MB EXAM 2 Terms Flashcards
Att sites
attP of the phage, splits and binds to the two parts or attB of the bacteria using integrase.
RNA polymerase 1
Specifically devoted to transcription of the three largest species of rRNAs, which are the 28S, 18S, and 5.8S.
RNA polymerase III
Transcribes genes for
tRNAs,
rRNA (5S rRNA)
snRNAs and scRNAs
RNA polymerase II
Transcribes: miRNA, and lncRNAs, mRNA
Lytic pathway
Lytic = propogation
Where the phage gets its DNA replicated using bacterial proteins and then the DNA is packaged into new virus particles. The bacteria is then lyzed and the new viruses will be released to go and infect other bacteria.
Lysogenic
Lysogenic =
The DNA from the bacteriophage lambda gets recombined with the bacterial DNA (integration). This event occurs at specific sites called ATT sites. Requires the phage encode enzyme “Integrase”
VDJ recombination
Occurs only in light chains, V-J-C segments.
V= variable:~250
J: joining = 4
C: constant = 1
Prokaryotes Mature rRNAs
16S, 23S, 5S
Eukaryotes Mature rRNA
18S, 5.8S, 28S
Prokaryote ribosomes
Small SU: 30S composed of 16S plus 21 proteins
Large SU: 50S composed of 5S rRNA and 23S rRNA plus 34 proteins.
Eukaryotes ribosomes
Small SU (40S) composed of 18S rRNA plus about 30 proteins Large SU (60S) 28S, 5.8S and 5S rRNA plus ~45 proteins when combined from the 80S ribosome.
Shine-Dalgarno sequence
The site of initiation of translation in prokaryotes
AGGAGGU
Drosha
nuclease, pri to prerRNA
Dicer
Nuclease, premirRNA to miRNA duplex
RISC miRNA induced silencing complexes
Two outcomes depend on binding completion.
- If binding is complete then it results in endonucleolytic cleavage
- If binding is incomplete then it results in translational repression or deadenylation.
Five types of DNA damage?
Deamination Depurination Exposure to UV Alkylation Reaction to carcinogen
Deamination
The loss of an amine group and replacing it with a ketone, by UV light or chemicals.
Exposure to UV light
Results in adduction of adjacent thymine dimers into a cyclobutane ring.
O6-methylguanine repair
Removal of CH3 from C6 is catalyzed by the enzyme 6 methylguanine methyltransferase.
CH3 group is transferred to a cysteine which becomes a methyl cysteine.
base excision repair
Aka, simple mismatch
- DNA glycosylase catalyzes the removal of the base.
- The AP endonuclease (AP stands for Apuric or Apyrimidic site) cleaves at the AP Site.
- The deoxyribose is removed by deoxyribosephophodiesterase, leaving a gap.
- The gap is then filled by DNA polymerase.
- The phosphate backbone is then regenerated by DNA ligase (ATP required).
Repair of thymine dimers
- The dimer is cleaved by a photoactivated enzyme photolyase, this removes the cyclobutane ring.
- After removal the DNA polymerase will replace the missing deoxynucleotides.
- There is also a generic option that can do the same thing known as NER.
Nucleotide Excision Repair (NER)
Cleavage 5’ and 3’
Unwinding by helicase
Filling by DNA pol and sealing by ligase.
NER in E. coli
uvrA, B and c are linked to light sensitivity to UV light.
uvrA recognizes damaged DNA and then recruits uvrB and C then cleave.
uvrA, B and c complex is known as exinuclease.
Exinuclease
The protein complex that excises damaged DNA during nucleotide-excision repair in bacteria.
