Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Biochemistry 2015 > Gene regulation (Chapter 38) > Flashcards

Gene regulation (Chapter 38) Flashcards

1
Q

What is a Type A response?

A

Gene expression is determined by the presence of the inducing signal.
Remove the inducing signal - stops the gene expression.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What is “Type B Response”?

A

Gene expression is done for a specific time regardless of whether inducing signal is still present.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is “Type C Response”?

A

This is when an inducing signal cause a permanent “turning on” of gene expression.
Found in differentiation of tissues.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What types of genes do we have?

A
  1. inducible genes:
    • low basal transcription rates
    • activators/repressors affect their transcription rate.
  2. Constitutive genes:
    • high basal rate. called the housekeeping genes.
    • They ARE NOT subjected to gene regulation.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is Constitutive Mutation

A

This occurs when a inducible gene has a mutation which makes it a Constitutive gene.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

what are the genes found in the Lac operon and what do they code for?
(start from left to right)

A 
LacL - produces lac repressor molecule
CRE - produces CAP protein
LacZ - B-galactidase
LacY - Permease
LacA - Thiogalactoside transferylase
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What type of response do we see when the Lac Operon is exposed to Lactose?

A

Type A response.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is “Catabolite Repression” and what causes it?

A

Catabolite repression basically means that when there is a presence of glucose and lactose, glucose will always be chosen.
This is due to CAP.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is the structure of the Lac Repressor molecule?

A
  • Lacl produces Lacl repressor molecules.

- 4 subunits join to form one LacL repressor molecule.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Where does the LacL repressor molecule bind to?

Consequence of LacL binding to the region?

A

2 of it’s 4 subunits are bound to the repressor on the major groove.
When Lacl repressor bound to Operator,
it prevents the expression of LacZ,Y,A

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

1) What are Gratituous Inducers?

2) give an example?

A

1) Gratituous inducers are lactose analogs.
- They activate the lac operon but are not substrate to B-galactidase.
2) IsopropylTHIOgalactidase (IPIG)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

How does “De-repression” of the Lac Operon occur?

A
  1. LacL repressors have high affinity to Inducers.
  2. Binding to inducer, causes them to have a conformational change.
  3. Therefore they dissociate off the operator, allowing RNAP to bind to it.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What complex is needed in Lac Operon for formation of Pre-Initiation Complex?

A

CAP-cAMP

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

How does Glucose presence affect Lac Operon.

A
  • Glucose presence causes “Catabolite repression”.
  • This is because [cAMP] is low in presence of glucose because:
         - Glucose inhibits the activity of Adenyly Cyclase.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What happens when the cell is starved of Glucose?

A

Then Adenyl Cyclase is NO longer inhibited thus there can be the formation of: cAMP.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

How does CAP-cAMP complex help form the: “Pre Initiation Complex”?

A
  • CAP-cAMP binds to CRE gene (immediately upstream of the promotor).
  • part of the CAP binds to alpha subunit of RNAP.
  • These Protein-Protein interactions facilitate the binding of RNAP to Promotor.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What is “Constitutive expression of Lac Operon”?

A
  • Constitutive Expression of Lac Operon occurs when there is a mutation in the lacL gene thus no repressor molecules formed.
  • SO no repression of the lac operon.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

what type of DNA does Lambda Bacteriophage secrete into cell?

A

single dsDNA.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

In which environment does Lambda Bacteriophage:

  1. Undergo Lysogenic pathway?
  2. Undergo Lytic Cycle?
A
  1. Poor conditions

2. Good Conditions (whatever good means…)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What happens in the “Lysogenic Pathway” of Lambda Bacteriophage?

A
  1. DNA integrates into the hosts DNA, where it remains dormant
  2. A DNA Damaging Agent will induce it and it will form proteins.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What type of response is inducing dormant DNA from the lysogenic pathway to the lytic cycle?

A

It’s a Type C response.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

1) How many Base Pairs long is the “Right Operator” in the Lambda Bacteriophage?|
2) What do we find on the left and to the right?

A

1) 80

2) cI gene on the left, CRO on the right.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Which gene is expressed during Prophage?

A

CI repressor gene is expressed.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What can the “Right Operator” of Lambda Bacteriophage be separated into?

A

Or3, Or2, Or1

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What can bind to the different parts of the Right Operator of Lambda Bacteriophage?

A

both cI and cro can bind, however they have different affinities to the different cis elements.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Structure of cI repressor molecule?

A

They always form a dimer.
The N-terminal is a DNA binding protein.
The C-terminal is the Dimerisation domain.

27
Q

Explain how repression occurs in Lambda Bacteriophage?

A
  • cI binds to Or1. This inhibits CRO gene expression.
  • Then via “Co-operative Binding” encourages another cI to bind to Or2.
  • This enhances RNAP binding to cI promotor.
28
Q

What are the total effects of cI repressor molecule?

A
  • Negative Regulation of Cro.

- Positive regulation of cI (itself…)

29
Q

What happens when cI concentration is too high?

A

When cI concentration is too high it can bind to Or3 which causes it’s own inhibition however soon cI concentration falls and it releases off the Or3.

30
Q

Explain the Switch from Prophage to Lytic cycle.

A

1) DNA-damaging agents causes generation of ssDNA.
2) these activate PROTEASE recA.
3) This cleaves cI from Or1 and Or2.
4) Therefore RNAP is able to bind to the promotor of CRO.
5) Cro binds to Or3 and Or2.

31
Q

Does Cro bind co-operatively?

A

nah.

32
Q

What does occupancy of Or3 by Cro do?

A

It causes inhibition of transcription of cI repressor molecules.

33
Q

How is Protease recA formed?

What is it important for?

A

Protease recA is formed due to single stranded DNA formed due to DNA Damaging agents.

It is important for cleaving cI repressor molecules from Or1 and Or2 - thus stoping the inhibition of Cro being transcribed.

34
Q

What is the final stage of Lytic cycle?

A

When [CRO] increases so much it binds to Or1 as well.

35
Q

What is similar between cI and CRO in terms of structure?

A

both have helix-turn-helix binding motiffs.

36
Q

Histone Modification:

What causes Activation/Inactivation?

A
  • Acylation of H3, H3
  • Methylation of Histones
  • Monoubiquitalyation
  • Sumolaytion
37
Q

Histone Modification:

What causes DNA repair?

A

ADP-Ribosylation.

38
Q

Histone Modification:

What causes Hetereochromatic silencing?

A

Monoubiquitaylation

39
Q

Histone Modification:

What causes Chromosomal Assembly?

A

Acylation of Histones

40
Q

Histone Modification:

Condensation of Chromosome in cell cycle?

A

Phosphorylation of H1

41
Q

How does Histone Acylation do?

A

Causes Gene activation/inactivation.

1) It occurs on the lysine residue, causing DNA to become less positive thus has less affinity to DNA.
2) It can provide binding site for co-regulators like:
- Chromatin Remodellers

42
Q

What are:

1) Code Writers
2) Code readers?
3) Code erasers?

A

1) Code writers are enzymes that catalyse PTMS on Histones.
2) Enzymes which recognise the PTMS of histones.
3) Code erasers are enzymes that remove PTMS of histones.

43
Q

What does Methylation of 5MeC do?

A

It makes transcription of chromatin impossible.

44
Q

Where do we find that demethylation increases transcription?

A

demethylation in steroid hormone inducible genes can INCREASe transcription.

45
Q

Properties of Enhancer?

A
  • Have many binding sites.
  • Can act upstream or downstream.
  • Act on Many Promotors.
  • Work by recruiting chromatin remodelling complexes.
  • Aid binding of basal transcription machinery to cis-related promotor.
46
Q

How do we study Tissue specific expression?

A

1) We use reporter genes, which we ligate the suspected enhancer including gene.
2) Place into embryo
3) Basal expression will increase if an Enhancer is present.

47
Q

What is HRE and MRE?

A

Hormone Response Element
Metal Response Element

Adding Hormones or Metal should increase the basal expression of a gene.

48
Q

Name some DNA binding motiffs found in Regulatory factors

A
  • Helix-Turn-Helix Motiff
  • Zinc Finger
  • Leucine finger
49
Q

What characteristics are found in these DNA binding motiffs?

A
  1. They are specific to certain DNA sequences.

2. Only part of regulatory protein binds to DNA, rest site for co-repressors etc.

50
Q

What are special characteristics about:

-Leucine and HTH Motiffs?

A

They both form dimers.

They both bind to Palindromic sequences.

51
Q

Give Examples of Helix-Turn-Helix containing regulatory proteins

A

-Cro
-LacL repressor molecules
-cI
-CAP
Homeobox proteins

52
Q

Give examples of Zinc Finger containing regulatory proteins

A
  • Gal4
  • TFIIIA
  • SP1
53
Q

Give examples of Leucine Zipper containing regulatory proteins

A

GCN4

  • CRE bidning proteins
  • c-myc (ANYTHING CONTAINING MYC)
54
Q

Structure of Helix-Turn-Helix Motiffs?

A

Each Cro molecule contains:

  • 3 Antiparallel B sheets
  • 3 Alpha Helices
  • DIMERISATION occurs between the 3 Antiparallel sheets
  • Recognition surface due to Alpha helices.
55
Q

What is the structure of Leucine Zipper?

How does it work?

A

Consists of ampiphatic alpha helix with a series of hydrophobic AA concentration one side.

We find Leucine at every 7th position forming a straight line.

56
Q

What does miRNA and siRNA do in terms of regulation?

A

-Inhibit translation

cause mRNA degradation

57
Q

Where does mirRNA modulation occur?

A

miRNA modulation occurs in the P-bodies.

58
Q

What happens when miRNA-mRNA Base-pairing is perfect match?

A

-TRANSLATION INHIBITED

59
Q

What happens when miRNA-mRNA Base-pairing is not perfect match?

A

-mRNA degradation

60
Q

What do Ribonucleoproteins (RNP) do in terms of regulation?

A

Either:

  • Protect mRNA from digestion
  • Encourage nuclease attack.
61
Q

How does: Deletion of 5UTR’ affect mRNA stability

A

deletion of 5UTR’ will increase the half life of mRNA.

62
Q

How does: Shortening of Coding region affect half life?

A

Shortening the coding region will increase the half life of mRNA.

63
Q

How does: A lack of 3’tail affect

A

It causes rapid degradation of mRNA.

Biochemistry 2015 (11 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions