Viral DNA and RNA Replication, Transcription, and Assembly Strategies

What are the exceptions for DNA viruses that replicate outside the nucleus?

Poxviruses and giant viruses replicate in the cytoplasm and encode their own transcription and replication enzymes.

Where in the cell do DNA viruses typically replicate?

In the nucleus, using host cell processes and enzymes.

Where do RNA viruses typically replicate?

In the cytoplasm, as they encode their own RNA-dependent RNA polymerase.

What is cap-snatching in the context of RNA viruses?

It is a process where some RNA viruses, like influenza, perform transcription in the nucleus by stealing capped host RNA fragments.

Why is viral DNA replication always delayed after infection?

Because early viral products must be transcribed and translated before genome replication can begin.

Do all DNA viruses encode their own DNA polymerases?

No, many do not; exceptions include very large DNA viruses like poxviruses.

What is the function of a viral origin of replication?

It is a sequence-based signal in the viral genome that marks where DNA replication initiates.

Why do viruses not replicate well in non-dividing cells?

Non-dividing cells have low nucleotide pools needed for DNA synthesis.

What is the first biosynthetic event after viral ssDNA enters the cell?

Synthesis of a complementary strand to make dsDNA, which occurs in the nucleus.

What is the initial biosynthetic event for dsDNA viruses after entering the cell?

Transcription of viral genes to produce viral mRNAs, which occurs in the nucleus.

What are the steps involved in the production and processing of mRNA?

1. Initiation: Transcription factors recruit RNA polymerase II. 2. Elongation: RNA polymerase synthesizes pre-mRNA. 3. Capping: A guanine cap is added. 4. Splicing: Introns are removed. 5. Polyadenation: A poly(A) tail is added. 6. Nuclear export: Mature mRNA is exported to the cytoplasm.

How is transcription regulated in viral infections?

Transcription is regulated by viral proteins that bind to promoter sequences and affect how tightly DNA is wound around histones.

What is alternative splicing?

It allows the generation of multiple different mRNAs from a single primary transcript, expanding coding capacity.

How do splicing and nuclear export relate to viral mRNAs?

Splicing marks cellular mRNAs for nuclear export, while unspliced viral mRNAs can also be marked for export through specific sequences.

Why is viral transcription temporarily regulated during the infection cycle?

To ensure that large quantities of viral proteins are produced at the right times for assembly and function.

What is the role of (+) strand RNA in viral replication?

It serves as mRNA that is translated immediately to produce proteins, including RNA-dependent RNA polymerase.

What is the significance of having proteins coat (-) strand RNA in viral particles?

It prepares the RNA for replication and ensures it is ready to make mRNA once inside the host cell.

True or False: All RNA viruses encode their own RNA replication system.

True, as they require an RNA-dependent RNA polymerase for RNA synthesis.

What happens to the flow of information in (+) and (-) strand RNA genomes?

(+) ssRNA is translated to proteins, while (-) ssRNA must be copied to (+) ssRNA before translation.

What is the role of transcription factors in viral transcription?

They bind to promoter sequences and recruit RNA polymerase II to initiate transcription.

What is the purpose of the guanine cap added during mRNA processing?

It protects mRNA from degradation and aids in ribosome recruitment for translation.

What is the role of introns in mRNA processing?

Introns are removed during splicing to produce mature mRNA that contains only exons.

What is the significance of polyadenation in mRNA processing?

It adds a poly(A) tail to the mRNA, which is important for stability and export from the nucleus.

How does alternative splicing benefit viral genomes?

It allows the production of different protein isoforms from a single transcript, enhancing the virus's adaptability.

What is the role of RDRP in RNA viruses?

RDRP (RNA-dependent RNA polymerase) is responsible for replicating the viral genome and synthesizing mRNA.

What is the significance of the primer in poliovirus replication?

The primer for poliovirus synthesis is crucial for the initiation of RNA synthesis, with secondary structures acting as caps.

How is poly(A) added to mRNAs of (+) ssRNA viruses?

In (+) ssRNA viruses, poly(A) is always encoded and added during RNA synthesis.

Why must viruses attach to receptors to enter cells?

Viruses are too large to diffuse through the cell membrane; they use receptors to facilitate entry.

How do enveloped viruses attach to cell receptors?

Enveloped viruses use fusion proteins displayed on their surface to bind to cell receptors.

What are the mechanisms by which nucleic acids exit a naked icosahedral capsid?

Nucleic acids exit via capsid disruption that allows the genome to be released into the cytosol.

What is the difference between enveloped and non-enveloped virus particle attachment?

Enveloped viruses use fusion proteins, while non-enveloped viruses use capsid proteins to bind to receptors.

What regulates the fusion of viral and cellular membranes?

Fusion is regulated to prevent premature fusion and requires conformational changes and receptor interactions.

How do viruses move within the crowded cytoplasm?

Viruses rely on active directed movement along microtubules rather than diffusion.

Do all viral nucleic acids get released from the capsid during entry?

No, some viruses, like the influenza virus, do not fully disassemble their capsid during entry.

How do DNA viruses enter the nucleus?

DNA viruses enter the nucleus via the importin system, while some RNA viruses, like influenza, require nuclear entry for cap-snatching.

What features must viral mRNAs present to be recognized by host ribosomes?

Viral mRNAs must have a 5' cap and a poly A tail.

What is a sub-assembly in viral replication?

A sub-assembly is an intermediate oligomeric structure assembled prior to final virus assembly.

What are the two strategies for making sub-assemblies?

Proteolytic processing of polyproteins and spontaneous self-assembly.

How do sequential and concerted assembly differ in viral replication?

Sequential assembly occurs in steps (e.g., poliovirus), while concerted assembly occurs when nucleic acid and capsid join later (e.g., influenza).

What are packaging signals in viral genomes?

Packaging signals are specific sequences on viral nucleic acids that interact with structural proteins for genome packaging.

How do enveloped viruses acquire their membranes?

Enveloped viruses acquire membranes from the host cell's plasma membrane or through vesicles from the ER.

What types of signals allow viral proteins to concentrate at budding sites?

Signals include lipidation, assembly proteins, and replication proteins that direct viral particles to appropriate locations.

How does the escort pathway facilitate viral budding?

The escort pathway mediates membrane deformation and assists in the budding of enveloped viral particles.

What is the monocistronic problem in RNA viruses?

RNA viruses manage this by using polyprotein processing and IRES elements to translate multiple proteins from a single RNA strand.

What are the two main differences between -1 and +1 ribosomal frameshift?

-1 frameshift involves the ribosome moving backward, while +1 frameshift involves advancing the nucleotide forward.

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