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Biochemistry Final Prep > Chapter 37&38: Eukaryotic Gene Expression, Regulation, & Processing > Flashcards

Chapter 37&38: Eukaryotic Gene Expression, Regulation, & Processing Flashcards

1
Q

Differences btw prokaryotic and eukaryotic gene expression/regulation:
structure of genome, size of genome, location of transcription/regulation

A

Prokaryotic Eukaryotic
Structure: single, circular genome chromosomes
Size of genome: small large
Location: coupled transcription- nuclear, translation- cytoplasm

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2
Q

What is constitutive gene expression?

A

Always on and important in housekeeping genes

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3
Q

What types of genes are only expressed at times needed?

A

Genes needed for cellular differentiation, cell-type specificity, in response to environmental signals

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4
Q

Gene expression in eukaryotes must respond both to conditions _________ and to _________.

A

conditions within the cell and to external stimuli

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5
Q

_______ hormones are one class of regulatory olecules that control gene expression.

A

Steroid

Ex: Estradiol (controls genes in the devlpmt of female secondary sex characteristics- must bind to estrogen receptor)

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6
Q

How many classes of hormone gene regulatory effects are there?

A

Two

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7
Q

Class 1 of hormone gene regulatory effects.

A

Hormone binds to nuclear receptor (cytoplasm) and causes dissociation of HSP (heat shock protein) with nuclear receptor.

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8
Q

How does hormone binding cause dissociation of HSP in class 1?

A
  1. Hormone binds nuclear receptor
  2. Nuclear receptor with bound ligand dimerizes and translocates to nucleus
  3. In nucleus, it complex binds to hormone response element (HRE)
  4. Recruits coactivator and proteins involved in transcription.
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9
Q

Class 2 of hormone gene regulatory effects.

A

Nuclear receptor is located on HRE on DNA bound by a corepressor.
Upon ligand binding (thyroid hormone), corepressor is release allowing coactivator to bind.

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10
Q

How do nuclear hormone receptors function?

A

Have 2 conserved domains:

  1. DNA binding domain- has zinc-finger domains that confer specific DNA binding
  2. Ligand binding domain- ligand binding causes structural change that enables receptor to recruit other proteins to regulate transcription
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11
Q

Do the structural changes that occur upon ligand binding affect the binding to the response element on DNA?

A

No

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12
Q

Steroid hormone receptors are targets for ____.

A

drugs

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13
Q

Three types of drugs that target steroid hormones.

A
  1. antagonist- binds, changes shape and recruits corepressors
  2. selective nuclear receptor modulator- binds, takes form intermediate btw inactive/active states
  3. agonist- binds, changes shape and recruits coactivators
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14
Q

Example of drug targeting steroid hormone receptor and how it works.

A

Ex: Tamoxifen

  1. some cancers require estradiol-receptor complex to grow.
  2. tamoxifen (antagonist of estradiol) binds AF1, causes differential structural changes to receptor that elicited by estradiol- less expression of the ER target genes
  3. OR estrogen can be depleted resulting in no expression of ER target genes
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15
Q

How does a corepressor prevent DNA opening?

A

Deacetylates chromatin so DNA becomes more compact (can’t open) so no gene expression.

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16
Q

What is an example of a corepressor?

A

HDACs

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17
Q

How does a coactivator encourage DNA opening?

A

Acetylates chromatin so DNA less compact (easier to open) so gene expression occurs

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18
Q

What is an example of a coactivator?

A

HATs

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19
Q

What is used by HATs (histone acetyltransferases) to modify histones?

A

acetyl CoA (made by ATP-citrate lyase)

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20
Q

How does acetylation allow for easier transcription?

A
  1. Acetylation reduces affinity of histones for DNA.
  2. Histone acetyllysine residues are interaction sites for many proteins which regulate transcription.
  3. Acetyllysine residues also bind/recruit chromatin remodeling proteins.
21
Q

All covalent modifications of histones are ______ and thus targeted for __________.

A

Are reversible and targeted for drug therapy

22
Q

________ is associated with active gene expression while _______ is associated with repressed gene expression.

A

Acetylation is associated with active gene expression while methylation is associated with repressed gene expression.

23
Q

What are the main 3 types of RNA molecules?

A
  1. messenger RNA (mRNA)- intermediates that carry genetic info from DNA to ribosomes, transcribed by RNA pol II
  2. transfer RNA (tRNA)- adaptors btw amino acids and codons in mRNA synthesized, transcribed by RNA pol III
  3. ribosomal RNA (rRNA)- structural and catalytic components of ribosomes, transcribed by RNA pol I
24
Q

What are 4 other types of RNA molecules?

A
  1. small nuclear RNA (snRNA)- structural components of spliceosomes, transcribed by pol II or pol III
  2. micro RNA (miRNA)- short single-stranded RNAs that block expression of complementary mRNAs, transcribed by pol II
  3. RNAi- similar to miRNA, RNA interference, transcribed by pol IV
  4. piRNA (Piwi-interacting RNA)- small non-coding RNA molecule
25
Q

The primary rRNA transcript contains what subunits?

A
  • it is about 7500nt, 45S RNA

- contains subunits 18S, 5.8S, 28S

26
Q

What are the 2 ways rRNA are modified?

A
  1. methylation- 80% O2-methylribose, 20% bases (A or G)

2. uredines in rRNA in human are converted to pseudouridine, may contribute to rRNA tertiary stability

27
Q

Processing of tRNA.

A
  1. removal of 5’ leader sequence by RNase P
  2. removal of 3’ tailer sequence by combination of endonucleases and exonucleases
  3. addition of CCA to 3’ end
  4. splicing of introns in some tRNAs
  5. numerous modifications at multiple residues
28
Q

First step in mRNA processing.

A

Addition of 5’ cap- 7-methylguanosine covalently attached to pre-mRNA
*occurs soon after RNA Pol II starts transcript (RNA chain about 20-30nt long)

29
Q

What functions does the 5’ cap serve (4)?

A
  1. protects mRNA from degradation
  2. important for splicing of 1st intron
  3. important for mRNA transportation to cytoplasm
  4. increases translational efficiency
30
Q

Second step in mRNA processing.

A

Addition of poly-A tail to 3’ end
Poly A Polymerase adds up to 250 adenylate residues to the 3’ end
*tail is progressively shortened by 3’exonucleases
*tail increases time required for nucleases to reach coding region

31
Q

Functions of the poly A tail.

A
  1. increases mRNA stability
  2. increases translational efficiency
  3. splicing of last intron
32
Q

Protein coding genes in eukaryotic DNA are organized in _________ fashion. Protein-coding sections are called ___ and are interrupted by noncoding sections called _____.

A

Organized in discontinuous fashion, coding sections called exons and noncoding sections called introns

33
Q

Final step of mRNA processing.

A

RNA splicing- removal of introns to make functional mRNA

34
Q

How are regions to be spliced determined?

A

Hypothesis is that cis elements or splice sites on RNA define regions to be spliced.
Exon-intron boundaries are marked by specific sequences: intron starts w/ GU, ends w/ AG

35
Q

Steps in intron splicing

A
  1. Binding of U1, U2 snRNPs
  2. Binding of U4, U5, U6 snRNPs
  3. Rearrangement of base-pair interactions btw snRNAs, release of U1 and U4 snRNPs
  4. Catalytic core (formed by U2, U6) catylzes 1st transesterification rxn
  5. Further rearrangements btw U2, U6, U5 lead to 2nd transesterification rxn
  6. Produces lariat intron
36
Q

What happens to the lariat intron?

A

Linearized by debranching enzymes and further degraded in exosomes.
*some introns end up as functional RNAs (different from mRNA)

37
Q

What is the importance of alternative splicing?

A

Increases protein diversity- a single gene can produce many proteins that may function differently

38
Q

Sex in Drosophila is largely determined by __________.

A

Alternative splicing
female- exons 1,3
male- exons 1,2,3

39
Q

Types of alternative splicing events

A

See notes.

40
Q

Do mRNAs also undergo editing?

A

YES

41
Q

How is mRNA processed?

A

RNA editing- refers to rxns that change the nucleotide sequence of mRNA molecule by nonsplicing molecules
*change may include nucleotide change, deletion, insertion

42
Q

Mutations in either ______ or _______ can result in pathological conditions

A

either pre-mRNA or splicing factors

43
Q

Defects in splicing or alternative splicing may cause up to __ of all genetic diseases.

A

15%

44
Q

What is retinitis pigmentosa?

A

A disease of acquired blindness, due to mutation in the U4-U5–U6 tri-snRNP

45
Q

Transcription and processing of mRNA are ____.

A

coupled

46
Q

What coordinates transcription and splicing?

A

The carboxyl-terminal domain (CTD) of RNA pol II

47
Q

3 functions of the CTD.

A
  1. recruiting enzymes to synthesize the 5’ cap
  2. recruiting components of splicing complex
  3. recruiting endonuclease that cleave pre-mRNA to expose site for polyA addition
48
Q

What happens to mRNA after it’s processed?

A

It’s packaged and exported from the nucleus to the cytoplasm for translation.

49
Q

What is transesterification?

A

Process in which an ester and alcohol react to give another ester with a different alkoxy group

Biochemistry Final Prep (6 decks)

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