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BIOL2520 > Unit 08: Control of Gene Expression > Flashcards

Unit 08: Control of Gene Expression Flashcards

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1
Q

define gene expression

A

the process by which cells selectively direct synthesis of proteins and RNA in their genome

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2
Q

what are housekeeping genes?

A

genes that code for proteins common to all cells of a multicellular organism

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3
Q

how much of a human’s 20 000 protein coding genes does a cell express?

A

5000 - 15 000 genes

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4
Q

what binds to DNA in bacteria to start transcription?

A

sigma factor

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5
Q

what binds to DNA in eukaryotes to start transcription?

A

general transcription factors

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6
Q

how do small regulatory nucleotide sequences work? how long are they?

A

10 nucleotides that act as a simple switch

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7
Q

how do long regulatory nucleotide sequences work? how long are they?

A

100 000 nucleotides that act as a complex microprocessor

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8
Q

what SPECIFICALLY acts as a switch to control transcription?

A

binding of transcription regulator to a regulatory DNA sequence

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9
Q

how many transcription regulators do the smallest bacteria have?

A

several hundred

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10
Q

how many transcription regulators do the humans have?

A

around 2000

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11
Q

describe the binding of transcription regulators to DNA

A
  • fits into major groove of DNA double helix by noncovalent interactions with nucleotide pairs within groove
  • 10-20 interactions on 6-8 nucleotides make fit specific and strong
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12
Q

are operons more commonly found in prokaryotes or eukaryotes?

A

prokaryotes

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13
Q

what are operons?

A

clusters of genes coordinately transcribed tgt

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14
Q

describe the Trp operon and its function.

A

controls transcription of 5 genes that code for tryptophan.

when tryptophan present, it binds to transcription regulator (called tryptophan repressor) which binds to operator within the promoter, blocking binding of RNA Pol, so no more tryptophan is produced.

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15
Q

the Trp operon follows what type of feedback loop?

A

feedback inhibition

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16
Q

what does a transcriptional repressor protein do?

A

block RNA Pol from binding to DNA, essentially switching genes off

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17
Q

what does a transcriptional activator protein do?

A

switches genes on by binding regulatory sequences and RNA Pol to initiate transcription.

often require binding to another molecule before can bind to DNA

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18
Q

what is an example of a transcriptional activator protein?

A

catabolite activator protein in bacteria binding to cAMP to activate

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19
Q

describe the Lac operon and its function.

A

controls the breakdown of lactose via the Lac repressor protein binding to DNA when lactose is NOT present.

when lactose is present it binds to the repressor so that the repressor does not bind to the DNA

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20
Q

how does the CAP activator protein work?

A

binds DNA when glucose is not present bc no glucose = high levels of cAMP which binds to CAP, allowing CAP to bind to DNA

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21
Q

what are enhancers? how far can they be from the transcription start site?

A

regions where eukaryotic gene activators bind, can be thousands of nucleotides up/downstream!

“action at a distance”

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22
Q

since enhancers can be so far away from the start site, how do they even work?

A

form loops to get close

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23
Q

what are mediators?

A

large complexes of proteins that serve as adaptors to close the loop made by enhancers doing their job

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24
Q

what is the transcription initiation complex?

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A

transcription regulators and RNA Pol positioned at transcription start site whos formation is prevented by repressors

25
what is the affect of a nucleosome being positioned over a promoter?
can inhibit transcription initiation by physically preventing assembly of initiation complex.
26
how can we get transcription even when histones are positioned above promoter?
either via ATP dependent remodeling complexes moving nucleosomes on the DNA OR histone acetyltransferases attaching lysine to histone tails, which attract general TFs.
27
what is the affect that the addition of lysine usually has?
loosening things up!
28
what is the affect that histone deacetylases have on transcription factors?
removal of acetyl groups from histone tails
29
what are some examples of large scale inactive chromatin caused by histone deacetylases?
heterochromatin, x-inactivation in mammalian females
30
on what scales can histone deacetylases work?
gene by gene or on large scale inactive chromatin
31
what is the function of looped domains in transcription?
to keep genes close to their enhancers, and ensuring that the genes and enhancers are paired up correctly
32
what can mutations preventing the formations of correct loops cause? ex. if enhancers r paired up with the wrong gene
genes being expressed at wrong time which can lead to disease/cancer
33
what is combinatorial control?
process by which LOTS of transcription regulators come together to control expression of a single gene
34
a typical gene is controlled by ______ of transcription regulators in eukaryotes
dozens
35
describe the structure of the mass exhibiting combinatorial control.
bimolecular condensate made of a LOT of transcription regulators and held tgt by scaffolds.
36
how does on protein control expression of many genes in bacteria?
operons
37
how does on protein control expression of many genes in eukaryotes? give an example
many transcription regulators being in place, all needing just one regulator to activate them all simultaneously. ex. cortisol increasing expression of genes in liver in response to starvation/prolonged stress
38
what are embryonic stem cells? what specific quality do they have?
undifferentiated cells that can become any type of cell. they are pluripotent
39
how many transcription regulators control 25 000 genes in humans?
1000
40
what are master transcription regulators?
cascade of regulators that tgt can lead to formation of whole organs!
41
describe the master transcription regulator that results in eye production in fruit flies.
Ey transcription regulator triggers differentiation of cell types that come tgt to form the eye! mutations = no eyes but if it activates in a region where eyes r NOT supposed to be.... we cna get fruit flies w eyes on their legs!
42
what are terminally differentiated cells?
highly specialized cells that never divide
43
what is cell memory?
when patterns of gene expression are remembered thru subsequent generations via feedback
44
how long is Xist? what is its function?
17000 nucleotides. base pairs w one of the X chromosomes in female mammals, coating it to make sure that absolutely nothing can reach the genetic material and transcribe it, while also condensing it
45
how long are long non-coding RNAs?
>200
46
how many long non coding RNAs are there in the human genome?
>5000
47
what are some methods of generating cell memory?
- positive feedback loop - histone modifications - DNA methylation
48
describe the positive feedback loop method of generating cell memory.
essentially, when we have a pluripotent cell that goes to divide, a signal will turn on a master transcription regulator. as the cell divides the presence of the protein produced by the transcription regulator will continue to keep it on.
49
describe the DNA methylation method of generating cell memory.
some nitrogenous bases are methylated, preventing the transcription of the subsequent genes. maintenance methyltransferase recognizes the patterns of methylation in a parent strand and copies the methylation patterns in the daughter strands
50
where does the ribosome bind in prokaryotes and eukaryotes?
eukaryotes - 5' cap prokaryotes - ribosome binding site
51
what happens when the ribosome binding site is blocked?
translation is blocked
52
what are microRNAs (miRNAs)?
22 nucleotide long (v small) segments of RNA that base pair with specific mRNAs that reduces their stability and translation
53
what is RNA-induced silencing complex (RISC)? what does it do?
miRNA packed with specialized proteins that can contain a nuclease, which degrades the complimentary mRNA or just bring the mRNA to another region where there are nucleases.
54
how many miRNAs do humans have?
>1000
55
what is the function of small interfering RNAs (siRNAs)? how long are they?
they are a cell defense against infection. they eliminate foreign RNA molecules.
56
describe the process of RNA interference (RNAi) when using RISC proteins?
foreign double stranded RNA gets recognized and cut by a dicer protein, turning them into siRNAs. these siRNAs are then taken up by the RISC protein, which discards one of the strands, and uses the other to find complimentary foreign RNA, which it then destroys
57
describe the process of RNA interference (RNAi) when using RITS proteins?
RITS takes foreign siRNAs and uses them to complimentary base pair with foreign RNA as it is coming out of RNA Polymerase. this attracts proteins that modify histones, turning that site where the DNA is into heterochromatin, stopping transcription.
58
describe the steps of CRISPR defense in a bacterial cell.
1.virus injects DNA into bacteria 2. short pieces of viral DNA are inserted into the bacterial genome at the CRISPR locus 3. the CRISPR remembers the DNA of the viruses 4. this info is then used to produce CRISPR RNAs (crRNAs) 5. crRNAs are loaded onto a Cas enzyme 6. Cas then uses these crRNAs to find and destroy complimentary viral nucleotide sequences

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