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Molecular Genetics > MCB Final > Flashcards

MCB Final Flashcards

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1
Q

Lytic Phase Definition

A

the phage makes more phage and kills its host cell

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2
Q

Lysogenic Phase Definition

A

the phage establishes a parasitic relationship with its host cell and does not kill its host

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3
Q

Prophage Definition

A

Phage DNA integrated into host genome

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4
Q

Lysogen Definition

A

Bacterium with integrated phage DNA

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5
Q

Is lysogeny reversible?

A

Yes

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6
Q

4 stages of lysogenic phase

A
  1. Commitment
  2. Integration to host chromosome
  3. Maintenance of lysogeny
  4. Exit from lysogeny (to lytic state)
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7
Q

What are the 3 transcriptional regulatory proteins?

A

Cl, Cll, Cro

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8
Q

Cl Repressor does what?

A
  • Represses expression of lytic genes (including cro)
  • Tanscriptional activator
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9
Q

PRM stands for what?

A

Promoter for repressor maintenance

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10
Q

PR stands for what?

A

Rightward promoter

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11
Q

Cl affinity binding order?

A

OR1 > OR2 or OR3

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12
Q

What happens when Cl binds?

A

Binding of Cl to OR1, OR2, OL1, OL2 blocks RNAP from binding @ PL and PR so NO TRANSCRIPTION OF LYTIC GENES OCCURS (INCLUDING CRO)

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13
Q

Are PL and PR weak promoters?

A

No, they are strong

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14
Q

Expression from PR and PL creates Cro and Cll and they race. What happens if Cll wins?

A

Cl gets made and represses LYTIC functions (including cro) ; it goes lysogenic

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15
Q

Cll Characteristics

A
  • activator of Cl
  • 97 AAs, unstable
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16
Q

How does Cll bind?

A

Binds to Cll binding site near PRE and recruits RNAP to transcribe Cl

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17
Q

PRE stands for

A

Promoter for repressor establishment

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18
Q

Is PRE a weak promoter?

A

Yes

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19
Q

Expression from PR and PL creates Cro and Cll and they race. What happens if Cro wins?

A

Cl is not made, lytic functions get repressed ; it goes lytic

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20
Q

Cro Characteristics

A
  • repressor of Cl gene
  • HTH Motif
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21
Q

Cro affinity binding order?

A

OR3 > OR1 or OR2

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22
Q

Where does Cro bind?

A

Cro binds to OR3 which blocks RNAP from binding at PRM so Cl is NOT transcribed

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23
Q

What factors influence the race?

A
  • The stability of Cll
  • Nutrient availability
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24
Q

When nutrients are abundant and the cells are growing well, lambda tends to go?

A

Lytic
- lots of bacteria present, low MOI, FtsH degrades Cll and keeps it at low levels

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25
Q

MOI meaning

A

the number of phage infecting a bacterial cell

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26
Q

When nutrients are low and the cells are not growing well, lambda tends to go?

A

Lysogenic
- little bacteria present, high MOI, too much Cll for FtsH to degrade

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27
Q

For integration into the host chromosome to occur, Site- specific recombination needs to occur between

A

attP and attB ; requires Int and IHF

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28
Q

Cll activates transcription from PRE and PI which makes

A

Integrase

28
Q

Potential problem with maintaining lysogeny (doesn’t actually happen)

A
  • as cell grows Cl repressor dilutes and if its too diluted it cannot repress lytic genes/cro so the phage will go lytic
29
Q

How is Cl maintained in lysogeny?

A

When bound to OR1/OR2 it activates its own gene expression at PRM

30
Q

What is prophage induction?

A

Switch from lysogenic to lytic state

31
Q

What is prophage induction triggered by?

A
  • DNA Damage
  • Spontaneity
32
Q

What happens in prophage induction?

A
  • Overcome repression by Cl
  • Expression of Cro to repress Cl synthesis
  • Excision of DNA from chromosome
  • Expression of lytic functions
33
Q

How does lambda exit lysogeny?

A

RecA senses DNA damage to make RecA filaments that activate autoproteolytic activity of Cl

34
Q

What happens when Cl gets cleaved when exiting from lysogeny?

A

It binds to operators with lower affinity and it no longer represses which allows RNAP to transcribe @ PR and PL

35
Q

Lambda negative control is done by

A

Cl and Cro

36
Q

Lambda positive control is done by

A

Cl and Cll

37
Q

Lambda cooperativity is done by

A

Cl monomers, dimers, and tetramers

38
Q

Lambda Autoproteolysis is stimulated by

A

RecA*

39
Q

Lambda protein stability and targeted degradation is done by

A

Cll and FtsH

40
Q

Two mechanisms of activation in eukaryotes

A
  1. Nucleosome remodeling
  2. Recruitment of RNA polymerase
41
Q

Examples of activation by recruitment of RNAP

A
  • Gal activation system in yeast
  • CREB system
  • Hormone response system
42
Q

In Gal activation, expression of the gal genes requires

A

Gal4 which forms dimers that bind to UAS sequence

43
Q

What are the roles that the Gal4 transcription factor plays

A
  1. When it binds to UAS it induces chromatin remodeling to insure GAL1 promoter is exposed
  2. Recruits transcriptional machinery to the exposed promoter
44
Q

Gal4 purpose

A

Transcriptional activator

45
Q

Gal80 purpose

A

Anti-activator, binds Gal4

46
Q

Gal3 purpose

A

Anti-activator, binds Gal80

47
Q

What senses galactose?

A

Gal3

48
Q

What happens when Gal3 binds galactose?

A

Gal3-galactose binds Gal80 and causes it to be released from Gal4

49
Q

Phosphorylation of a protein occurs on

A

Serine, threonine, tyrosine, or histidine residues

50
Q

Components of ligand binding hormone systems

A
  1. Hormone receptor
  2. Hormone response element
51
Q

Mechanisms of ligand binding hormone systems

A
  1. Hormone activates receptor in the cytoplasm
  2. Hormone activates receptor in the nucleus
52
Q

In prokaryotes, negative control directly blcoks RNAP from binding via

A

Occlusion

53
Q

Inactivation of a female X chromosome involves

A

hypermethylation of its DNA and hypoacetylation of its histones. The inactivated chromosome condenses into heterochromatin (barr body)

54
Q

Combinatorial control

A

More than one signal controls expression of a given gene. The more activators that bind, the greater the transcription

55
Q

Splicing with alternate promoter results

A

Proteins with different N-terminal sequences

56
Q

Splicing with alternate polyadenylation sites results

A

Proteins with different C-terminal sequences

57
Q

Splicing with intron retaining mode results

A

Retain intron in some transcripts

58
Q

Splicing with exon cassette mode results

A

Internal deletion or insertion in protein

59
Q

When iron is low, Tfr mRNA is

A

stable and translated

60
Q

When iron is high, Tfr mRNA is

A

unstable and degraded

61
Q

Iron Response Protein (IRP) is aconitase which is

A

an iron-containing enzyme

62
Q

RNA Interference (RNAi) is a mechanism involved in what two processes?

A
  1. protecting cells from drRNA viruses
  2. regulating gene expression
63
Q

dsRNA triggers RNAi. Where does the dsRNA come from?

A
  • dsRNA virus
  • microRNA genes
  • transgenes (inadvertent, planned antisense)
64
Q

What is antisense RNA?

A

An RNA complementary to an mRNA

65
Q

Antigen definition

A

Foreign substances recognized by the body as being different

66
Q

VDJ Recombination DNA Sites

A
  • Recombination Signal Sequences (RSS)
  • Found next to V,D, and J segments
  • Bind recombinase
67
Q

VDJ Recombination Protein Factors

A
  • RAG1/RAG2 (recombination activating gene)
  • HMG (DNA bending protein)

Molecular Genetics (4 decks)

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