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Bioinformatics > Gene Expression and Regulation (Khan Academy) > Flashcards

Gene Expression and Regulation (Khan Academy) Flashcards

1
Q

What is chromatin?

A

Coiled DNA with histone protein and non-histone protein.

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2
Q

What are nucleosomes?

A

It’s the basic repeating subunit of chromatin packaged inside the cell’s nucleus.
It’s 146 base pairs of DNA wrapped around a core of 8 histones.

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3
Q

What are the types of histones?

A

H2A, H2B, H3, H4

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4
Q

What is histone acetylation and deacetylation?

A

It’s the uncoiling and coiling of the chromatin.

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5
Q

What is the enzyme responsible for histone acetylation?

A

HAT - histone acetyltransferase

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6
Q

What is the enzyme responsible for histone deacetylation?

A

HDAC - histone deacetylase

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7
Q

What is heterochromatin?

A

Densely packed, transcriptionally inactive DNA

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8
Q

What is euchromatin?

A

Less densely packed, transcriptionally active DNA

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9
Q

What is the role of DNA methylation?

A

It’s a method of down regulating the transcription of a gene - “gene silencing”. It happens e.g. when stem cells are differentiated into various cells.

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10
Q

What is the DNA methylation process?

A

Adding a methyl group (CH3) to cytosine DNA base in regions called CpG sites.

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11
Q

What are CpG sites?

A

Sites in DNA where C and G are immediately next to each other in a DNA sequence.

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12
Q

What is a promoter sequence?

A

A sequence upstream of a gene to which RNA polymerase binds to start transcription.

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13
Q

What is an operator sequence?

A

A sequence upstream of a gene, between promoter and the gene itself, to which Transcription Factor protein binds.

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14
Q

What are activators?

A

Proteins that enhance interaction between RNA polymerase and a promoter encouraging the expression of a gene.

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15
Q

What is a enhancer sequence?

A

A DNA sequence that can be bound by activators to increase the likelihood that transcription of a particular gene will occur. It might be located upstream or downstream of the enhanced gene, not necessarily close to it.

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16
Q

What are repressors?

A

One of transcription regulation factors, a protein that bind to the operator and impede RNA polymerase’s progress on the DNA strand and thus impeding expression of a gene.

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17
Q

What is a silencer sequence?

A

A sequence that binds repressors, preventing RNA polymerase from transcription. It can be located upstream or downstream a gene, not necessarily close to it.
When repressor binds to the silencer sequence, RNA polymerase cannot bind to the promoter.

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18
Q

What is asymmetric segregation of cellular determinants?

A

When a cell divides in a zygote, transcription factors are not uniformly distributed among daughter cells, causing cellular differentiation.

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19
Q

What is induction in cell differentiation?

A

A group of cells “pressures” another group of cells to differentiate.

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20
Q

What are the types of induction in cell differentiation?

A
  1. diffusion
  2. direct contact
  3. gap junction (using connexon proteins)
21
Q

What is an operon?

A

A combination of a regulatory DNA sequence (e.g. a promoter) with the genes whose transcription it promotes.
Found in bacteria.

22
Q

What does it mean that an operon is inducible?

A

When an operon is usually “off”, it can be “switched on” by a molecule called the inducer.

23
Q

What does it mean that an operon is repressible?

A

An operon that is usually “on” can be “turned off: by a molecule called the repressor.

24
Q

What is lac operon?

A

In E. coli, it’s an operon which contains genes involved in lactose metabolism.

25
Q

What regulatory proteins are involved in regulation of the lac operon?

A
  1. the lac repressor - acts as a lactose sensor
  2. the CAP (catabolite activator protein - acts as a glucose sensor
26
Q

What are the parts of the lac operon?

A

CAP binding site, promoter, opertor, and 3 genes (lacZ, lacY, lacA).

27
Q

What is the role of a promoter?

A

It is RNA polymerase binding site.

28
Q

What is the role of an operator in lac operon?

A

It is a negative regulatory site bound by the lac repressor protein. The operator overlaps with the promoter, and when the lac repressor is bound, RNA polymerase cannot bind to the promoter and start transcription.

29
Q

What is the role of the CAP binding site in the lac operon?

A

It is a positive regulatory site that is bound by catabolite activator protein (CAP). When CAP is bound to this site, it promotes transcription by helping RNA polymerase bind to the promoter.

30
Q

What happens to lac repressor when lactose is present?

A

It loses its ability to bind to the operator (it binds to allolactose instead).

31
Q

Why is the role of CAP (catabolite activator protein in lac operon?

A

RNA polymerase doesn’t bind very well to the lac operon promoter, CAP attaches to the CAP binding site and helps RNA polymerase bind and perform transcription.

32
Q

What is the role of cAMP (cyclic AMP) in the lac operon?

A

It acts as a “hunger signal” in E. coli.
It changes the shape of CAP and thus activates it, allowing CAP to bind to its binding site in the lac operon. It is produced when glucose levels are low.

33
Q

What is a corepressor?

A

It’s a molecule which attaches to a repressor and thus allows it to attach to DNA.

34
Q

What is attenuation?

A

Is a gene expression regulation mechanism which prevents completion of transcription - it causesRNA polymerase to stop prematurely when transcribing a gene.

35
Q

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

A
  1. chromatin accessibility
  2. transcription
  3. RNA processing
  4. RNA stability
  5. translation
  6. protein activity
36
Q

How is gene expression regulated through chromatin accessibility?

A

More”relaxed” chromatin makes genes available for expression.

37
Q

How is gene expression regulated during transcription?

A

Sets of transcription factor proteins bind to specific DNA sequences in or near a gene and promote or repress its transcription into an RNA.

38
Q

How is gene expression regulated during RNA processing?

A

Splicing, capping, and addition of a poly-A tail to an RNA molecule can be regulated, and so can exit from the nucleus. Different mRNAs may be made from the same pre-mRNA by alternative splicing.

39
Q

How is gene expression regulated through RNA stability?

A

The lifetime of an mRNA molecule in the cytosol affects how many proteins can be made from it. Small regulatory RNAs called miRNAs can bind to target mRNAs and cause them to be chopped up.

40
Q

How is gene expression regulated during translation?

A

Translation of an mRNA may be increased or inhibited by regulators.

41
Q

How is gene expression regulated through protein activity?

A

Proteins can undergo a variety of modifications, such as being chopped up or tagged with chemical groups. These modifications can be regulated and may affect the activity or behavior of the protein.

42
Q

What are general (basal) transcription factors?

A

In eukaryotes, RNA polymerase cannot bind to the promoter without a general transcription factor protein.

43
Q

What are activators?

A

Transcription factors which activate transcription, e.g. they may help the general transcription factors and/or RNA polymerase bind to the promoter.

44
Q

What are repressors?

A

Transcription factors which repress transcription. For example, a repressor may get in the way of the basal transcription factors or RNA polymerase, making it so they can’t bind to the promoter or begin transcription.

45
Q

What are gene enhancers?

A

Binding sites for activators.

46
Q

What are gene silencers?

A

Binding sites for repressors.

47
Q

What are tissue-specific enhancers?

A

Enhancers that control gene expression in a specific part of the body.

48
Q

What is combinatorial regulation?

A

When a gene is controlled by multiple different transcription factors and the expression is regulated by a logical operations on those factors.

Bioinformatics (7 decks)

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