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BI304 Molecular Biology > Lecture 13 and 14 Transcriptional regulation of gene expression. > Flashcards

Lecture 13 and 14 Transcriptional regulation of gene expression. Flashcards

1
Q

Every cell in the body contains the same set of chromosomes, i.e. the same genetic material.
So, what makes a hepatocyte different from a fibroblast, different from a lymphocyte

A

They regulate the expression of their genes

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2
Q

Different genes have different expression levels depending on what?

A

cell type and on environmental conditions

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3
Q

DNA is essentially a storage molecule that contains

A

all of the instructions a cell needs to sustain itself.

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4
Q

What step Is the information in DNA is decoded in

A

transcription

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5
Q

what are genes

A

genes are sections of DNA made up of specific sequences of nucleotides, that give instructions to the cell.

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6
Q

in order to implement these instruction in the genes what has to occur?

A

The instructions stored within DNA are read and processed by a cell in two steps: transcription and translation

The instructions contained within genes must be expressed, or copied into a form that can be used by cells to produce the proteins needed to support life.

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7
Q

What is the specific type of RNA that carries the information stored in DNA to other areas of the cell called?

A

Messenger RNA (mRNA)

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8
Q

in transcription how is an RNA molecule created

A

During transcription, a portion of the cell’s DNA serves as a template for creation of an RNA molecule.

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9
Q

what causes regulation in the expression levels in the steps from transcription of the gene to translation of the mRNA

A

developmental and environmental signals.

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10
Q

How is transcription catalysed by RNA Polymerase?

A
  • RNA polymerase moves along the gene and generates a complementary RNA strand to the DNA template strand.
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11
Q

Prokaryotic RNA polymerase

A
  • Only one RNA polymerase for all genes.
  • Guided to promoters by associated sigma factor, which makes contact with the nucleotide bases in the promoter region.
  • Different prokaryotic genes have promoters that differ in strength (based on nucleotide sequence).
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12
Q

How do bacteria respond to such variations in their environment?

A

Alter their gene expression pattern;
- express different enzymes depending on the carbon sources and other nutrients available to them.
- E.g. wasteful to synthesise, lactose metabolising enzymes in the absence of lactose. BUT when lactose is the only available carbon source, bacteria must quickly induce lactose-metabolizing enzymes, or else they will die.

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13
Q

In bacteria, where Is this genetic regulation mediated?

A

At the level of transcription.

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14
Q

What is an operon?

A

Gene clusters of metabolic genes that are coordinately transcribed.

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15
Q

What is the regulation of metabolic genes in bacteria dependent on?

A

Availability of nutrient sources

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16
Q

Expression of the gene clusters is controlled by..

A

an operator region embedded into the promoter.

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17
Q

How is transcription enhanced?

A

binding of activatory factors to the promoter

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18
Q

How can transcription be blocked?

A

Binding of repressor proteins to the operator which blocks RNA polymerase access.

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19
Q

What are genes in clusters transcribed as?

A

single polycistronic mRNA molecule.

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20
Q

Polycistronic mRNA molecule.

A

An mRNA that encodes multiple genes whose expression is also controlled by a single promoter and a
single terminator.

Polycistronic mRNAs are also called operons.

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21
Q

Are eukaryotic mRNAs Polycistronic or Monocistronic?

A

Monocistronic

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22
Q

why does E.coli use lactose at times?

A

E.coli prefer to metabolise glucose and will only switch to lactose in the absence of glucose

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23
Q

What are the functions of the genes in the lac operon (E.coli)?

A

The lac operon contains genes that regulate the metabolic breakdown of lactose.

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24
Q

How does lactose promote transcription

A

lactose binds to the lac repressor protein and induces a conformation change, which makes it unable to bind to the operator. Thus transcription can occur.

25
Q

How is the expression of the lac operon genes also controlled by glucose.

A

E.coli prefers to metabolise glucose, so there is no transcription of the lac genes.
When glucose is absent, cAMP levels in the cell rise and binds to the CAP, enabling it to bind to the lac promoter.
CAP then enhancing recruitment of RNA polymerase on the promoter promoting transcription.

26
Q

what are the positive and negative regulators of the lac operon (E.coli)?

A

CAP is a positive regulator (activated by absence of glucose).
Lac repressor is a negative regulator (inactivated by presence of lactose).

27
Q

what Is the tryptophan operon (E.coli)

A

A gene cluster containing five genes that encode proteins involved in tryptophan biosynthesis.

28
Q

where is tryptophan found?

A

tryptophan is abundant in the environment and it is imported into the E.coli cells

29
Q

What effect does tryptophan taken up Into cells have on transcription?

A

it binds to the tryptophan repressor protein causing a conformational change allowing binding to the tryptophan operator region. This switches off transcription

30
Q

How is the repressor protein a ‘sensor’ for tryptophan levels in the cells?

A

When tryptophan is present, the repressor binds and transcription is off.
When tryptophan levels drop, the repressor becomes unoccupied and frees up the operator region to allow for transcription.

31
Q

Differences between Lactose and Tryptophan

A

Both the lac and tryptophan repressor protein switch off transcription when bound to the operator.

BUT: allolactose binding to the lac repressor leads to its release from the operator, whereas tryptophan binding to the trp repressor induces its binding to the operator
Thus:
- lactose switches on transcription
- tryptophan switches off transcription

32
Q

What are the two distinct differences between RNA polymerase in the prokaryotic and eukaryotic systems.

A
  • all genes are transcribed by a single RNA polymerase in bacteria, eukaryotic cells contain multiple different RNA polymerases that transcribe distinct classes of genes.
  • Eukaryotic RNA polymerases need to interact with a variety of additional proteins to specifically initiate transcription. Prokaryotes can bind directly to promoter sequences.
33
Q

What do eukaryotes usually have as opposed to gene clusters?

A

one promoter, one gene, one mRNA, one protein.

34
Q

RNA polymerase binding is guided by….

A

general transcription factors and inducible transcription factors

35
Q

what regulate gene expression in conjunction with transcriptional regulators

A

Long Promoter and Enhancer sequences

36
Q

What is a Promoter?

A

Promoter is a region of DNA that facilitates the transcription of a particular gene it is located near, the genes they regulate are on the same strand and typically upstream (5’ region)

37
Q

What are the 3 types of RNA polymerase in eukaryotes and what do they make?

A

RNA polymerase I makes large rRNA
RNA polymerase II makes mRNA and miRNAs
RNA polymerase III makes small rRNA and tRNA

38
Q

What is needed by RNA polymerase II in order for it to attach to the promoter

A

a basal (general) transcription factors.

39
Q

what are basal (general) transcription factors?

A

They are part of the cell’s core transcription toolkit, needed for the transcription of any gene.

40
Q

What is the function of core elements?

A

core elements recruit the general transcription factors and thereby position the RNA polymerase II complex at the transcription start site.

41
Q

What are the common elements in eukaryotic core promoters (look at slide 31- 33)

A

BRE
TATA
INR
DPE

42
Q

What do general transcription factors assemble on?

A

core promoter

43
Q

what do proteins that bind to Dustan enhancer regions do?

A

interact with transcription machinery in looped DNA structure.

44
Q

What can recognise specific sequences within the wider promoter and enhancer regions of genes?

A

Inducible transcription factors (gene regulatory proteins)

45
Q

What is a mediator?

A

a large multiprotein complex conserved in eukaryotes that is needed to regulate transcription.

46
Q

A lot of signalling cascades culminate in transcription factor activation

A

look at slide 35 for the signalling cascade

47
Q

what are the ways that Inducible transcription factors can be activated in the cell?

A
  • in response to external stimuli (changes in the environment).
  • post-translational modification (phosphorylation, ubiquitination…)
  • dimerisation
  • nuclear translocation…
48
Q

how is the NF-KB transcription factor activated?

A

External stimulus activates kinase complex that phosphorylates inhibitor of kB (IKB) protein. This leads to K48-linked ubiquitination of IkB and proteasomal degradation. This releases active NFKB, which can then translocate to the nucleus.
-Phosphorylation of NF-kB subunits also regulates transcription.

49
Q

NF-KB subfamily contains how many members ?

A

five members: p65 (RelA), RelB, c-Rel p105/p50, p100/p52, in which homo- and heterodimers can form.

50
Q

What does p50 and p52 need to do to become transactivated?

A

p50 and p52 contain no activation domain, so need to dimerise with a Rel family member to transactivate.

51
Q

What are the common features of inducible transcription factors?

A
  • They bind to specific short DNA sequences in promoter regions of genes.
  • usually act as dimers (homo- and heterodimers).
  • contain an activation domain which regulates the activation of transcription when bound to DNA.
  • Through the activation domain, they interact with the RNA polymerase complex, directly or indirectly. Or they recruit proteins that modulate chromatin structure.
  • They are often cytoplasmic, and translocate to the nucleus after activation.
52
Q

Transcription factors are modular: DNA-binding domain

A

Binds to the promoter region of a gene in a sequence-specific manner.

53
Q

Transcription factors are modular: Activation domain

A

Mediates transactivation of the gene, by interacting with RNA pol II complex and/or by recruiting chromatin remodelling enzymes.
Often, the activation domain has to be phosphorylated to become active

54
Q

Transcription factors are modular: Dimerisation domain

A

A lot of transcription factors act as dimers.

55
Q

Summary: How is transcription regulated?

A

Transcription is regulated by binding of inducible transcription factors (aka gene regulatory proteins) to the promoter region of a gene.

56
Q

Summary: How is the activity of inducible transcription factors regulated?

A

The activity of inducible transcription factors is regulated by signalling cascades stimulated in response to environmental or cell-intrinsic stimuli.

57
Q

Summary: Gene regulatory proteins affect the level of transcription from a gene in what way.

A

positively or negatively

58
Q

Summary: The overall activity of a gene promoter depends on what?

A

the integration of signals from a large number of different gene regulatory factors that act in conjunction at the gene promoter.

BI304 Molecular Biology (5 decks)

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