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Biochem Final > Gene Regulation > Flashcards

Gene Regulation Flashcards

1
Q

When is lac operon most active?

A

When glucose is low and lactose is high.

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2
Q

What are inducers of lac operon?

A

Allolactose and IPTG

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3
Q

What two regions does the promoter region have?

A

Operator, LacO and cAMP repressor protein binding site, CRP

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4
Q

What is upstream of the operator region?

A

LacI repressor gene, when it is active repressor protein will black bind to operator region and block transcription

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5
Q

How is the repressor-inducer complex negative control?

A

The active regulatory element, the repressor is an inhibitor of transcription

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6
Q

What is a helix-turn-helix?

A

The structure of the lac repressor and how it binds to the DNA at high speceficity ( in the major groove)

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7
Q

What are the two domains of transcription factors?

A

DNA binding and activation domains

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8
Q

What is the difference between negative and positive regulation?

A

Negative = block transcription and Positive means promote transcription

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9
Q

When glucose is low, cAMP is abundant. cAMP binds to CRP/CAP, what happens next?

A

It will bind to CRP binding site which recruits RNA pol. You need cAMP need turn on transcription.

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10
Q

How do you turn on the Trp operon?

A

Low levels of tryptophan, so you can make more tryptophan

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11
Q

How is the trp repressor different from the lac repressor?

A

The trp repressor needs a corepressor to be able to bind to the operator region. Tryptophan is the corepressor. Transcription is only inhibited when Trp levels are high

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12
Q

What does the eukaryotic core promoter region consist of? What are proximal control elements?

A

Initiator and TATA box. Proximal control elements are the CAAT box and the GC box

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13
Q

What is a mediator complex and what is its function?

A

They are multi-protein complexes that function as transcriptional coactivators in all eukaryotes by linking upstream regulatory sequences, such as enhancers, with RNA Pol II and general transcription factors at the promotor region. Its function is to transmit signals from the transcription factors to the polymerase

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14
Q

How can transcriptions factors respond to hormones and other signals?

A

hormon and hormone receptor inside a cell. cAMP (inactive) binding to protein kinase A to activate. Cell signaling via the receptor on the outside of the cell activating a transcription factor through phosphorylation.

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15
Q

How do nucleosomes affect transcription?

A

The default state is off and promotors are blocked. Chromatin must be remodeled to initiate transcription.

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16
Q

How can histone tails affect transcription?

A

Modification of the tails allows it to condense or relax, thus affecting transcription

17
Q

What is the function of the histone fold domain?

A

Allows histone to interact with each other

18
Q

What can DNA and H3 and H4 do with each other?

A

They can H bond with each other in the minor groove of the DNA

19
Q

How does DNA wrap around histones? Why?

A

Left handed wrapping to generate the negative supercoiling to better resolve for transcription

20
Q

What is acetylation generally associated with?

A

Transcriptionally active genes, causes unwinding of DNA aka euchromatin

21
Q

What is methylation generally associated with?

A

Inactive gene, tighter packing

22
Q

What enzyme brings in and remove methyl groups? Acetyl groups?

A

Methyl transferase and histone acetyl transeferase.

23
Q

What can be methylated or acetylated?

A

Amino groups can be acetylated or methylated

24
Q

What is histone code?

A

Specific cominations of histone modifications control different chromatin eg.) Gene silencing or promote transcription elongation - methylation after transcription has begun

25
Q

What do acetylated residues recruit?

A

Bromodomain proteins that further allow for loosening of DNA / more relaxed. It is a remodeling engine

26
Q

What do methylated residues recruit?

A

Chromodomain proteins that makes it pack tighter / more condensed. It is a remodeling engine.

27
Q

Why do eukaryotes methylate their DNA?

A

To cause gene silencing / block transcription of a specific gene.

28
Q

What is epgenetic inheritance?

A

When DNA is methylated and is preserved during replication

29
Q

What is genomic imprinting?

A

When methylated DNA is to the next generation via egg or sperm

30
Q

What is an example of DNA methylation silencing?

A

DNA methylation silencing of one X chromosome for a female. More permanent than chromatin remodeling.

31
Q

How do you silence gens by targetting mRNA?

A

By using Small interfering RNAs (siRNAs) and microRNAs (miRNAs)

32
Q

Where do miRNAs come from?

A

Theyre embedded within the genome and get transcribed as pri-mRNA with stem loops

33
Q

What does Drosha do to Pri-mRNAs?

A

Cuts off the cap and tail and turns it into a Pre-mRNA and binds to CPO5 to be exported to the cytoplasm.

34
Q

What does Dicer do to Pre-mRNA?

A

It cuts off the stem loop resulting in two strands, the guide strand and the passenger strand. The least stable of the two strands will get loaded onto the RISC (RNA-induced Silencing Complex) complex.

35
Q

What is the guide strand doing after its loaded?

A

It binds to its complementary bases on mRNA and argonaute cleaves where it binds to and the remaining strand gets degraded.

36
Q

What do siRNAs do and Where do siRNAs come from?

A

siRNAs are a cellular defense mechanism, they come from double stranded viral RNA.

37
Q

How does Dicer make siRNAs? And what happens next?

A

Dicer recognizes the foreign dsRNA and cleaves the dsRNA into siRNAs. Also results in a passenger strand and guide strand. Guide strand is loaded onto RISC. siRNA and RISC complex bind to the viral mRNA and degrades it.

Biochem Final (5 decks)

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