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Regulation Of Gene Expression > Lesson 7 > Flashcards

Lesson 7 Flashcards

1
Q

what creates the difference between cells in the same organism?

A

the regulation of gene expression → how the transcriptome and the proteome is regulated

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2
Q

what is the function of the promotor region?

A

essential part of the gene → region that allows the binding of the RNA polymerase with all the accessory transcription factors

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3
Q

what are regulatory sequences?

A

sequences on the DNA which allow the binding of the regulatory proteins ; not usually part of the promoter in terms of spatial occupancy, but they also can be very far from the basal promoter

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4
Q

what can control gene expression besides regulatory proteins and transcription factors?

A

RNA

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5
Q

what types of RNA can regulate gene expression besides protein transcription factors?

A

interferring RNA and regulatory RNA

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6
Q

what are the two main actors in regulation of the genome in complex eukaryotes?

A

trans-acting proteins and cis-acting proteins

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7
Q

what is the function of trans-acting proteins?

A

transcription factors

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8
Q

what is the function of cis-acting proteins?

A

sequences recognized by the transcription factor on the DNA (also on the DNA themselves)

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9
Q

what is transcription ultimately controlled by in complex eukaryotes?

A

the binding of trans-acting proteins to cis-acting regulatory DNA sequences

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10
Q

what was the goal of the ENCODE project?

A

to identify all the elements on the DNA and do all the annotations on them in a functional way in order to discover their functions

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11
Q

cis-regions usually act in genes that are involved in what four activities?

A
  1. DNA replication
  2. chromatin condensation
  3. chromosome segregation
  4. gene expression
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12
Q

describe the regulatory regions in simple eukaryotes?

A

very short sequences that are easy to study as they are close to the core and the basal promotor

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13
Q

why is it more difficult to study enhancers, insulators, and silencers in complex eukaryotes?

A

these elements are very interspersed in the genomic DNA and can be very far from each other

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14
Q

when distal elements like enhancers or silencers are far away from each other, what must occur?

A

the interactions with elements on the promotor must be mediated by other proteins (must have something to mediate the cross-talking between elements)

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15
Q

what are the main actors of regulation on the DNA?

A

enhancers

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16
Q

what are enhancers classified as?

A

cis-acting elements

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17
Q

what are enhancers defined as?

A

sequences on the DNA which offer multiple binding sites for transcription factors

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18
Q

where is the enhanceosome usually located and what does it define?

A

located in the soma of the enhancer and defines all the transcription factors that are bound to the same enhancer (it had multiple blinding sites for transcription factors)

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19
Q

during evolution, what has increased complexity?

A

an increase in the number of transcription factors → increase in regulation increases complexity

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20
Q

what three categories do proteins regulating transcription fall into?

A

sequence-specific DNA binding proteins, general transcription factors (GTFs), and chromatin remodeling and modification complexes

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21
Q

describe sequence-specific DNA binding proteins:

A

they should have a DNA binding domain and they recognize specific bases on DNA

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22
Q

what two groups are sequence-specific DNA binding proteins divided into?

A

activators and repressors

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23
Q

what is the function of general transcription factors?

A

recognize the same sequence in all genes

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24
Q

what larger complex are GTFs part of?

A

RNA polymerase II → recognize a sequence that is the same in all promotors

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25
Q

what is the function of chromatin remodeling and modification complexes?

A

changing chromatin by assisting the transcriptional machinery in order to facilitate the access of proteins to DNA → regulatory proteins need to see the sequence for the binding and
these complexes are able to facilitate the reading of the DNA.

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26
Q

Enzymes for the synthesis of RNA, in particular RNA pol 2 (that transcribes for mRNA) can’t initiate transcription without the general transcription factors, why not?

A

RNA polymerase has some affinity for DNA, but without them it cannot bind in a specific way → TFs bring the specific polymerase to the specific region (otherwise initiation is not specific)

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27
Q

where does the +1 region refer to?

A

where transcription starts and promoter is usually 200 bp upstream

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28
Q

what does RNA pol 2 control?

A

regulation of messenger RNA

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29
Q

where is a promotor located?

A

region of the upstream the coding region for the +1

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30
Q

what is the core promotor?

A

the minimal sequence needed for effective transcription and in order to identify the promotor

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31
Q

describe the position of the TATA box:

A

fixed position in eukaryotes and prokaryotes from the transcriptional start sites

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32
Q

how are upstream sequences connotated?

A

-

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33
Q

how are downstream sequences connotated?

A

+

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34
Q

what is the TATA box?

A

the TATA binding protein sequence

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35
Q

what has a specific sequence rich in G and C, that is also the binding site for TF2B (general transcription factor for pol2)?

A

BRE

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36
Q

what is BRE?

A

the TF2B recognition element

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37
Q

what are two essential components of the promotor?

A

TATA Box and BRE

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38
Q

besides the TATA Box and BRE, what else can be present in eukaryotes?

A

an initiator and the DCE / DPE

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39
Q

where is the initiator located?

A

it is in the middle of the sequence and includes the +1 (so is not upstream
sequence like the TATA box) → has a couple of nucleotides upstream and 4 nucleotides downstream the +1

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40
Q

what are DCE and DPE bound to?

A

TF2D

41
Q

what is TF2D?

A

one of the other general transcription factors working with RNA pol 2

42
Q

what is a characteristic of the TATA box that allows the probability to find this specific sequence of bases in this exact position very high?

A

it is a consensus sequence

43
Q

if a gene in the human genome does not have a TATA box, what other combinations might serve as the promotor?

A

DPE + the initiation factor or an initiator + a CPG island (sequence made of repeating C and G in the promotor)

44
Q

we need the TATA box in order to bind TBP (TATA binding protein), which has what function?

A

to bind DNA

45
Q

once TBP binds to the Tata box, what occurs?

A

the bending of DNA

46
Q

where does DNA bending occur?

A

at the level of the minor groove of the double helix

47
Q

what is the purpose of DNA bending?

A

works like a marker on the chromatin → like a flag for all the other transcription factors to mark the promotor gene

48
Q

what is the function of TBP?

A

recruits RNA polymerase and tells it where to bind = essential protein

49
Q

what is the role of RNA polymerase I?

A

enzyme that transcribes ribosomal RNA

50
Q

what is the role of RNA polymerase III?

A

transcribes all tRNA and 5S rRNA

51
Q

what are the three rRNA in eukaryotes?

A

5S, 18S, and 28S

52
Q

what are the smallest RNA?

A

tRNA

53
Q

what makes the genes encoding for ribosomal RNA unique?

A

they are some of the few genes in the eukaryotic genome which have repeated sequences in tandem

54
Q

in the first step of transcription, what needs to bind to RNA polymerase II?

A

we need the binding of other proteins such as TBP but also TF2B that binds to BRE in order to let pol 2 reach the promotor

55
Q

besides TF2B, what other transcription factors is RNA poly 2 associated with?

A

TF2F, TF2E, and TF2H

56
Q

what is TF2H and why is it important?

A

it is a helices → needed to open the double stranded of DNA to start transcription

57
Q

once transcription is initiated and enters the elongation phase, what occurs?

A

all factors that facilitate transcription are released because they are no longer needed

58
Q

what is the major change on pol II when transcription enters the elongation phase?

A

phosphorylation of the C-term domain is needed in order to change the kinetics from transcription initiation to transcription elongation

59
Q

what happens simultaneously as pol II moves along the DNA transcribing mRNA?

A

splicing also happens cotranscriptionally

60
Q

where are all factors required for the splicing of RNA associated?

A

C-term of the enzyme → so that splicing occurs co-transcriptionally in order to make the process very efficient

61
Q

what are cofactors?

A

large complexes that interact with either activators or repressors of transcription and RNA pol II to enhance or repress transcription

62
Q

what is a mediator?

A

one big complex made by more than 25 subunits, and mediates the interaction between transcription factors (activators) and RNA polymerase II

63
Q

what is the main function of mediator complexes?

A

transmit signals from the transcription factors to the polymerase, acting as a big co-activator in all eukaryotes

64
Q

where have mediator complexes been found?

A

both simple (yeast) and complex (human) eukaryotes

65
Q

what must happen in order to facilitate the the interaction between proteins near the transcription start site (TSS) and proteins that might be bound to distal DNA sequences?

A

DNA bending

66
Q

what is the the complex mediating this protein-to-protein interaction and that conveys the signal from activators to RNA pol II in order to promote bending?

A

mediator

67
Q

what must transcription factors be able to recognize on the outer part of the double helix?

A

the pattern of particular chemical groups

68
Q

where do transcription factors recognize the pattern of particular chemical groups on the outer part of the double helix?

A

only in major grooves

69
Q

why do transcription factors only recognize the pattern in major grooves?

A

only in major grooves are the patterns marked different for each of the four base pair arrangements

70
Q

what also determines the overall geometry of the double helix by creating distortions of the helix that can be recognized by proteins?

A

nucleotide sequences

71
Q

what three features must regulatory proteins have?

A

a DNA binding domain, an active domain, and a flexible domain

72
Q

describe the dna binding domain of a regulatory protein:

A

can be present in the N-ter/C-ter/middle part of the protein and is responsible for the interaction with the DNA

73
Q

what is the function of the active domain in regulatory proteins?

A

interacts with other proteins

74
Q

what is the function of a flexible domain in regulatory proteins?

A

links together other domains

75
Q

dna-binding domains can be structured in different motifs, however, every TF must have one of which motifs?

A
  • Helix-turn-helix
  • Homeodomain
  • Zinc-finger
  • Winged helix (forkhead)
  • Leucine-zipper
  • Helix-loop-helix
76
Q

what is the simplest DNA binding motif, and how is it structured?

A

helix-turn-helix → presence of an alpha helix, a small turn, and another alpha helix

77
Q

what is a prominent dna binding motif widely used in molecular engineering, and what is its structure?

A

zinc-finger → a zinc atom linked to a cysteine or histidine residue

78
Q

what is another important dna binding motif?

A

leucine-zipper → high leucine frequency, form homodimers or heterodimers: this can alter the specificity of the DNA-binding ability of the transcription factor and is also a way to expand the regulation

79
Q

what are nucleosomes composed of?

A

DNA wrapped around a protein complex (usually a histone)

80
Q

because the N-terminal tail of histones protrudes outside the nucleosome, how can it be modified?

A

post-transcriptionally

81
Q

how are nucleosome modifications added and removed?

A

enzymes

82
Q

what is the most well-known nucleosome modification?

A

acetylation of lysines

83
Q

what happens during the acetylation of lysines?

A

removes the charge from lysine thus promoting the formation of euchromatin and allowing the transcription of nearby genes

84
Q

what is hyperacetylation directly related to?

A

activation

85
Q

what is de-acetylation related to?

A

repression

86
Q

what is one of the most famous acetyltransferases?

A

p300/CBP complex

87
Q

what is the function of the p300 CBP complex?

A

responsible for the acetylation on histone 4

88
Q

what is the function of the acetyltransferase protein PCAF?

A

preferentially acetylates histone 3

89
Q

what is acetylation ALWAYS related to?

A

enhanced expression

90
Q

describe the status of chromatin in the presence of euchromatin:

A

transcriptionally active

91
Q

describe the status of chromatin in the presence of heterochromatin:

A

transcriptionally repressed

92
Q

why do we need actors that remodel nucleosomes?

A

the positions of adjacent nucleosomes vary a lot

93
Q

what use the energy of ATP hydrolysis to change the structure of nucleosomes temporarily so that DNA becomes less tightly bound to the histone core?

A

chromatin remodeling complexes

94
Q

what is the most famous chromatin remodeling complex family?

A

SWI/SNF family → very much conserved among different species

95
Q

what do the SWI/SNF families of different species have in common?

A

presence of an ATPase domain

96
Q

when is the only time that we need to disrupt the nucleosomes structure when transcribing RNA?

A

during dna replication

97
Q

what is the function of ATP-dependent remodeling complexes?

A

loosen the interaction between dna and histones thus permitting the entrance of dna binding proteins

98
Q

after dna binding proteins have done their job, what occurs?

A

another dna binding protein restores the normal nucleosome structure

99
Q

both histone-modifying enzymes and chromatin remodeling complexes work together to do what?

A

release and recondenes stretches of chromatin

Regulation Of Gene Expression (28 decks)

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