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Biochem FINAL > Chapter 37 and 38: Eukaryotic Gene Expression, Regulation and Processing > Flashcards

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

1
Q

Differences between prokaryotes and eukaryotes: Genome?

A

Prokaryotes: Circular, like “plasmids”
Eukaryotes: Found in chromosomes; nucleosome structure limits DNA accessibility

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2
Q

Differences between prokaryotes and eukaryotes: Size of genome?

A

Prokaryotes: Small
Eukaryotes: Large

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3
Q

Differences between prokaryotes and eukaryotes: Location of gene transcription and translation?

A

Prokaryotes: Coupled; no nucleoid envelope
Eukaryotes: Nuclear transcription and cytoplasmic translation

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4
Q

Differences between prokaryotes and eukaryotes: Gene clustering?

A

Prokaryotes: Operons where genes with similar function are grouped together
Eukaryotes: Operons generally not found; each gene has its own promotor element

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5
Q

Differences between prokaryotes and eukaryotes: Default state of transcription

A

Prokaryotes: On
Eukaryotes: Off

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6
Q

Differences between prokaryotes and eukaryotes: DNA structure?

A

Prokaryotes: Highly supercoiled DNA with some associated proteins
Eukaryotes: Highly supercoiled chromatin associated with histones and nuclesomes

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7
Q

What is constitutive gene expression?

A

Always on and important in housekeeping genes

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8
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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9
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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10
Q

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

A

Steroid

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11
Q

An example of a steroid is: Estradiol - describe

A

Controls genes in the development of female secondary sex characteristics - must bind to estrogen receptor to exert its gene regulatory effect

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12
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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13
Q

How does hormone binding cause dissociation of HSP in class 1? (4)

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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14
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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15
Q

How do nuclear hormone receptors function?

Have 2 conserved domains:

A
  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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16
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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17
Q

Steroid hormone receptors are targets for ____.

A

Drugs

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18
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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19
Q

Example of drug targeting steroid hormone receptor and how it works.
Ex: Tamoxifen (3)

A
  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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20
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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21
Q

What is an example of a corepressor?

A

HDACs

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22
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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23
Q

What is an example of a coactivator?

A

HATs

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24
Q

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

A

acetyl CoA (made by ATP-citrate lyase)

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25
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.
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26
Q

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

A

Are reversible and targeted for drug therapy

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27
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.

28
Q

What are the main 3 types of RNA molecules?

A
  1. messenger RNA (mRNA)
  2. transfer RNA (tRNA)
  3. ribosomal RNA (rRNA)
29
Q

mRNA

A

intermediates that carry genetic info from DNA to ribosomes, transcribed by RNA pol II

30
Q

tRNA

A

adaptors btw amino acids and codons in mRNA synthesized, transcribed by RNA pol III

31
Q

rRNA

A

structural and catalytic components of ribosomes, transcribed by RNA pol I

32
Q

What are 4 other types of RNA molecules?

A
  1. small nuclear RNA (snRNA)
  2. micro RNA (miRNA)
  3. RNAi
  4. piRNA (Piwi-interacting RNA)
33
Q

snRNA

A

structural components of spliceosomes, transcribed by pol II or pol III

34
Q

miRNA

A

short single-stranded RNAs that block expression of complementary mRNAs, transcribed by pol II

35
Q

RNAi

A

similar to miRNA, RNA interference, transcribed by pol IV

36
Q

piRNA

A

small non-coding RNA molecule

37
Q

The primary rRNA transcript contains what subunits?

A
  • it is about 7500nt, 45S RNA

- contains subunits 18S, 5.8S, 28S

38
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

39
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
40
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)

41
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
42
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

43
Q

Functions of the poly A tail.

A
  1. increases mRNA stability
  2. increases translational efficiency
  3. splicing of last intron
44
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

45
Q

Final step of mRNA processing.

A

RNA splicing - removal of introns to make functional mRNA

46
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

47
Q

Steps in intron splicing (6)

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
48
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)

49
Q

What is the importance of alternative splicing?

A

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

50
Q

Sex in Drosophila is largely determined by __________.

A

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

51
Q

Types of alternative splicing events

A

See notes pg. 20

52
Q

Do mRNAs also undergo editing?

A

YES

53
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

54
Q

Mutations in either ______ or _______ can result in pathological conditions

A

either pre-mRNA or splicing factors

55
Q

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

A

15%

56
Q

What is retinitis pigmentosa?

A

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

57
Q

Transcription and processing of mRNA are ____.

A

Coupled

58
Q

What coordinates transcription and splicing?

A

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

59
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
60
Q

What happens to mRNA after it’s processed?

A

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

61
Q

What is transesterification?

A

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

62
Q

Which statement about splicing is TRUE?
A. splicing occurs on tRNA, rRNA and mRNA
B. splicing is carried out by the ribosome
C. splicing removes exon sequences
D. splicing occurs in the cytoplasm
E. splicing requires the 5’ cap

A

Splicing requires the 5’ cap

63
Q

If the polyA polymerase in a cell contained a mutation which made it add very short (approximately 50 nucleotides) poly A tails to mRNA, what would be the most likely effect on mRNA half-life?
A. the average mRNA half-life would not be effected
B. the average mRNA half-life would be increased
C. the average mRNA half-life would be decreased
D. the half-life of housekeeping messages would not be changed, but the half-life of other messages would be decreased
E. the half-life of housekeeping messages would not be changed, but the half-life of other messages would be increased

A

The average mRNA half-life would be decreased

64
Q 
Acetylation of \_\_\_\_\_\_\_\_\_ in histones is involved in activation of transcription.
A.	serine residues
B.	threonine residues
C.	arginine residues
D.	lysine residues
E.	tryptophan residues
A

Lysine residues

65
Q 
The bond formed between GMP and the 5’ end of the mRNA during capping is called:
A.  a 3’-5’ phosphodiester bond
B.  a disulfide bond
C.  a 5’-5’ triphosphate bond
D.  a hydrogen bond
E.  a 3’-5’ carbonyl bond
A

A 5’-5’ triphosphate bond

Biochem FINAL (6 decks)

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