E2 Gene Expression Questions

Why must DNA be packaged in an orderly manner?

Fits ~2 m of DNA into the tiny nucleus while organizing and regulating access to genes

What is a nucleosome?

~146 bp of DNA wrapped ~1.75 times around histone proteins

What is euchromatin?

Loosely packed chromatin that allows RNA polymerase II access and active transcription

What is heterochromatin?

Tightly packed chromatin that restricts RNA polymerase II access and reduces transcription

Why is little new gene transcription expected in maximally condensed mitotic chromosomes?

Highly compact DNA limits access of transcription machinery to genes

Why do nucleosomes naturally form higher-order structures?

Interactions among histones, histone tails, and DNA promote further compaction and organization

How does histone acetylation loosen chromatin?

HATs acetylate lysines, reducing their positive charge and weakening ionic attraction to negatively charged DNA, promoting euchromatin

What do HATs and HDACs do?

HATs add acetyl groups to histones and generally loosen chromatin

How does histone methylation promote heterochromatin?

Methylation of H3K9 or H3K27 can block acetylation and recruit HP1, promoting tighter packing

What does HP1 do?

Recognizes methylated histones and helps pack chromatin into transcriptionally repressive heterochromatin

What do histone demethylases (HDMs) do?

Remove histone methyl groups, potentially permitting acetylation and a more open chromatin state

What happens if a histone acetyltransferase (HAT) loses function?

Less histone acetylation, tighter chromatin, reduced access to affected genes, and potentially reduced transcription

What happens if a histone deacetylase (HDAC) loses function?

Histones may remain more acetylated, chromatin may stay more open, and transcription of affected genes may increase

What happens if HP1 loses function?

Heterochromatin formation or maintenance may weaken, making normally silenced genes more accessible and potentially increasing transcription

What happens if DNA methyltransferase loses function?

Less DNA methylation can weaken transcriptional repression, allowing some normally silenced genes to be expressed

How does DNA methylation repress transcription?

DNA methyltransferases add methyl groups to cytosines

How does DNA methylation differ from histone modification?

DNA methylation is generally longer-lasting, whereas histone-tail modifications are generally more dynamic

What are the major parts of a eukaryotic gene?

Enhancer, proximal promoter, TATA box or equivalent promoter element, transcription start site (+1), 5′ UTR, exons, introns, and cleavage/polyA signal near the 3′ end

What does an enhancer do?

Binds regulatory transcription factors that can recruit HATs and help make promoter DNA accessible for transcription

What does the proximal promoter do?

Provides nearby regulatory DNA sequences that help control transcription-factor binding and RNA Pol II access

What does the TATA box do?

Helps general transcription factors assemble and recruit RNA Pol II to initiate transcription at the correct location

What is the transcription start site (+1)?

The first DNA nucleotide transcribed into RNA

What are exons and introns?

Exons are sequences retained in mature mRNA

What is the transcriptional stop/3′ cleavage region?

The region containing the cleavage/polyadenylation signal that helps define the mRNA 3′ end and coordinates transcription termination

Why can a TATA-box mutation cause transcription errors?

It can disrupt general transcription-factor binding and RNA Pol II recruitment, reducing transcription or altering where transcription starts

How does TATA-box position help define the first transcribed nucleotide?

Its position helps orient and position the transcription machinery relative to the +1 start site

What happens if RNA Pol II cannot interact with TFIIH?

Initiation may fail because TFIIH helps open the DNA transcription bubble, allowing the template to be transcribed

What happens if RNA Pol II occasionally inserts the wrong nucleotide?

The resulting RNA may contain incorrect sequences, potentially producing abnormal proteins or reducing protein function

What happens if the cleavage/polyadenylation signal mutates?

The cleavage/polyA complex may not recognize the signal properly, disrupting 3′-end formation, polyadenylation, and termination

What happens if poly(A) polymerase loses activity but cleavage still works?

The RNA can be cleaved but cannot receive a normal poly(A) tail, reducing stability, nuclear export, and translational efficiency

What are the three major types of mRNA processing?

5′ capping, intron splicing, and 3′ polyadenylation

Why is the 5′ cap important?

It protects mRNA, helps nuclear export, and supports translation initiation

Why is the poly(A) tail important?

It protects mRNA from degradation, assists nuclear export, and contributes to translational re-initiation

Why is intron splicing important?

It removes introns and joins exons to produce mature mRNA

Why can't mature mRNA begin or end with an intron?

Introns are removed and exons joined during splicing, so mature mRNA retains exon sequences at both ends

Why must the first exon begin at the transcription start site?

The first exon contains the beginning of the transcribed RNA sequence

What is the 5′ UTR?

The transcribed region before the start codon that is not translated into protein

Must the first exon contain the start codon?

No. The 5′ UTR can occupy part or all of exon 1, with the start codon located in a later exon

What are the four common isoforms from alternative inclusion of exons 2 and 3?

1-2-3-4, 1-2-4, 1-3-4, and 1-4

How does alternative splicing change protein function?

Different exon combinations can include or omit functional domains, producing proteins with different activities, regulation, or cellular locations

What happens if a transcription factor that recruits a HAT to the Hsc70 enhancer/promoter loses function?

Reduced chromatin opening can lower Hsc70 transcription, impair protein-folding support, and cause toxic protein aggregates to accumulate

What is the overall sequence of gene expression?

Open chromatin → transcription initiation → elongation and termination → mRNA processing and nuclear export → translation