Reverse Transcription and Integration - Vocabulary Flashcards

A vocabulary-focused set of terms and concise definitions covering reverse transcription and integration in retroviruses as presented in the lecture notes.

Reverse Transcriptase (RT)

RNA-dependent DNA polymerase carried by retroviruses that converts the single-stranded RNA genome into double-stranded proviral DNA; also has RNase H activity and RNA template unwinding capability.

Proviral DNA

Double-stranded DNA copy of the viral genome produced by reverse transcription that becomes integrated into the host genome.

Integrase (IN)

Viral enzyme that covalently inserts proviral DNA into the host genome; part of the pol gene and forms multimeric complexes (intasomes) for integration.

Long Terminal Repeats (LTRs)

Flanking sequences at both ends of proviral DNA that function as the promoter (5' LTR) and polyadenylation/terminator signals (3' LTR) and provide ends for integration.

Gag gene

Retroviral gene encoding structural proteins for virion assembly; expressed as part of unspliced transcripts and cleaved into mature proteins.

Pol gene

Retroviral gene encoding enzymes required for replication, including reverse transcriptase, integrase, and protease.

Env gene

Retroviral gene encoding envelope proteins (surface SU and transmembrane TM) involved in host cell entry.

Simple retrovirus

Retrovirus with only three essential genes: gag, pol, and env.

Complex retrovirus

Retrovirus with gag, pol, and env plus additional non-structural regulatory genes affecting replication and pathogenesis.

Protease (PR)

Viral enzyme that cleaves the Gag-Pol polyprotein to produce mature viral proteins during virion maturation.

tRNA primer

Host cell tRNA that is selectively packaged and used to prime DNA synthesis by RT during reverse transcription.

Primer Binding Site (pbs)

Viral genome sequence where the tRNA primer anneals to initiate minus-strand DNA synthesis.

RNase H

Endonuclease domain of RT that degrades RNA in RNA-DNA hybrids during reverse transcription.

R region

Repeat sequences at the ends of the RNA genome that enable first template exchange during reverse transcription.

Strong-stop DNA

Early product of minus-strand DNA synthesis (approximately 100 nt) generated after initiation and RNA template degradation.

Polypurine tract (ppt)

RNA sequence left after RNase H digestion that serves as a primer for plus-strand DNA synthesis.

Double-stranded provirus

Complete proviral DNA after reverse transcription, flanked by identical LTRs, ready for integration.

Copy choice

Recombination during reverse transcription via template switching between the two RNA genome copies.

Quasispecies

Group of related but distinct viral genotypes arising from the high mutation rate of RT, leading to diverse phenotypes.

LEDGF/p75 (LEDGF)

Cellular factor that tethers integrase to chromatin and influences integration site selection, often favoring active genes.

BAF (Barrier-to-autointegration Factor)

Cellular protein that prevents autointegration of proviral DNA; supports productive replication as a cofactor.

Intasome

A tetrameric integrase complex that binds viral DNA ends to catalyze concerted integration.

Preintegration Complex (PIC)

Nuclear-transport complex containing proviral DNA, RT, capsid/nucleocapsid proteins, and integrase prior to integration.

Terminal dinucleotides (5'-TG-3' and 3'-CA-5')

Conserved dinucleotide ends of proviral DNA required for proper processing and joining during integration.

Processing step

First step of integration: removal of terminal dinucleotides to generate 5' overhangs and prepare ends for joining.

Joining step

Second step of integration: staggered cleavage of host DNA and ligation to proviral DNA ends.

Repair step

Final step of integration: host DNA repair fills single-strand gaps and ligates ends to form continuous proviral DNA.

Concerted integration

Integration event where both ends of proviral DNA are inserted into the host genome in a coordinated manner.

HIV-1 reservoir

Cells harboring integrated proviral DNA with no active viral expression, capable of reactivation and contributing to persistence.

Endogenous proviruses

Endogenous retroviral elements integrated in host DNA; replication-defective vestiges of past infections.

Retroid viruses

Non-retroviruses that employ reverse transcription (e.g., Hepadnaviruses) as part of their replication.

Hepadnaviruses

Virus family (e.g., HBV) that uses reverse transcription during replication, despite being DNA viruses.

RNA genome dimer

Retroviral genome packaged as two RNA copies that form a dimer, enabling template exchanges and recombination.