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Biochemistry and molecular science > Module 11 > Flashcards

Module 11 Flashcards

gene regulation

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Biology 101 flashcards
1
Q

The lowest level of chromosome organisation in a eukaryotic chromosome

A

nucleosome

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2
Q

A core nucleosome is composed of

A

two copies each of histone H2A, H2B, H3 and H4

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3
Q

An activator which positively regulates the expression of one or more genes

A

DNA-binding protein, transcription rates increase when an activator is bound to the DNA

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4
Q

Repressor proteins

A

Impede access of RNA polymerase to the promoter

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5
Q

The name of the major eukaryotic coactivator consisting of 20 or more polypeptides

A

mediator

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6
Q

When a regulatory protein represses transcription at specific promoters

A

Negative regulation

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7
Q

The role of an enhancer in eukaryotic gene transcription is to

A

Facilitate the expression of a given gene

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8
Q

What is underwound

A

lesser wound and it is strained

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9
Q

What happens when its underwound,

A

supercoil forms

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10
Q

What is type I topoisomerase purpose

A

Cut one strand and turn it to another side, phospahte bind to Tyr in the topoisomerase. covalent linkage, connected with no errors

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11
Q

What is type II topoisomerase

A

Holding two double stranded DNA, two monomer cutting the C gate and pass it through the other strand.

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12
Q

When does sister chromosome appear

A

metaphase

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13
Q

What does chromatin contain

A

1/3 DNA, 2/3 protein by mass

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14
Q

How many protein are in the histones

A

8

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15
Q

How many types are there in histones

A

5

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16
Q

Where is histone H1

A

outside, act as a clip to stabilise it

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17
Q

What are amino tails

A

from histones, allow the tail to interact with each other. binds to enzyme easier to modify and regulate them

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18
Q

Where does modification occur

A

histone tails and in the body of the histones

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19
Q

How is it modified

A

structure and packing of the chromatin

access to the DNA of DNA binding proteins

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20
Q

What does histone acetylation do

A

regulates chromatin condensation, wind by histones deacetylases and unwind by histone acetyl transferases HAT(decondensed chromatin)

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21
Q

What is chromatin remodlling

A

change section of chromatin for it to move around more. can remove histone, change histone variants, covalent modification of histones(by enzyme) change the accessibility of the DNA

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22
Q

How histone are read

A

scaffold protein, protein complex with catalytic activities and additional binding site to change the histones usage(modification.

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23
Q

What are the use of histone modification

A

Silencing genes, change expression, dna repair

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24
Q

When was chromatin more condensed

A

In mitosis

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25
Q

What are the stages of compaction

A

First level: when being transcript. 7 fold compaction

SEcond level: 30nm fibre, solenoid model, nucleosome are attach to one histone each, inaccessible DNA, cannot be transcripted.

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26
Q

What control the lose dna

A

chromosomal scaffold, loop 30nm fibre around the scaffold. may be transcript.

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27
Q

Are the grenes controlled?

A

yes

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28
Q

What can dna by transcript more easily

A

moving genes to another region, different nuclear neighbourhood. looped into an active region

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29
Q

What is one way to modify DNA

A

DNA methylation in eukaryotes(adding methyl group), it does not have effect of base pairing. when there is a CG dinucleotides. can be methylated on both strands

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30
Q

What is CpG islands

A

CpG change the way it interacts. a group of GC methylation. large sequences. Found in promoters to regulate transcription

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31
Q

Waht is one use of methylation

A

represses the expression of a gene

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32
Q

What is the use of DNA methyltransferases

A

to shutdown the expression of a gene

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33
Q

What happens when the new strand of the replicated ones dont not have CpG

A

maintenance DNa methyltransferases is used to methylate the new strand

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34
Q

What does epigenetic changes

A

no changes to DNA sequence
Are maintained in the cell but can by altered by signals.
Inherited from cell to cell
switches gene on or off
aceytlation in the histone tails and methylation of the cytosine
Does not change the bases

35
Q

What direction does the outer ring of the E. coli genome go

A

Clockwise

36
Q

What direction does the inner ring of the E. coli genome go

A

anti-clockwise

37
Q

How are genes regulated

A

using UP element and other regions

38
Q

Why must the genes be regulated

A

Does not have to express all the genes

39
Q

What are transcription factors

A

elements(sequences in the gene), repress transcription or activates them.

40
Q

How are bacterial genes being controlled together

A

operons( not in out genome)

41
Q

How are operans operated

A

transcript multiple genes together as a unit

42
Q

what is trp operon

A

to produce tryptophan,gaps are start and stop codons.

43
Q

What happens when there is trp

A

cause repressor to active, block the transcription from making trp

44
Q

what produces Lac repressor

A

LacI, made in a active state

45
Q

What is Lac operon for

A

when there is no lactose, the active Lac repressor will stop Lac operons from producing

When there is lactose present, aldolactose will bind to the repressor, this will produce the gene.

46
Q

What is B-galactosidase for

A

to form glucose as a energy source

47
Q

What is the difference between trp operon and lac operon

A

With both have corepressor bound, trp will stop gene expression, while allolactose will express the gene. Both negative regulation

48
Q

What does the operator sequence do

A

3 operators, palindrome.

49
Q

How is Lac repressor bound

A

it binds as a dimer, work together as a tetremer. forms a loop, prevent polymerase to transcript

50
Q

How many regulators are there for a single gene

A

multiple

51
Q

How are gene activation like

A

synergistic, works together and does more transcription when lack of operon

52
Q

Why is glucose a good energy source

A

does not take a lot of energy to breakdown compared to lactose. it will prioritise glucose first.

53
Q

How does E. Coli use glucose first

A

when low glucose, there will be low ATP, cAMP increase, binds to CAP to activate it. binds to promoter of the lac operon to use lactose pathway. CAP overwrite lac operon

54
Q

What are the 4 situations for cAMP production for prokaryote

A

When glucose high, cAMP is low, low level of gene expression when lactose is present. (no expression when lactose is absent)
When Glucose is low, cAMP high, high level of gene expression when Lac is present(none when lactose are not present)

55
Q

How does cells change in the eukaryotic cell of the same DNA

A

difference in the regulation of the gene

56
Q

What are the difference between eukaryotic and prokaryotic gene regulation

A

• Separation of transcription and translation
• Chromatin can block RNA polymerase access
• Basal transcription is low (eukaryote)
• Majority of regulation is positive, not negative
• There are more proteins involved in transcriptional regulation
• There are more transcription factors that control each gene
– on average 6 binding sites, but could be many more
- Combinatorial control

mostly are regulated in eukaryotic cell

57
Q

What are the chromatin regulation

A

Methylation of DNA (prevent expression)

Histone acetylation ( allow transcription factors to bind and genes to expressed)

58
Q

How eukaryotic transcriptional regulation work

A

+1 onwards are transcripted

regulatory element- DNA sequence that transcription factors bind to

Repressors bind to sequences called silencer

Activators find to sequence called enchancer or enhancer element

very regular

59
Q

What is regulatory element

A

DNA sequence that transcription factors bind to

60
Q

What is the use of an enhancer

A

it is where the activator is going to bind

61
Q

How do you change the structure of the chromotin

A

Histone modification/ nucleosome remodelling complexes

62
Q

What is the use of a mediator

A

It mediates between activators and the general transcription factor, facilitates binding of TBP, TFIIB. Makes transcription initiate.

63
Q

What is the downstream of the gene

A

further region of the coding strand

64
Q

Are shape of the dna constant

A

no

65
Q

What is the major and minor groove

A

The large gaps and smaller gaps of the DNA, to bind to transcription factor.

66
Q

What does the major grove do

A

DNA-binding protein will be able to bind to the DNA sequence without affecting the sequence

67
Q

What are the features of eukaryotic transcription factors

A
  • Transcription factors are usually made up of several domains
  • There is only a small number of possible DNA binding domains
  • Most Transcription Factors exist in large gene families
68
Q

What is an example of a DNA binding domain

A

Helix-loop-Helix, it is a dimer(most do)

69
Q

What is the use of Max

A

involved in cell growth and division

70
Q

What can be formed in transcription factor

A

heterodimers(MYCMAX)

71
Q

What is the use of the MYC MAX

A

involve in cell growth, activates, open chromatin for transcription

72
Q

What is the use of MADMAX

A

repressed, not expressed, differentiation

73
Q

What are the eukaryotic transcription factors like

A

Modular, members of the TF family can homo-dimerise or heterodimerise, control by the binding of many TF(combinarial control

74
Q

How can there be so many protein produced

A

By alternative splicing, different protein produced from one gene

75
Q

How does cell produce differennt mRNA

A

regulated for splicing repressor(harder for the splicing machinery from detecting)

Or Splicing activator to promote splicing

76
Q

What is gene expression serparated into

A

1 Transcription initiation (how much)

2 post transcriptional precessing(how it is processed)

3 RNA stability (where does it go)

4 translational regulation (How it is translated)

5 Protein modification(how much is need to modify)

6 protein transport (where it is transported

7 Protein degradation (how long it should stay for)

77
Q

How is transcription initiation regulated

A

by micro RNA (mi RNA)

78
Q

where are mi RNA form

A

in the genes(multiple of them)

79
Q

How is mi RNA formed

A

transported out to cytoplasm from nucleus, one will be removed.if mRNA is same as mi RNA, it will be broken down and destroy the RNA. If is it different, it will be repressed

80
Q

What may be ask about a gene

A
  1. What cell types express gene1?
  2. Under what conditions do these cells express gene1?
  3. What can change or control the expression of gene1?
81
Q

How to find whether a experiemtn is consistent

A

QRT-PCR

82
Q

How is QRT-PCR done

A

extract RNA, get only mRNA, treat it with DNase, Run RT reaction, generate c-DNA. Run PCR, add it into a quantitative machine using light detection

83
Q

How does QRT-PCR work

A

find the midpoint of the cycle graph. set a level and measure the number of cycle to reach the threshold. Or use a probe that base pair that are needed to be bind to, detect the florescent when the probe is bound.

Biochemistry and molecular science (12 decks)

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