause carcinogenesis
Term
p53
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
Term
Li-Fraumeni syndrome
Definition
single copy of p53 mutant gene
predisposition to carcinoma, sarcoma, leukemia, brain tumor
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