DNA-Directed RNA Synthesis

What is transcription?

The process of copying DNA into RNA.

What is the product of transcription?

RNA (usually mRNA)

What is a DNA-dependent RNA polymerase?

An enzyme that synthesizes RNA using DNA as a template

What does RNA polymerase II transcribe?

pre-mRNAs and mRNA

In what direction does RNA polymerase synthesize RNA?

5’ → 3’ direction

What is a transcription activator?

A DNA-binding protein that increases transcription by recruiting transcription machinery

What is a co-activator?

A non-DNA-binding protein that helps activators stimulate transcription

What is a transcription enhancer element?

A DNA sequence that increases transcription, often located far from the promoter

What binds to enhancer elements?

Transcription activators (enhancer-binding factors)

How do enhancer elements increase transcription?

By recruiting activators and co-activators that help assemble the transcription machinery.

Can enhancer elements function far from the gene they regulate?

Yes, they can act at a distance and in either orientation

What is a positive transcription regulatory loop?

A feedback loop where a gene product enhances its own transcription or that of a partner gene.

What is a negative transcription regulatory loop?

A feedback loop where a gene product inhibits its own transcription or that of a related gene

What is the function of a positive loop?

To amplify or sustain gene expression

What is the function of a negative loop?

To limit or stabilize gene expression

What is the 5’ cap made of?

A 7-methylguanosine linked to the 5’ end of mRNA via a 5’ to 5’ triphosphate bridge

What are the main functions of the 5’ cap?

mRNA protection, nuclear export, translation initiation, and aiding splicing

What is the poly(A) tail made of?

A stretch of adenine nuleotides added to the 3’ end of mRNA

What are the main functions of the poly(A) tail?

mRNA stability, translation efficiency, nuclear export, and lifespan regulation

What is the purpose of splicing in RNA processing?

To remove introns and join exons, forming mature mRNA.

What are introns?

non-coding regions of pre-mRNA that are removed during splicing

What are exons?

Coding regions of pre-mRNA that are retained and joined to form mature mRNA

What is alternative splicing?

a process that allows different combinations of exons to be joined, producing multiple mRNA variants from one gene

How can alternative splicing affect viral gene expression?

Viruses can use it to produce multiple proteins from a single gene, helping them conserve genome space

What are the three temporal classes of viral gene expression?

Immediate early (IE), early (E), and late (L) genes

What is the role of immediate early (IE) genes?

They activate early gene transcription and modulate the host cell environment

Do immediate early genes require prior viral protein synthesis?

No, they are expressed immediately using host machinery

What doe early (E) genes encode?

Proteins needed for viral DNA replication and host cell modification

When are late (L) genes expressed?

After viral DNA replication has begun

What do late (L) genes encode?

Structural proteins for virion assembly and components for virus release

What is the main structural difference between pre-mRNA and mature mRNA?

Pre-mRNA contains introns and exons; mature mRNA has only exons

Where does transcription of mRNA occur in the cell?

In the nucleus

What three modifications are made to pre-mRNA and mature mRNA?

5’ capping, splicing, and 3’ polyadenylation

Where does mRNA go after RNA processing?

It is exported from the nucleus to the cytoplasm for translation

What does temporal regulation of viral transcription refer to?

The timed expression of viral genes in a specific order: IE and L

What is the role of SV40’s large T antigen?

It inhibits early transcription, activates DNA replication, and stimulates late gene transcription

How many promoters does SV40 use for transcription?

One bidirectional promoter near the origin of replication

What triggers late gene expression in SV40?

The onset of viral DNA replication.

What do SV40 late genes encode?

Structural proteins (VP1, VP2, VP3) for virion assembly.

Why do DNA viruses use temporally regulated transcription?

To coordinate gene expression efficiently and ensure successful replication. 

What do immediate early genes typically do?

Activate transcription of early genes and prepare the host cell. W

Why are late genes expressed after DNA replication?

Because they encode structural proteins needed to package newly replicated genomes.

How does temporal regulation help viruses evade the immune system?

By delaying expression of immunogenic structural proteins until later in infection. W

Why are retroviruses dependent on host transcription?

DNA integrates into the host genome and use host transcription machinery.

What is a provirus?

Integrated retroviral DNA within the host genome.