KGI - Viruses and Host Cells Lecture 2

Flashcards covering core concepts from the lecture notes on viruses and host cell interactions, replication, transcription, and antiviral strategies.

What are the main steps in viral infection as outlined in the lecture notes?

Adsorption and penetration, uncoating, synthesis (nucleic acid replication and protein production), assembly, and release.

What cellular 'rules' do viruses need to abide by or work around?

Monocistronic messages, structure of mRNAs, and the lack of viral-specific polymerases for genome replication.

Which virus families were noted as differing in how they deal with cellular rules?

Orthomyxoviridae, Flaviviridae, and Coronaviridae.

What activities does reverse transcriptase perform?

RNA-directed DNA polymerase activity and RNase H activity, enabling second-strand DNA synthesis to form a DNA copy.

Why do RNA viruses have a high mutation rate?

RNA polymerases are error-prone, leading to greater genetic diversity.

List some targets for antiviral therapies.

Virus–cell receptor interactions; entry; uncoating; genome processing; protein synthesis; packaging & assembly; and egress (with immunomodulation as a broader approach).

What happens to the proteasome in an infected cell?

Viral proteins become substrates for proteasomal degradation, integrating viral components into turnover.

What are the key steps in MHC-I antigen processing?

Ubiquitination of proteins, proteasomal degradation to peptides, transport of peptides into the endoplasmic reticulum, trimming by ER aminopeptidases (ERAP), and presentation by MHC-I.

Name two RNA virus translation strategies mentioned.

Polyprotein strategy with cleavage by host or viral proteases; translation of a 5′ ORF (often with cleavage sites) to produce multiple proteins.

What is an IRES and when is it used?

Internal Ribosome Entry Site; used by RNA viruses that do not enter the nucleus to initiate translation without a 5′ cap.

How does the influenza virus obtain a 5′ cap for its mRNA?

It enters the nucleus and snatches the 5′ cap from host mRNAs (cap-snatching).

Where do most dsDNA viruses perform DNA replication and transcription?

In the host cell nucleus.

What alternative replication route do some DNA viruses use involving RNA?

Some DNA viruses use an RNA intermediate (reverse transcription) during replication.

When a virus makes a DNA copy from an RNA template, what enzyme is used?

Reverse Transcriptase (RNA-dependent DNA polymerase activity).

Where do RNA viruses primarily replicate, and are there exceptions?

Primarily in the cytoplasm; not always—some RNA viruses replicate in the nucleus or utilize other pathways.

What is a dsDNA intermediate in +ssRNA virus replication?

Some +ssRNA viruses use a dsDNA intermediate to replicate.

Where is DNA replicated and transcribed

in the nucleus of eukaryotic cells; transcription occurs in the nucleus while DNA replication takes place prior to cell division.

mRNAs are translated

in the cytoplasm of cells to synthesize proteins.

What do viruses have to do to replicate themselves?

Get into cell( penetration and adsorption)

remove capsid protein (uncoating)

Replicate viral genome

make mrna to produce viral proteins

assemble and encapsidate genome

exit cell and release

Orthomyxoviridae

is a family of viruses that includes the influenza viruses. They are characterized by their segmented RNA genome and ability to cause annual epidemics. multi component genome

Flaviviridae

is a family of viruses known for their single-stranded RNA genomes. This family includes notable viruses such as Zika, dengue fever, and West Nile virus. single genome produces on protein that is subsequently cleaved into multiple proteins using host or viral proteasesThese viruses are primarily transmitted by arthropod vectors like mosquitoes and ticks, and they can cause various diseases in humans and animals.

Coronaviridae

virus makes an RNA directed polymerase that can make multiple mRNAs from viral genome

What do we not have that viruses must bring with them

rna dependent rna polyermase or RNA-dependent RNA polymerase

Ubiquitination

tagging proteins for disposal

proteasome

a protein complex that degrades ubiquitinated proteins to maintain protein homeostasis.

ERAP

(endoplasmic reticulum aminopeptidase) enzyme that trims peptides forpresentation on MHC class I molecules in immune response.

what takes peptides to ERAP and where is ERAP located

Transporter associated with antigen processing (TAP)

Where does MHC I go to

the cell surface after peptide loading in the endoplasmic reticulum. and goes through the golgi apparatus before being expressed on

IRES

(internal ribosome entry site) sequence in mRNA that allows for translation initiation during conditions where cap-dependent translation is inhibited. it substitutes for a cap structure that can bind to the 40 s Ribosome

what do all mRNA have and what do viruses do with one of the components of the mRNA

a 5' cap structure and an A poly tail. viruses snatch these caps to facilitate their own translation and evade host defenses.

some DNA viruses use an RNA intermediate why?

These DNA viruses use an RNA intermediate because:

1. Their DNA is incomplete/unstable and cannot directly replicate efficiently.

2. Using an RNA step allows them to exploit reverse transcriptase to regenerate their DNA genome.

episome

a circular or linear DNA molecule that exists independently of the chromosomal DNA within the host cell and can replicate autonomously or integrate into the host genome.

Reverse Transcriptase

RNA dependent DNA polymerase

RNase H activity( degrades RNA from DNA/RNA hybrids)

DNA dependent DNA polymerasean enzyme that synthesizes DNA from an RNA template.

dsRNA viruses

carry there own Reverse transcriptase for replication. within virion particle

cDNA

complementary DNA synthesized from an RNA template by reverse transcription, often used in cloning and gene expression studies.

Retrovirus viral genome is reverse transcribed and integrated as

cDNA into hosts CHROMOSOME

Example of Retrovirus

HIV

RNA viruses mutate more rapidly than DNA Why?

Because RNA polymerases lack proofreading capability, leading to more frequent errors during replication.

What do antiviral drugs target

Various stages of viral replication, including enzymes like proteases and reverse transcriptases. and cant be toxic to us

Acyclovir

is an antiviral drug primarily used to treat infections caused by certain types of viruses, notably herpes viruses. It works by inhibiting viral DNA synthesis.

AZT for HIV

is an antiretroviral medication used to treat HIV by inhibiting reverse transcriptase, preventing viral replication.

What mutates more RNA viruses or DNA viruses

RNA viruses tend to mutate more frequently than DNA viruses due to their error-prone replication processes.