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

Question 1

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

Answer 1

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

Question 2

What is constitutive gene expression?

Answer 2

Always on and important in housekeeping genes

Question 3

What types of genes are only expressed at times needed?

Answer 3

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

Question 4

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

Answer 4

conditions within the cell and to external stimuli

Question 5

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

Answer 5

Steroid

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

Question 6

How many classes of hormone gene regulatory effects are there?

Answer 6

Two

Question 7

Class 1 of hormone gene regulatory effects.

Answer 7

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

Question 8

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

Answer 8

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.

Question 9

Class 2 of hormone gene regulatory effects.

Answer 9

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

Question 10

How do nuclear hormone receptors function?

Answer 10

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

Question 11

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

Answer 11

No

Question 12

Steroid hormone receptors are targets for ____.

Answer 12

drugs

Question 13

Three types of drugs that target steroid hormones.

Answer 13

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

Question 14

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

Answer 14

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

Question 15

How does a corepressor prevent DNA opening?

Answer 15

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

Question 16

What is an example of a corepressor?

Answer 16

HDACs

Question 17

How does a coactivator encourage DNA opening?

Answer 17

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

Question 18

What is an example of a coactivator?

Answer 18

HATs

Question 19

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

Answer 19

acetyl CoA (made by ATP-citrate lyase)

Question 20

How does acetylation allow for easier transcription?

Answer 20

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.

Question 21

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

Answer 21

Are reversible and targeted for drug therapy

Question 22

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

Answer 22

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

Question 23

What are the main 3 types of RNA molecules?

Answer 23

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

Question 24

What are 4 other types of RNA molecules?

Answer 24

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

Question 25

The primary rRNA transcript contains what subunits?

Answer 25

- it is about 7500nt, 45S RNA | - contains subunits 18S, 5.8S, 28S

Question 26

What are the 2 ways rRNA are modified?

Answer 26

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

Question 27

Processing of tRNA.

Answer 27

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

Question 28

First step in mRNA processing.

Answer 28

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)

Question 29

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

Answer 29

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

Question 30

Second step in mRNA processing.

Answer 30

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

Question 31

Functions of the poly A tail.

Answer 31

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

Question 32

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

Answer 32

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

Question 33

Final step of mRNA processing.

Answer 33

RNA splicing- removal of introns to make functional mRNA

Question 34

How are regions to be spliced determined?

Answer 34

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

Question 35

Steps in intron splicing

Answer 35

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

Question 36

What happens to the lariat intron?

Answer 36

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

Question 37

What is the importance of alternative splicing?

Answer 37

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

Question 38

Sex in Drosophila is largely determined by __________.

Answer 38

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

Question 39

Types of alternative splicing events

Answer 39

See notes.

Question 40

Do mRNAs also undergo editing?

Answer 40

YES

Question 41

How is mRNA processed?

Answer 41

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

Question 42

Mutations in either ______ or _______ can result in pathological conditions

Answer 42

either pre-mRNA or splicing factors

Question 43

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

Answer 43

15%

Question 44

What is retinitis pigmentosa?

Answer 44

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

Question 45

Transcription and processing of mRNA are ____.

Answer 45

coupled

Question 46

What coordinates transcription and splicing?

Answer 46

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

Question 47

3 functions of the CTD.

Answer 47

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

Question 48

What happens to mRNA after it's processed?

Answer 48

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

Question 49

What is transesterification?

Answer 49

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