Ch 8: Control of Gene Expression Flashcards

You may prefer our related Brainscape-certified flashcards:
1
Q

What is true/not true of liver cells and kidney cells in the same organism?

A

True: They contain different proteins
True: They express different genes
True: They contain the entire set of instructions needed to form the whole organism
False: They contain different genes

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

What would be the best method for determining which genes are bring transcribed in a particular cell type?

A

RNA sequencing

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

In eukaryotes, where do transcription regulators bind?

A

Upstream, downstream, or within the genes they control. Gene activation can occur at a distance in eukaryotes

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

What is an operon?

A

A set of genes transcribed as a single mRNA from a single promoter

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

Which does not affect gene expression at the post-transactional level? (small interfering RNAs, microRNAs, nucleotide sequences in the untranslated regions of an mRNA, DNA methylation)?

A

DNA methylation

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

When is gene expression controlled?

A

It can be controlled at any of the steps between a gene and its ultimate functional product. However, most of the control happens with initiation of transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

How and where is the transcription of individual genes switched on and off, and how is this different between eukaryotes and bacteria?

A

Transcription of individual genes is switched on and off by transcription regulators, which are proteins that bind to short stretches of DNA called regulatory DNA sequences.

In bacteria, the regulatory DNA sequences are usually close to where the RNA polymerase could bind. In Eukaryotes, regulatory DNA sequences are often separated from the promoter by many thousands of nucleotide pairs

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

Transcription regulators in eukaryotes

A

They usually act in one of two main ways:
1) they direct the assembly process that requires RNA polymerase and the general transcription factors at the promoter
2) The locally modify the chromatin structure of promoter regions.

The expression of the gene is usually controlled by a combination of different transcription regulators.

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

How does cellular memory work?

A
  • One prominent mechanism in multicellular organisms is positive feedback: transcription regulators that perpetuate transcription of their own gene.
  • Patterns of DNA methylation and chromatin structure can be transmitted from one cell generation to the next
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

DNA methylation

A

the enzymatic addition of methyl groups to cytosine bases in DNA. This covalent modification generally tuns off genes by attracting proteins that block gene expression

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

Epigenetic inheritance

A

the transmission of a heritable patters of gene expression from one cell to its progeny that does not involve altering the nucleotide sequence of the DNA

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

long noncoding RNA

A

class of RNA molecules more than 200 nucleotides in length that does not encode proteins. Often used to regulate gene expression

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

microRNA

A

miRNA, small noncoding RNA that controls gene expression by base-pariing with a specific mRNA to regulate its stability and translation

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

post-transcriptional control

A

regulation of gene expression that occurs after transcription has already begun. Examples include RNA splicing and translational control

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

promoter

A

DNA sequence that initiates gene transcription. Includes sequences recognized by RNA polymerase and its accessory proteins

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

regulatory DNA sequence

A

DNA sequence to which a transcription regulator binds to determine where, when, and in what quantities a gene is to be transcribed into RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

reporter gene

A

gene encoding a protein whose activity is easy to monitor experimentally; used to study the expression patters of a target gene or the localization of its protein product

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

RNAi

A

RNA interference; cellular mechanism that results in the destruction of RNAs containing a similar nucleotide sequence. It is widely exploited as an experimental tool for preventing the expression of selected genes (gene silencing)

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

siRNA

A

small interfering RNA: short length of RNA produced from double-stranded RNA during the process of RNA interference. It base-pairs with complementary sequences in other RNAs, leading to he inactivation or destruction of the target RNA.

20
Q

transcriptional activator

A

a protein that binds to a specific regulatory region of DNA to stimulate transcription of an adjacent gene

21
Q

transcriptional repressor

A

a protein that binds to s specific regulatory region of DNA to prevent transcription of an adjacent gene

22
Q

transcription regulator

A

protein that binds specifically to a regulatory DNA sequence to switch a gene either on or off

23
Q

What is a zinc-finger?

A
24
Q

What is a genetic switch?

A

Transcriptional control based on a genetic switch requires two things:
1) short stretches of defined DNA sequence
2) gene regulatory proteins that recognize and bind to the sequences

25
Q

What are the steps at which gene expression can be regulated?

A

1) transcriptional control
2) RNA processing control
3) RNA transport and localization control
4) mRNA degradation control
5) translational control
6) protein degradation control
7) protein activity control

26
Q

Proteins that recognize DNA sequences

A

helix-turn-helix
zinc finger

27
Q

Describe the zinc finger

A

modular proteins that bind to specific DNA sequences

28
Q

What could be some of the applications for designer proteins that bind to DNA with predetermined sequences?

A

They could be used to recognize specific DNA sequences, which allos site specific genetic editing, and allow regulation of gene expression. Can make a double-stranded break anywhere you want.

29
Q

If you have to do a knockout gene sequence, where would you do it?

A

The exon–the intron gets spliced out. If you do it early enough in the sequence, you could cause a codon shift

30
Q

Describe the tryptophan repressor

A

When tryptophan is abundant, it binds to the inactive form of the repressor, and makes it active. This then binds to the operator site. The tryoptophan is low, there is not enough to bind to the repressors, so the repressor is in its inactive form, and so the gene can be transcribed again.

31
Q

What is the significance of the -35 and -10 regions?

A

Those are the regions that the RNA polymerase binds to in prokaryotes (counting backwards from the transcription start site.). This means that the sequence in between can be variable, so there can be regulatory sequences that will interfere with the polymerase binding

32
Q

negative feedback loop

A

when an end product of a reaction shuts down the production of that end product. (Example: tryptophan repressor, where trypotophan activates the repressor)

33
Q

Explain the control of the Lac operon

A

When there is glucose, the CAP activator is in its inactive form. When there is no glucose, cAMP binds to the CAP activator, causing it to be able to bind to the DNA, stabilizing and promoting the DNA polymerase.

When there is no lactose, LacI binds to the operator site, blocking transcription. There there is lactose, the lactose binds to the LacI, inactivating it an allowing transcription to happen.

So the gene should only be transcribed where there is no glucose, and there is lactose.

34
Q

What are two mutations that can happen that both stop a repressor from working?

A

The repressor can be mutated, or the repressor binding site can be mutated

35
Q

How do eukaryotes regulate gene expression?

A

1) RNA polymerase uses multiple transcription factors to begin transcription
2) they lack operons, so regulate every gene individually
3) they can be controlled by many (sometimes hundreds) or regulatory proteins which act over very large distances (in terms of base-pairs..the folds mean they are physically close)
4) Chromatin provides an additional opportunity for gene regulation

36
Q

Is is possible for a transcription factor to be both an activator and a repressor for the same cell, or even for the same gene?

A

Upstream: it can recruit DNA polymerase
Downstream: it can still recruit DNA polymerase, but at the wrong spot, or it can physically block it

37
Q

Insulator

A

DNA sequences what pervent eukaryotic gene regulatory proteins from influencing distant genes (they block transcription from happening beyond a certain point)

38
Q

positive feedback

A

a transient signal turns on a gene, which then produces activators for itself.

One common way that cell memory happens

39
Q

Transcription circuits

A

they allow the cell to carry out logic operations (measure duration of a signal).
Both A and B are needed to turn on output. A produces B. So when the input to turn on A is only there briefly, A is not around long enough to turn on B, so there is no output. When the signal for A is on long enough, A has time to produce B, so the end output is produced as well.

40
Q

DNA methylation

A

can turn genes off, typically completely off, and it can stay that way.

Because DNA replication is semi-conservative, methylation is inherited

41
Q

Examples of translational regulation

A
42
Q

How can you tell whether a protein binds to a DNA sequence?

A

protein slows down DNA’s movement through gel electrophoresis

43
Q

Ubiquitin

A

a molecule that binds to protein to mark it as targeted for desctruction

44
Q

What are some of the most common protein structures used by nature to find and bind to DNA sequences?

A

zinc fingers
helix turn helix
(and CRISPR)

45
Q

TrpR and LacI are repressors or activators?

How are they different?

A

they are repressors

TrpR: whey tryptophan is present, it binds to DNA and represses the gene expression

LacI: Binds to DNA in the absence of lactose. When lactose is present, it prevents the repressor from binding to DNA

46
Q

What is the promoter, enhancer, insulator?

A

Promoter is where the RNA polymerase binds and initiated transcription. Enhancer (sequence) is a DNA sequence where transcription activator binds, and promotes transcription to occur.
Insulator is a DNA sequence that prevents transcription from occuring.

47
Q

Methylation

A

a methyl group (CH3) is added to something–DNA, histone, or other proteins.