BIOS 220 Genetics Unit 2(Eukaryotic Gene expression)

What is the fundamental difference between monocistronic and polycistronic mRNA, and how does this divide prokaryotes and eukaryotes?

A) Monocistronic mRNA codes for multiple proteins and is unique to eukaryotes; polycistronic mRNA codes for one protein and is found in prokaryotes.

B) Monocistronic mRNA codes for a single protein (characteristic of eukaryotes); polycistronic mRNA carries information for multiple proteins from a single operon transcript (characteristic of prokaryotes).

C) Both prokaryotes and eukaryotes predominantly use polycistronic mRNA to coordinate gene regulation.

D) Polycistronic mRNA contains multiple 5′ caps, whereas monocistronic mRNA has a single poly(A) tail.

B) Monocistronic mRNA codes for a single protein (characteristic of eukaryotes); polycistronic mRNA carries information for multiple proteins from a single operon transcript (characteristic of prokaryotes).

Explanation: Prokaryotes group related genes into operons transcribed onto a single polycistronic mRNA. Eukaryotes transcribe genes individually as monocistronic mRNAs and generally lack operons.

Which enzyme catalyzes histone acetylation, and what is the net effect on chromatin structure and transcription?

A) Histone deacetylase (HDAC); adds acetyl groups to positively charged lysine tails, tightening DNA binding and repressing transcription.

B) Histone acetyltransferase (HAT); adds acetyl groups to neutralize positive charges on lysine tails, relaxing chromatin into euchromatin to stimulate transcription.

C) DNA methyltransferase (DNMT); adds acetyl groups directly to cytosines in DNA to open up promoters.

D) Histone methyltransferase (HMT); removes acetyl groups to condense chromatin into heterochromatin.

B) Histone acetyltransferase (HAT); adds acetyl groups to neutralize positive charges on lysine tails, relaxing chromatin into euchromatin to stimulate transcription.

Explanation: Neutralizing the positive charge on histone tails prevents them from tightly binding the negatively charged DNA backbone. Deacetylases (like FLD in plants) remove acetyl groups, promoting condensation and repression.

Where does DNA methylation typically occur in eukaryotic genomes, and what is its primary regulatory effect?

A) Adenine bases near the TATA box; stimulates transcription by attracting RNA polymerase II.

B) Cytosine bases in CpG dinucleotides (and CHG/CHH in plants); represses transcription by making DNA inaccessible and recruiting deacetylases.

C) Guanine bases in coding exons; enhances mRNA splicing efficiency.

D) Uracil residues in pre-mRNA; tags transcripts for nuclear export.

B) Cytosine bases in CpG dinucleotides (and CHG/CHH in plants); represses transcription by making DNA inaccessible and recruiting deacetylases.

Explanation: Methylation of cytosine (5-methylcytosine) leads to chromatin condensation and gene silencing. DNA methyltransferases maintain these CpG patterns on newly replicated daughter strands during cell division.

Which statement accurately describes the roles of enhancers, silencers, and insulators in eukaryotic transcription initiation?

A) Enhancers bind repressors far from the promoter, while insulators bind basal transcription factors at the TATA box.

B) Enhancers bind activators to stimulate transcription; silencers bind repressors to inhibit initiation; insulators block an enhancer's effect if positioned between the enhancer and the promoter.

C) Insulators increase transcription rates regardless of their position relative to enhancers or promoters.

D) Enhancers only function when placed downstream of the gene in a forward orientation.

B) Enhancers bind activators to stimulate transcription; silencers bind repressors to inhibit initiation; insulators block an enhancer's effect if positioned between the enhancer and the promoter.

Explanation: Enhancers can work at long distances and in any orientation, but their range of action is restricted by position-dependent insulator-binding proteins.

What defines an epigenetic modification, and what are the three primary molecular mechanisms that establish epigenetic marks?

A) Alterations to the DNA base sequence; caused by point mutations, insertions, and deletions.

B) Heritable changes in gene expression without altering the underlying DNA sequence; mediated by DNA methylation, histone modifications, and non-coding RNA molecules.

C) Irreversible changes to ribozyme activity caused by temperature shifts, environmental toxins, and GTP depletion.

D) Modifications to the ribosome structure during translation initiation, elongation, and termination.

B) Heritable changes in gene expression without altering the underlying DNA sequence; mediated by DNA methylation, histone modifications, and non-coding RNA molecules.

Explanation: Epigenetics alters how genetic information is used (accessibility) rather than changing the code itself. These marks can be passed down during cell division (and across generations).

How do microRNAs (miRNAs) and small interfering RNAs (siRNAs) differ in their origins, even though both utilize Dicer and RISC to mediate RNA interference?

A) miRNAs originate from foreign viral RNA; siRNAs are encoded directly within the host genome.

B) miRNAs are transcribed from endogenous host genes; siRNAs derive from exogenous or double-stranded RNA sources (e.g., viruses, transposons, synthetic constructs).

C) miRNAs are processed by Slicer/Argonaute; siRNAs bypass Dicer completely.

D) miRNAs increase mRNA stability; siRNAs destroy the 5′ cap and poly(A) tail.

B) miRNAs are transcribed from endogenous host genes; siRNAs derive from exogenous or double-stranded RNA sources (e.g., viruses, transposons, synthetic constructs).

Explanation: Both are cleaved into ~21-25 nucleotide fragments by Dicer and incorporated into RISC (containing Argonaute/Slicer) to target mRNAs for degradation or translational repression, but their sources differ.

While both miRNA and siRNA use Dicer and RISC to silence genes, how do their functional outcomes and target binding specificities differ?

A) miRNA generally exhibits imperfect base pairing with mRNA targets to inhibit translation; siRNA typically exhibits exact complementary base pairing to induce cleavage and degradation of mRNA.

B) miRNA cleaves target mRNA directly; siRNA only represses translation without degrading the transcript.

C) miRNA targets foreign viral RNA; siRNA exclusively targets endogenous host mRNA.

D) miRNA binds to the 5′ cap; siRNA binds exclusively to the poly(A) tail.

A) miRNA generally exhibits imperfect base pairing with mRNA targets to inhibit translation; siRNA typically exhibits exact complementary base pairing to induce cleavage and degradation of mRNA.

Explanation: Because miRNA often has imperfect complementarity with its target (usually in the 3′ UTR), it primarily represses translation. Because siRNA has exact match complementarity, Argonaute (Slicer) within RISC cleaves the mRNA, leading to rapid degradation.

What are the enzymes responsible for histone acetylation and deacetylation, and what are their respective effects on chromatin structure and transcription?

A) HAT (Histone Acetyltransferase) adds acetyl groups to lysine residues, neutralizing positive charges to relax chromatin (euchromatin) and stimulate transcription; HDAC (Histone Deacetylase) removes acetyl groups, restoring positive charges to condense chromatin (heterochromatin) and repress transcription.

B) HDAC adds acetyl groups to promote open chromatin; HAT removes acetyl groups to condense chromatin.

C) DNMT acetylates histones to activate transcription; Slicer deacetylates histones to degrade pre-mRNA.

D) HAT methylates DNA cytosines to stimulate transcription; HDAC deacetylates RNA polymerase to stop initiation.

Asnwer:A

Explanation: Lysine tails on histones are positively charged and attract negatively charged DNA. HAT neutralizes this charge (opening chromatin -> transcription ON). HDAC (like FLD in plants) removes the acetyl group, allowing histones to bind DNA tightly again (condensing chromatin -> transcription OFF).

Which statement correctly pairs the enzyme and outcome for DNA methylation with the general characteristics of histone methylation?

A) DNMT (DNA Methyltransferase) methylates cytosine bases (e.g., CpG dinucleotides) to repress transcription; HMT (Histone Methyltransferase) can either stimulate or repress transcription depending on which specific amino acid residue is methylated.

B) DNMT methylates histone tails to always activate transcription; HMT methylates adenine bases to always repress transcription.

C) Both DNA methylation and histone methylation exclusively activate gene expression by opening up promoters.

D) HDAC methylates DNA cytosines, whereas Dicer methylates histone lysine tails.

Answer: A

Explanation: DNA methylation (via DNMT) forms 5-methylcytosine, recruiting deacetylases to lock down chromatin and silence genes. Histone methylation (via HMT) is context-dependent: methylating Lysine 4 of Histone H3 (H3K4me3) activates transcription, whereas methylating Lysine 9 (H3K9me3) represses it.

How do insulators block an enhancer from activating a promoter?

A) Insulator-binding proteins (like CTCF) form a chromatin loop that physically separates the enhancer and promoter into different domains.

B) Insulators bind to RNA polymerase II and stop it from starting transcription.

C) Insulators destroy the enhancer sequence using Dicer.

D) Insulators prevent the mRNA from leaving the nucleus.

A) Insulator-binding proteins (like CTCF) form a chromatin loop that physically separates the enhancer and promoter into different domains.

Explanation: By anchoring DNA into a loop, the insulator acts as a physical barrier. An enhancer inside one loop cannot bend across the loop boundary to reach a promoter in another loop.