Viruses, Replication Cycles & Antiviral Strategies

Vocabulary cards summarizing key virology terms, life-cycle stages, enzymes, drug classes, specific antivirals and important concepts discussed in the lecture transcript.

Attachment

First step of viral infection in which a virion’s surface proteins bind to specific receptors on a host cell.

Penetration

Entry of viral genetic material (and sometimes capsid) into the host cell after attachment.

Synthesis (viral)

Stage where host machinery is re-programmed to make viral genome copies and viral proteins.

Assembly (maturation)

Newly made genomes and proteins self-assemble into complete virions inside the host cell.

Release

Exit of mature virions from the host cell by lysis, budding, or exocytosis.

Lytic life cycle

Replication scheme in which infection quickly proceeds through synthesis, assembly and release, killing the host cell.

Lysogenic life cycle

Replication scheme in which viral DNA first integrates into the host genome and can remain silent before later entering lytic steps.

Provirus

Integrated viral DNA that has become a permanent part of the host genome.

Latent infection

Lysogenic outcome in which proviral genes are completely silent between episodic outbreaks.

Persistent infection

Lysogenic outcome in which an infected cell continuously releases low numbers of virions while remaining alive.

Oncogenic infection

Integration event that disrupts host oncogenes or tumor-suppressor genes, potentially leading to cancer.

Capsomere

Individual protein subunit that joins with others to form a viral capsid.

Capsid

Protein shell composed of capsomeres that encloses the viral genome.

Nucleocapsid

Capsid together with the enclosed genome (and any packaged enzymes).

Peplomer (spike)

Viral envelope glycoprotein that protrudes from the membrane and mediates attachment.

Tegument / Matrix protein

Layer of proteins that lines the inside of some viral envelopes and helps organize assembly.

Budding

Process by which enveloped virions acquire their envelope as they push through a host membrane.

Endocytosis (viral entry)

Host membrane engulfs the virion, forming a vesicle that brings it into the cytoplasm.

Fusion (viral entry)

Envelope merges directly with the host membrane, releasing the nucleocapsid into the cytoplasm.

Exocytosis

Secretion process by which virions in vesicles exit the cell without bursting it.

Lysozyme (phage enzyme)

Bacteriophage enzyme that drills a hole for genome injection and later digests peptidoglycan to lyse the cell.

Integrase

Viral enzyme that covalently inserts viral DNA into host DNA during lysogeny.

Reverse Transcriptase

Enzyme that synthesizes DNA from an RNA template; essential for retroviruses.

RNA-dependent RNA polymerase

Virus-coded enzyme that makes RNA from an RNA template—required by RNA viruses that replicate in the cytoplasm.

Protease (viral)

Enzyme that cleaves viral polyproteins into functional individual proteins during assembly.

Nucleoside analog

Chemically altered nucleotide that can be incorporated into viral DNA, terminating chain elongation.

Base analog

Synonym for nucleoside analog—fake base that disrupts viral nucleic-acid synthesis.

Chain terminator

Any nucleotide analog lacking a 3′-OH; once inserted, no further nucleotides can be added.

Protease inhibitor

Antiviral drug class that blocks viral protease, preventing maturation of proteins (e.g., Paxlovid components).

Integrase inhibitor

Drug class that blocks insertion of viral DNA into host DNA (e.g., raltegravir).

Tamiflu (oseltamivir)

Influenza drug that blocks neuraminidase, preventing budding/release of new virions.

Paxlovid

COVID-19 therapy (nirmatrelvir + ritonavir) that inhibits SARS-CoV-2 protease.

Acyclovir

Guanosine analog used chiefly against herpesviruses; acts as a DNA chain terminator.

AZT (zidovudine)

Thymidine analog used against HIV; terminates reverse-transcribed DNA chains.

Remdesivir

RNA-dependent RNA polymerase inhibitor used for Ebola and COVID-19 treatment.

Molnupiravir

Oral antiviral that induces lethal mutagenesis in SARS-CoV-2 RNA.

Positive-sense RNA (+RNA)

Single-stranded viral RNA that can serve directly as mRNA for translation.

Negative-sense RNA (-RNA)

Single-stranded RNA complementary to mRNA; must be transcribed into +RNA before translation.

Reverse transcription

Synthesis of DNA from an RNA template, catalyzed by reverse transcriptase.

RNA-dependent RNA transcription

Copying of RNA from an RNA template; performed by RNA-dependent RNA polymerase.

Central dogma

Flow of genetic information: DNA → RNA (transcription) → protein (translation).

Template strand

DNA (or RNA) strand used as a guide to synthesize a complementary strand.

Genome copies

Newly synthesized viral nucleic acids destined to be packaged into progeny virions.

Trigger (lysogenic induction)

Stress or stimulus that ends dormancy and initiates lytic synthesis in a lysogenic virus.

UV radiation trigger

Ultraviolet light can activate silent herpes proviruses, causing cold-sore outbreaks.

Lysine

Dietary amino acid that tends to suppress herpes outbreaks when abundant relative to arginine.

Arginine

Dietary amino acid that can promote herpes reactivation when high relative to lysine.

Retrovirus

RNA virus (e.g., HIV-1) that uses reverse transcriptase and integrase to establish a provirus.

Double-stranded DNA virus

Virus whose genome is dsDNA; may enter directly into transcription or integrate via integrase.

Single-stranded DNA virus

Virus with ssDNA genome; must first make the complementary strand to form dsDNA before transcription.