MB EXAM 2 Terms

Question 1

Att sites

Answer 1

attP of the phage, splits and binds to the two parts or attB of the bacteria using integrase.

Question 2

RNA polymerase 1

Answer 2

Specifically devoted to transcription of the three largest species of rRNAs, which are the 28S, 18S, and 5.8S.

Question 3

RNA polymerase III

Answer 3

Transcribes genes for
tRNAs,
rRNA (5S rRNA)
snRNAs and scRNAs

Question 4

RNA polymerase II

Answer 4

Transcribes: miRNA, and lncRNAs, mRNA

Question 5

Lytic pathway

Answer 5

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.

Question 6

Lysogenic

Answer 6

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”

Question 7

VDJ recombination

Answer 7

Occurs only in light chains, V-J-C segments.
V= variable:~250
J: joining = 4
C: constant = 1

Question 8

Prokaryotes Mature rRNAs

Answer 8

16S, 23S, 5S

Question 9

Eukaryotes Mature rRNA

Answer 9

18S, 5.8S, 28S

Question 10

Prokaryote ribosomes

Answer 10

Small SU: 30S composed of 16S plus 21 proteins

Large SU: 50S composed of 5S rRNA and 23S rRNA plus 34 proteins.

Question 11

Eukaryotes ribosomes

Answer 11

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.

Question 12

Shine-Dalgarno sequence

Answer 12

The site of initiation of translation in prokaryotes

AGGAGGU

Question 13

Drosha

Answer 13

nuclease, pri to prerRNA

Question 14

Dicer

Answer 14

Nuclease, premirRNA to miRNA duplex

Question 15

RISC miRNA induced silencing complexes

Answer 15

Two outcomes depend on binding completion.

1. If binding is complete then it results in endonucleolytic cleavage
2. If binding is incomplete then it results in translational repression or deadenylation.

Question 16

Five types of DNA damage?

Answer 16

Deamination
Depurination
Exposure to UV
Alkylation
Reaction to carcinogen

Question 17

Deamination

Answer 17

The loss of an amine group and replacing it with a ketone, by UV light or chemicals.

Question 18

Exposure to UV light

Answer 18

Results in adduction of adjacent thymine dimers into a cyclobutane ring.

Question 19

O6-methylguanine repair

Answer 19

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.

Question 20

base excision repair

Answer 20

Aka, simple mismatch

1. DNA glycosylase catalyzes the removal of the base.
2. The AP endonuclease (AP stands for Apuric or Apyrimidic site) cleaves at the AP Site.
3. The deoxyribose is removed by deoxyribosephophodiesterase, leaving a gap.
4. The gap is then filled by DNA polymerase.
5. The phosphate backbone is then regenerated by DNA ligase (ATP required).

Question 21

Repair of thymine dimers

Answer 21

1. The dimer is cleaved by a photoactivated enzyme photolyase, this removes the cyclobutane ring.
2. After removal the DNA polymerase will replace the missing deoxynucleotides.
3. There is also a generic option that can do the same thing known as NER.

Question 22

Nucleotide Excision Repair (NER)

Answer 22

Cleavage 5’ and 3’

Unwinding by helicase

Filling by DNA pol and sealing by ligase.

Question 23

NER in E. coli

Answer 23

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.

Question 24

Exinuclease

Answer 24

The protein complex that excises damaged DNA during nucleotide-excision repair in bacteria.

Question 25

NER in yeast

Answer 25

NER is also a UV-light damage repair system, and the genes are called RAD.

Question 26

NER in Mammals: mechanism

Answer 26

NER shares components with transcription machinery.

1. XP-C and hHR23B recognize DNA damage and recruit XPB, XPD, and TFII-H (Helicase activity)
2. XP-G (endonuclease) is then added, TFII-H maintains the region unwound and XPB, XPD maintain the DNA single stranded.
3. XP-A, XP-F, and ERCC1 are recruited and act as endonucleases.
4. The fragment is cleaved and released.
5. DNA poly fills the gap and DNA ligase seals the backbone.

Question 27

NER in Mammals: what does XP stand for?

Answer 27

Xeroderma Pigmentsosom

It is a skin disorder that causes sensitivity to light; myth of vampires.

Disorder was used to study discover NER in humans.