chapter 12

Question 1

What are the molecular mechanisms of gene regulation in eukaryotes?

Answer 1

Involves numerous regulatory proteins, chromatin modifications, and RNA molecules.

Key factors include transcription factors, chromatin remodeling complexes, and epigenetic modifications.

Question 2

How do eukaryotes generate many different patterns of gene expression?

Answer 2

Through a limited number of regulatory proteins that interact in combinatorial ways to control various genes.

This allows for complex gene regulation despite fewer proteins compared to prokaryotes.

Question 3

What role does chromatin play in eukaryotic gene regulation?

Answer 3

Chromatin affects the accessibility of regulatory proteins to DNA sequences, requiring modifications for gene expression.

Chromatin structure can be dynamically altered to expose or hide regulatory sites.

Question 4

What are epigenetic marks?

Answer 4

Chemical modifications to DNA or histones that influence gene expression without altering the DNA sequence.

Examples include DNA methylation and histone acetylation.

Question 5

What roles do RNA molecules play in repressing eukaryotic gene expression?

Answer 5

Small RNAs, such as miRNAs, can bind to messenger RNAs to inhibit translation or promote degradation.

This is a form of post-transcriptional regulation.

Question 6

Contrast gene regulation in prokaryotes and eukaryotes.

Answer 6

Prokaryotes use single activators/repressors; eukaryotes use numerous regulatory proteins and lack operons.

Eukaryotic gene regulation is more complex due to chromatin structure.

Question 7

What is the ‘ground state’ of gene expression in prokaryotes?

Answer 7

The ground state is ON, meaning genes are generally accessible for transcription.

This contrasts with eukaryotes, where the ground state is OFF.

Question 8

What is the ‘ground state’ of gene expression in eukaryotes?

Answer 8

The ground state is OFF, requiring chromatin modification for gene accessibility.

Eukaryotic genes are packaged in chromatin, making them less accessible.

Question 9

What is a nucleosome?

Answer 9

A fundamental unit of chromatin composed of a histone octamer and approximately 150 base pairs of DNA.

Nucleosomes help package DNA into a compact structure.

Question 10

What is the function of histone acetyltransferases (HATs)?

Answer 10

Enzymes that add acetyl groups to histone tails, leading to gene activation.

HATs are crucial for modifying chromatin and facilitating transcription.

Question 11

What are coactivators?

Answer 11

Proteins or protein complexes that assist in the activation of gene expression without binding to DNA.

Examples include the Mediator complex which aids in recruiting RNA polymerase.

Question 12

How does the GAL system in yeast regulate gene expression?

Answer 12

GAL genes are turned ON in the presence of galactose and OFF when it is absent, controlled by GAL3, GAL4, and GAL80 proteins.

GAL4 acts as a transcription factor that activates GAL gene expression.

Question 13

What is the role of the SWI/SNF complex?

Answer 13

A chromatin remodeling complex that reposition nucleosomes to expose regulatory sequences.

It is essential for making DNA accessible for transcription factors.

Question 14

What is the effect of histone deacetylases (HDACs)?

Answer 14

Enzymes that remove acetyl groups from histones, leading to gene repression.

HDACs play a critical role in turning off gene transcription.

Question 15

What is DNA methylation?

Answer 15

The addition of methyl groups to cytosine residues in DNA, influencing gene expression and chromatin structure.

Methylation patterns can be inherited and affect gene accessibility.

Question 16

What are enhancers in gene regulation?

Answer 16

Cis-regulatory elements that can increase gene expression levels in a flexible manner.

Enhancers can function like a ‘dimmer switch’ for gene expression.

Question 17

What is combinatorial regulation?

Answer 17

The process by which combinations of transcription factors control the expression of specific genes.

This is key for generating diverse cell types and functions in multicellular organisms.

Question 18

What is the significance of the GAL4 protein?

Answer 18

It is a key transcription factor that activates the transcription of GAL genes in yeast.

GAL4 binds to upstream activation sequences to enhance transcription.

Question 19

Fill in the blank: The presence of a _______ in eukaryotic promoters is often crucial for initiating transcription.

Answer 19

TATA-box

Question 20

True or False: Eukaryotic gene expression can occur without chromatin modifications.

Answer 20

False

Question 21

Fill in the blank: The fundamental unit of chromatin is the _______.

Answer 21

nucleosome

Question 22

What is the role of the MCM1 transcription factor in yeast?

Answer 22

It turns on the expression of ‘a’-specific genes in yeast mating types.

MCM1 interacts with other proteins to regulate gene expression.

Question 23

What does hyperacetylation of histones indicate?

Answer 23

It is often associated with highly expressed genes.

This modification reduces the interaction between DNA and histones, facilitating transcription.

Question 24

What is the function of enhancers in gene expression?

Answer 24

Enhancers adjust the level of gene expression, functioning like a ‘dimmer switch’.

Question 25

Define enhanceosome.

Answer 25

A large protein complex that acts synergistically to activate transcription.

Question 26

What is required for high levels of transcription in enhanceosomes?

Answer 26

All proteins must be present and physically interacting.

Question 27

What does the β-interferon enhanceosome recruit?

Answer 27

It recruits the coactivator protein CBP.

Question 28

List the two functions of CBP.

Answer 28

* Modifies nucleosomes to make promoter region accessible * Recruits transcriptional machinery (RNA polymerase II)

Question 29

What do enhancer-blocking insulators do?

Answer 29

They prevent enhancer activation by blocking transcriptional activation at the promoter.

Question 30

What is the significance of 'position effect' in gene silencing?

Answer 30

Gene silencing depends on the chromatin neighborhood where a gene is located.

Question 31

Differentiate between heterochromatin and euchromatin.

Answer 31

* Heterochromatin: highly condensed chromatin * Euchromatin: less condensed chromatin

Question 32

What are silent information regulators (SIR) mutants?

Answer 32

Mutants that express both HMLα and HMRa gene information, which are normally silent.

Question 33

What role does Sir2 play in chromatin regulation?

Answer 33

Sir2 is a histone deacetylase that facilitates chromatin condensation into an inactive domain.

Question 34

What is epigenetic silencing?

Answer 34

Gene is shut off due to spreading of repressive chromatin into the gene region, not due to mutation.

Question 35

What is position-effect variegation (PEV)?

Answer 35

A phenomenon where expression is repressed due to the gene's position in a chromosome.

Question 36

What is genomic imprinting?

Answer 36

A genetic phenomenon where certain genes are expressed in a parent-of-origin specific manner.

Question 37

What causes an allele to be imprinted?

Answer 37

Imprinting is determined by the parent from whom the allele was inherited, not by DNA sequence.

Question 38

Define maternal imprinting.

Answer 38

An allele of the Igf2 gene is expressed only if inherited from the father; maternal allele is inactive.

Question 39

What is the imprinting control region (ICR)?

Answer 39

The region between the Igf2 and H19 genes, methylated in male but not female gametes.

Question 40

What is the Barr body?

Answer 40

The inactive X-chromosome in female mammals, which is epigenetically marked.

Question 41

Fill in the blank: Gene expression often correlates with the number of gene copies, known as _______.

Answer 41

dosage

Question 42

What is dosage compensation?

Answer 42

A mechanism that adjusts X-chromosome gene dosage to be equal between sexes.

Question 43

What is the role of the MSL complex in Drosophila?

Answer 43

It doubles male X-chromosome gene expression.