Epigenetics (Practice MC Questions)

Which of the following best defines epigenetics?

A. Mutations in the DNA sequence

B. Heritable changes in gene expression without altering DNA sequence

C. Random changes in nucleotide order

D. Genetic recombination events

E. Permanent modifications of the DNA backbone

B

Which of the following is not an epigenetic mechanism?

A. DNA methylation

B. Histone modification

C. Long noncoding RNA (lncRNA)

D. Alternative splicing

E. Chromatin remodeling

D

DNA methylation primarily occurs on which base?

A. Adenine

B. Cytosine

C. Guanine

D. Thymine

E. Uracil

B

DNA methyltransferases (DNMTs) add a methyl group at what position on cytosine?

A. 3' carbon

B. 2' carbon

C. 5' carbon

D. 1' carbon

E. N7 position

C

CpG dinucleotides are regions where:

A. Cytosine is bonded to phosphate

B. Cytosine is followed by guanine

C. Guanine precedes adenine

D. Thymine pairs with adenine

E. Guanine is methylated

B

Which type of DNMT adds methyl groups to previously unmethylated DNA?

A. Maintenance DNMT

B. De novo DNMT

C. CpG DNMT

D. TET DNMT

E. Passive DNMT

B

Which enzyme removes methyl groups during active DNA demethylation?

A. HDAC

B. DNMT

C. TET enzyme

D. RNA polymerase

E. HAT

C

The enzyme Dnmt1 is primarily responsible for:

A. De novo methylation

B. Maintenance methylation after replication

C. Histone acetylation

D. Adding phosphate groups

E. Removing methyl groups

B

Which of the following correctly describes passive demethylation?

A. Direct enzymatic removal of methyl groups

B. Failure to maintain methylation after DNA replication

C. Random addition of methyl groups

D. Enzymatic conversion of cytosine to thymine

E. Loss of histone acetylation

B

The process by which cytosine is converted to 5-hydroxymethylcytosine involves:

A. DNMT

B. HDAC

C. TET enzymes

D. RNA polymerase

E. Ligase

C

Highly methylated promoters are generally associated with:

A. Active transcription

B. Increased translation

C. Gene silencing

D. Chromatin decondensation

E. Histone acetylation

C

Which statement about CpG islands is true?

A. They make up most of the genome

B. They are usually unmethylated

C. They occur near promoters

D. They are located only in mitochondria

E. They cannot be demethylated

C

Which of the following factors can influence epigenetic changes?

A. Environment

B. Age

C. Lifestyle

D. Disease

E. All of the above

E

Which term describes the gradual loss of epigenetic marks over time?

A. Epigenetic drift

B. Genetic mutation

C. Chromosomal inversion

D. Methylation burst

E. Reprogramming

A

Which enzyme class adds modifications to histone tails?

A. Readers

B. Erasers

C. Writers

D. Recruiters

E. Binders

C

Histone acetylation occurs on which amino acid residue?

A. Arginine

B. Lysine

C. Serine

D. Threonine

E. Histidine

B

Which enzyme removes acetyl groups from histones?

A. HAT

B. DNMT

C. HDAC

D. TET

E. HKMT

C

Histone acetylation generally causes:

A. Chromatin condensation and gene silencing

B. Chromatin relaxation and gene activation

C. DNA methylation

D. Protein degradation

E. Chromosome loss

B

Which enzyme adds methyl groups to histones?

A. HDAC

B. HAT

C. HKMT

D. DNMT

E. TET

C

Histone methylation can lead to:

A. Only activation

B. Only repression

C. Either activation or repression

D. No change in expression

E. Permanent DNA mutation

C

What does "H3K4me3" represent?

A. Histone 3 lysine 4 tri-methylated

B. Histone 4 lysine 3 mono-methylated

C. Histone 3 lysine 3 acetylated

D. Histone 4 lysine 3 phosphorylated

E. Histone 2 lysine 4 tri-methylated

A

Which term describes enzymes that remove histone modifications?

A. Writers

B. Readers

C. Erasers

D. Activators

E. Transferases

C

Which is an example of a histone "reader" domain?

A. Chromodomain

B. HAT

C. HDAC

D. DNMT

E. TET

A

When chromatin is tightly packed and histones are deacetylated, transcription is:

A. Increased

B. Inhibited

C. Unaffected

D. Irregular

E. Randomized

B

Which histone modification most directly competes with acetylation on lysine residues?

A. Methylation

B. Phosphorylation

C. Ubiquitination

D. Glycosylation

E. SUMOylation

A

The Agouti gene in mice demonstrates that:

A. DNA mutations control fur color

B. Methylation of DNA can affect phenotype

C. RNA splicing determines color

D. Gene duplication causes obesity

E. Recombination changes coat color

B

The offspring of BPA-exposed mice were rescued by:

A. Gene knockout

B. Methyl-rich maternal diet

C. RNA interference

D. Vitamin D supplements

E. Removing the Agouti gene

B

Which of the following best describes extrinsic histone modification?

A. Originates within the cell

B. Caused by environmental or mechanical factors

C. Occurs in the mitochondria

D. Only affects cytosolic proteins

E. Irreversible

B

Which enzyme class interprets histone marks and recruits other modifiers?

A. Writers

B. Erasers

C. Readers

D. Synthases

E. Ligases

C

Which of the following best defines non-coding RNA (ncRNA)?

A. RNA molecules that code for proteins

B. RNA molecules that do not code for proteins

C. Ribosomal RNA only

D. Mitochondrial RNA only

E. Messenger RNA

B

Which of the following is not a type of ncRNA?

A. rRNA

B. tRNA

C. miRNA

D. lncRNA

E. mRNA

E

Long noncoding RNAs (lncRNAs) are involved in:

A. Protein translation

B. Gene silencing and chromatin remodeling

C. Ribosome assembly

D. RNA splicing

E. mRNA degradation only

B

Which function is associated with guide lncRNAs?

A. Repress gene activation

B. Bring protein complexes to specific genomic locations

C. Form chromatin loops

D. Block miRNAs

E. Scaffold multiple proteins

B

Which lncRNA function involves repressing gene activation?

A. Guide

B. Scaffold

C. Decoy

D. Sponge

E. Loop formation

C

lncRNAs that "sponge" miRNAs result in:

A. Decreased gene expression

B. Increased gene expression

C. Gene silencing

D. DNA methylation

E. Histone deacetylation

B

The formation of chromatin loops by lncRNA helps:

A. Block transcription

B. Physically bring promoters and regulatory regions together

C. Unwind DNA helices

D. Create double-stranded RNA

E. Degrade histones

B

Which of the following enzymes adds acetyl groups to histones?

A. HDAC

B. DNMT

C. HAT

D. HKMT

E. TET

C

Which category of histone modification relies on effector proteins?

A. Intrinsic

B. Extrinsic

C. Effector-mediated

D. Indirect

E. Post-replicative

C

What is the overall charge effect of histone acetylation?

A. Increases histone positive charge

B. Reduces positive charge, loosening DNA interaction

C. Increases DNA-histone affinity

D. Neutralizes DNA charge

E. Adds negative charge to histones

B

Which statement about histone modifications is false?

A. They are covalent

B. They are reversible

C. They ONLY occur on histone tails

D. They can regulate transcription

E. They can influence DNA repair

C

Which pairing correctly matches the modifier enzyme with its function?A. DNMT - adds acetyl groups

B. HDAC - removes methyl groups

C. HKMT - adds methyl groups

D. HAT - removes phosphate groups

E. TET - adds methyl groups

C

Which process is used by CRISPR-Cas9 for DNA repair using a template?

A. Non-homologous end joining

B. Homology-directed repair

C. Base excision repair

D. Nucleotide excision repair

E. Replication-coupled ligation

B

Which component of CRISPR recognizes the target DNA sequence?

A. Cas9 enzyme

B. PAM site

C. gRNA

D. RNA polymerase

E. dCas9

C

The Cas9 protein's main function is to:

A. Bind RNA

B. Make double-stranded DNA cuts

C. Add methyl groups

D. Ligate fragments

E. Degrade mRNA

B

Which of the following is required for Cas9 to bind DNA?

A. Guide RNA

B. PAM site

C. Both A and B

D. DNA methylation

E. None of the above

C

CRISPRoff is designed to:

A. Cut DNA and insert new genes

B. Silence genes by methylation

C. Activate transcription factors

D. Remove histone acetylation

E. Create DNA breaks

B

The protein used in CRISPRoff is:

A. Active Cas9

B. Deactivated Cas9 (dCas9)

C. PAMase

D. gRNAase

E. TET enzyme

B

CRISPRoff-induced silencing is reversible by:

A. DNA ligase

B. Modified Cas9 demethylase

C. RNA polymerase

D. HDAC

E. DNMT

B

The "information theory of aging" proposes that:

A. Mutations cause aging

B. Telomere length directly causes aging

C. RNA decay shortens lifespan

D. Epigenetic information loss leads to aging

E. Protein folding errors accumulate

D

Epigenetic drugs can work by:

A. Inhibiting DNA methyltransferases

B. Increasing mutation rates

C. Blocking transcription factors

D. Degrading histone proteins

E. Cutting DNA strands

A

A population of genetically identical mice exhibits different coat colors despite having the same agouti gene. Researchers find that differences in maternal diet alter methylation patterns in the offspring. Which conclusion is most consistent with this observation?

A. DNA sequence mutations caused the phenotypic variation

B. Environmental factors induced heritable epigenetic changes

C. Random genetic drift caused the color variation

D. The agouti gene was deleted in some mice

E. Post-translational modification of histones was permanently lost

B

A tumor cell line shows hypermethylation at the promoter region of a tumor suppressor gene. Which of the following outcomes would most likely result?

A. Increased transcription of the tumor suppressor gene

B. Decreased expression of the tumor suppressor gene

C. Activation of DNA repair enzymes

D. Overproduction of histone acetyltransferases

E. Chromatin opening and gene activation

B

A scientist treats cells with a histone deacetylase (HDAC) inhibitor. Which change in chromatin structure and gene activity would you expect?

A. Chromatin condensation; decreased transcription

B. Chromatin relaxation; increased transcription

C. Chromatin condensation; unchanged transcription

D. No change in chromatin but decreased transcription

E. DNA methylation increases

B

A researcher uses a CRISPRoff system to silence a gene in stem cells. Which best explains the mechanism by which CRISPRoff achieves gene repression?

A. It removes promoter methylation

B. It cuts DNA at a specific locus

C. It recruits dCas9 to add methylation at the target site

D. It acetylates histones near the gene promoter

E. It prevents DNA replication

C

In a study on aging, scientists observe that aged cells show loss of DNA methylation in specific regions and gain in others, causing misexpression of developmental genes. Which concept does this illustrate?

A. Genetic mutation theory

B. Epigenetic drift

C. Genomic imprinting

D. Non-homologous repair

E. Transcriptional interference

B

A mutation in a "reader" protein's bromodomain prevents it from binding acetylated histones. Which process would most likely be disrupted?

A. Recognition of active gene regions

B. Addition of methyl groups to histones

C. Conversion of 5mC to 5hmC

D. Synthesis of noncoding RNAs

E. DNA replication initiation

A

Scientists discover that a particular lncRNA brings a chromatin-modifying complex to silence a cluster of genes on one chromosome, similar to X-inactivation. This lncRNA most likely functions as a:

A. Decoy

B. Scaffold

C. Guide

D. Sponge

E. Enhancer RNA

C

A researcher notes that demethylation of CpG islands in a normally silent gene leads to histone acetylation and transcriptional activation. What can be concluded about the interaction between DNA methylation and histone modification?

A. They are independent processes with no cross-talk

B. Demethylation promotes chromatin opening through histone acetylation

C. Histone acetylation inhibits demethylation

D. DNA methylation directly causes histone methylation

E. Both always lead to transcriptional repression

B

After CRISPR-Cas9 treatment, a cell repairs a DNA cut by inserting a new DNA template sequence provided by the scientist. Which DNA repair pathway was used?

A. Base excision repair

B. Non-homologous end joining (NHEJ)

C. Homology-directed repair (HDR)

D. Mismatch repair

E. Translesion synthesis

C

A diet rich in folate, vitamin B12, and choline increases the availability of methyl donors in cells. What long-term epigenetic effect might this have on gene expression?

A. Increased global methylation and potential gene silencing

B. Decreased methylation and global gene activation

C. Permanent mutations in DNA

D. Loss of histone modifications

E. Inhibition of DNMT enzymes

A