ch 16 & 17 quiz

Describe how epigenetic changes can be targeted via transcription factors or noncoding RNAs (Figure 16.1)

TFs and ncRNAs recognize specific sequences and recruit other proteins (ex: DNA methyltransferase and histone-modifying enzymes) to change chromatin structure - alters expression of the gene and changes are maintained in subsequent generations

Explain the function of reader domains (Figure 16.5)

reader domains recognize a particular PTM in histones and binds to it - can catalyze addition of PTMs with writer domain, or removal with eraser domain

Explain how epigenetic changes can occur via environmental factors (Figures 16.13, 16.14)

- mutation in agouti gene caused by a TE upstream from the normal agouti promoter - DNA methylation inhibits agouti gene - darkness of color correlates to increased methylation of CpG islands w/in the TE, due to chemicals in diet

Describe the steps in the mechanism of RNA interference (RNAi) (Figure 17.6).

- presiRNA (exogenous) and premiRNA (endogenous) recognized by dicer and chopped into 20-25 ds nucleotide pieces - RISC protein complex binds trimmed RNAs and gets rid of 1 of 2 strands - mismatches from miRNAs inhibits translation; perfect match from siRNAs degrades mRNA

List the 5 general functions of ncRNAs (Figures 17.2, 17.3)

- scaffold: binds to group of proteins - guide: binds to protein and guides it to specific site in cell (causes complex to form) - ribozyme: RNA has catalytic function - blocker: physically blocks a cellular process from happening - decoy: recognizes another ncRNA sequence and sequesters it

Explain how epigenetic changes can occur during development: genomic imprinting Igf2 gene (Figure 16.9)

- Igf 2 de novo methylated during sperm formation only - methylation inhibits CTCF-binding factor, which allows Igf2 to be stimulated by nearby enhancer (males) - contrast: CTCF-binding factor binds to unmethylated gene and inhibits transcription by forming loop (females)

Compare and contrast the similarities and differences between constitutive and facultative heterochromatin

- constitutive heterochromatin: regions of heterochromatin at the same location in all cell types - facultative heterochromatin: heterochromatin that varies in its location among different cell types

Analyze the results of Fire and Mello and describe how they are consistent with the idea that double-stranded RNA is a more potent inhibitor of mRNA compared to antisense RNA (Figure 17.5)

- embryos that received antisense RNA, mex-3 mRNA levels were decreased, but detectable - embryos that received double-stranded RNA, no mex-3 mRNA detected - the double-stranded RNA caused the mex-3 mRNA to be degraded

List the phases of heterochromatin formation (Figure 16.8)

1. nucleation: short chromosomal site bound by chromatin-modifying enzymes and chromatin-remodeling complex 2. spreading: adjacent euchromatin turned to heterochromatin 3. barrier: spreading stops when interphase chromosomes reach a barrier

Explain how epigenetic changes can occur during development: the formation of specific cell types (Figure 16.11)

2 types of polycomb group complexes - PG1: can inhibit transcription with chromatin compaction, covalent modification of histones, or interaction with TFs - PG2: binds to polycomb response element and leads to trimethylation of Lys 27 on histone 3

When mice carrying the Avy allele exhibit a darker coat, this phenotype is thought to be caused by dietary factors that result in A. a higher level of DNA methylation and a decrease in the expression of the Agouti gene. B. a lower level of DNA methylation and a decrease in the expression of the Agouti gene. C. a higher level of DNA methylation and overexpression of the Agouti gene. D. a lower level of DNA methylation and overexpression of the Agouti gene.

A

During the process of XCI, which chromosome expresses the Xist gene and which one expresses the Tsix gene? A. Xist is expressed only by Xa, and Tsix is expressed only by Xi. B. Xist is expressed only by Xi, and Tsix is expressed only by Xa. C. Xist is expressed by Xa, and Tsix is also expressed by Xa. D. Xist is expressed by Xi, and Tsix is also expressed by Xi

B

In one cell, gene C is expressed, whereas in another cell, gene C is inactive. After the cells are fused experimentally, both copies of gene C are expressed. This observation could be explained by A. a cis-epigenetic mechanism. B. a trans-epigenetic mechanism. C. DNA methylation. D. both a and b.

B

Scientists propose that the first macromolecules in protobionts were A. DNA molecules. B. RNA molecules. C. proteins. D. all of the above.

B

When an ncRNA functions as a decoy, it A. contains binding sites for many different proteins, thereby promoting the formation of a large complex. B. recognizes other ncRNAs and sequesters them, thereby preventing them from functioning. C. can alter its conformation, allowing it to switch between active and inactivate conformations. D. may physically prevent or block a cellular process from happening.

B

A form of chromatin that silences gene expression and varies in location among different types of cells is A. euchromatin. B. constitutive heterochromatin. C. facultative heterochromain. D. Both b and c are forms of chromatin with these characteristics.

C

An epigenetic modification to a specific gene may initially be established by A. a transcription factor. B. a non-coding RNA. C. either a or b. D. none of the above.

C

For the Igf2 gene, where do de novo methylation and maintenance methylation occur? A. De novo methylation occurs in sperm, and maintenance methylation occurs in egg cells. B. De novo methylation occurs in egg cells, and maintenance methylation occurs in sperm cells. C. De novo methylation occurs in sperm, and maintenance methylation occurs in the somatic cells of offspring. D. De novo methylation occurs in egg cells, and maintenance methylation occurs in the somatic cells of offspring.

C

If the VIN3 gene had a loss-of-function mutation, how do you think that would affect the phenotypes of summer-annual and winter-annual Arabidopsis plants? A. Neither type would flower. B. Both types would flower at the proper time. C. The summer type would flower, but the winter type would not. D. The winter type would flower, but the summer type would not.

C

In the CRISPR-Cas system, what does tracrRNA bind to? A. crRNA and Cas1 protein B. crRNA and Cas2 protein C. crRNA and Cas9 protein D. Cas1 and Cas2 proteins

C

Which of the following is not an important function of heterochromatin formation? A. Gene silencing B. Prevention of viral proliferation C. Splicing of pre-mRNA D. Prevention of movement of transposable elements

C

Epigenetic changes may A. be programmed during development. B. be caused by environmental factors. C. involve changes in the DNA sequence of a gene. D. Both a and b are true of epigenetic changes.

D

Heterochromatin is characterized by which of the following? A. Higher level of compaction B. Silencing of gene transcription C. Localization at the periphery of the cell nucleus D. All of the above are characteristics of heterochromatin.

D

The process of RNA interference may lead to A. the degradation of an mRNA. B. the inhibition of translation of an mRNA. C. the synthesis of an mRNA. D. both a and b.

D

When facilitating the methylation or pseudouridylation of an rRNA, a snoRNA functions as A. a decoy. B. a scaffold. C. a guide. D. both b and c

D

Which of the following components are needed for the adaptation phase of the CRISPR-Cas system? A. crRNA and Cas1 protein B. crRNA and Cas2 protein C. crRNA and Cas9 protein D. Cas1 and Cas2 proteins

D

Which of the following function(s) is/are carried out by piRITS or piRISC? A. Inhibits transcription of TEs B. Causes the degradation of TE RNA C. Causes chromosome breakage D. Both a and b are functions of piRITS or piRISC.

D

Which of the following functions does HOTAIR perform? A. Decoy B. Scaffold C. Guide D. Both b and c

D

Which of the following mechanisms may be involved when PRC1 complexes silence gene expression? A. The compaction of nucleosomes B. The attachment of ubiquitin to histone proteins C. The direct inhibition of transcription factors, such as TFIID D. Any of the above may be involved in silencing of gene expression by PRC1 complexes.

D

Which of the following statements is/are true regarding a barrier? A. A barrier stops the spreading of heterochromatin. B. A barrier forms a boundary between euchromatin and heterochromatin. C. A barrier prevents DNA replication. D. Both a and b are true

D

List the possible molecular mechanisms that maintain heterochromatin during cell division

DNA methylation, histone modification, DNA poly recruits chromatin-modifying complex, higher order structure favoring reformation of heterochromatin

Explain how epigenetic changes can occur during development: X-chromosome inactivation (Figure 16.10)

DO THIS OR LOOK

Describe the higher order structure of heterochromatin in the cell nucleus, including the role of HP1 protein (Figure 16.7)

HP1 protein forms a dimer binding two nucleosomes carrying H3K9me3 modification, holding them in close association - formation of loop domains follows - heterochromatin binds to the nuclear lamina (fibrous layer of proteins lining inner nuclear membrane)

Which of the following can bind to ncRNAs? A. DNA B. RNA C. Proteins D. Small molecules E. All of the above

E

Which of the following are examples of molecular changes that can have an epigenetic effect on gene expression? A. Chromatin remodeling B. Covalent histone modification C. Localization of histone variants D. DNA methylation E. Feedback loops F. All of the above can have an epigenetic effect on gene expression

F

Explain how HOTAIR ncRNA inhibits transcription (Figure 17.4)

acts as a scaffold that guides histone-modifying complexes to their target genes - PRC2 complex and LSD1 complex binds to 5' and 3' end of HOTAIR - HOTAIR binds to GA-rich region next to a target gene

Explain how the CRISPR-Cas system provides bacteria with defense against bacteriophages (Figure 17.9)

adaptation - when bacteriophage infects a cell, Cas1 and Cas2 are expressed and the proteins form a complex that cleaves bacteriophage into small pieces expression - piece of bacteriophage inserted into Crispr gene - genes encoding tracrRNA and precrRNA transcribed - tracrRNAs bind to precrRNAs and cleave them to crRNAs - Cas9 gene expressed; tracrRNA-crRNA complex binds to Cas 9 protein interference - tracrRNA-crRNA-Cas9 complex recognizes bacteriophage DNA - Cas9 cleave bacteriophage DNA into pieces, inactivating it

Describe the ability of ncRNAs to bind to other molecules (Figure 17.1)

can bind to - DNA and other RNAs via complementary base pairing - proteins by forming stem-loop structures