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74 Cards in this Set

  • Front
  • Back
HIV infected macrophage
-cell has very large vacuoles filled with virus partciles, followed by release and cell death
Retroviruses
-human and animal pathologies
-interacations between host and virus are specific
-overall do not tend to kill cell, only use cellular machinery for viral replication
-go against central dogma, proven by inhibiting retrovial replciation with DNA synthesis inhibitors
Oncoretroviruses
-group of retroviruses
-cause cancer
-acquire host sequences and present them as oncogenes
-cause activation or inactivation different genes
-similarily act as transposable elements
Lenti viruses
-group of retroviruses
-chronic disease causer
-mild to severe immunodefiencies
Spuma viruses
-group of retroviruses
-infect and accumulate in vacuoles, giving foamy look
-foamy viruses
-no known pathology
-co-exist with host
HERV
"-group of retroviruses"
-human endogenous retroviruses
-no known pathology
-ancestral relics retroviruses
Inner Core retroviruses
-composed of capsid proteins
-bullet shaped, circular or icosahedral
-2 ssRNA +
-diploid genome loosely associated with each ohter at 5' end forming kissing loop structure
-nucleic acid coated with nucleocapsid protein providing protection and regulation in ushering RNA into virion
-includes reverse transcriptase proteins, tRNA molecule (primers), integrase proteins
Lipid Bilayer retroviruses
-derived from host cell bud
-within are surface and transmembrane glycoproteins essential for recognition of host cells and mediation of fusion
-inner side coated with matrix proteins providing structural role and regulatory role in virus assembly before budding
Attachment retroviruses
-receptor to glycoprotein provides specificity
-receptors used by viruses usually involved in cellular metabolism
-specificity provides level at which restriction viral infection can occur
Murine and Feline Leukemia Viruses
-recognise different amino acid transporters as receptors
Reverse Transcription retroviruses
-core particle dissociates adn reverse transcriptase converts RNA to proviral DNA
-DNA can be linear or circular and is transported to nucleus
-cell can restrict viral replication by altering its RNA structure through proteins like Apo3G and TRIM5
-restriction viral replciation can occur at cellular surface through receptors as well
Apo3G and TRIM5
-used by cell to restrict viral replication by altering its RNA structure
-proteins
Integration retroviruses
-integrase catalyses integration proviral DNA into host in random location
Production viral proteins and new virions of retroviruses
-integrated viral DNA act as transcription unit for host cell machinery, producing viral mRNA, translated then packed into new virions
-glycoproteins produced travel to host cell membrane surfaces where picked up by budding virions
Late stage maturation retroviruses
-virion buds, then viral protease produces mature and infections virion
-protease important target for drug development
Retroviral genomes
-all have 3 main coding regions: gag, pol, env
-UTRs
-3' Poly A tail
-methyl 5' cap
-some contain additional coding regions, number proteins increases with complexity virus (HIV)
gag
-group specific antigen
-codes for antigenic molecules recognised by immune response, distinct between viruses
-codes for structural proteins: matrix, capsid, nucleocapsid proteins
pol
-codes for enzymatic activity: reverse transcriptase, integrase, protease
env
-codes for surface and transmembrane glycoproteins in envelope
UTRs
-regulatory regions
-R: repeat unit important for process of reverse transcription
U3: unique to 3' end, important for regulation of integrated proviral DNA
U5: unique to 5' end, important for regulation of integrated proviral DNA
3' Poly A tail
-part of viral RNA, very similar to cellular mRNA
methyl 5' cap
-part of viral RNA, very similar to cellular mRNA
Reverse Transcriptase
-heterodimeric protein, 66 and 51 kDa polypeptides
-right hand as polymerase activity (groove region where RNA or DNA sits)
-thumb portion has RNAase H enzymatic activity
-DNA dependent polymerase,RNA dependant polymerase activity as well
-no proofreading, high mutations, 10 mistakes/10 000bp
RNAase H enzymatic activity
-degrade RNA in RNA-DNA hybrids
-part of reverse transcriptase enzyme
Reverse Transcription
1. tRNA binds PBS and elongation
2. first jump
3. RNAase H activity and ppt
4. second jump and ds completion
tRNA to PBS and elongation of reverse transcription
-prepackaged cellular tRNA packaged in core binds to PBS and acts as primer for reverse transcriptase, which extends primer
-RT extends tRNA primer from 3' OH, copying + ssRNA to 5' end, generating - DNA complementary to U5 and R of 5' end (strong stop DNA)
PBS
-primer binding site
-18 nt
-5'
-tRNA binds and acts as primer for reverse transcriptase
"strong stop DNA"
-- DNA strand complementary to U5 and R of 5' end RNA
-3-400 nt
-abundant a few hours after RT initiation
First jump in reverse transcription
-strong stop DNA dissociates from RNA template through circular mechanism and hybridises to R sequence on 3' end
-RT elongates DNA from 5' to 3'
RNAaseH activity and ppt
-RNAaseH degrades most RNA except small region at 3' end called ppt and tRNA
-RT uses DNA dependant polymerase activity to begin synthesising second strand DNA
-elongation finished, ppt and tRNAdegraded by RNAaseH activity
Retroviral genomes
-all have 3 main coding regions: gag, pol, env
-UTRs
-3' Poly A tail
-methyl 5' cap
-some contain additional coding regions, number proteins increases with complexity virus (HIV)
gag
-group specific antigen
-codes for antigenic molecules recognised by immune response, distinct between viruses
-codes for structural proteins: matrix, capsid, nucleocapsid proteins
pol
-codes for enzymatic activity: reverse transcriptase, integrase, protease
env
-codes for surface and transmembrane glycoproteins in envelope
UTRs
-regulatory regions
-R: repeat unit important for process of reverse transcription
U3: unique to 3' end, important for regulation of integrated proviral DNA
U5: unique to 5' end, important for regulation of integrated proviral DNA
3' Poly A tail
-part of viral RNA, very similar to cellular mRNA
methyl 5' cap
-part of viral RNA, very similar to cellular mRNA
Reverse Transcriptase
-heterodimeric protein, 66 and 51 kDa polypeptides
-right hand as polymerase activity (groove region where RNA or DNA sits)
-thumb portion has RNAase H enzymatic activity
-DNA dependent polymerase,RNA dependant polymerase activity as well
-no proofreading, high mutations, 10 mistakes/10 000bp
RNAase H enzymatic activity
-degrade RNA in RNA-DNA hybrids
-part of reverse transcriptase enzyme
Reverse Transcription
1. tRNA binds PBS and elongation
2. first jump
3. RNAase H activity and ppt
4. second jump and ds completion
tRNA to PBS and elongation of reverse transcription
-prepackaged cellular tRNA packaged in core binds to PBS and acts as primer for reverse transcriptase, which extends primer
-RT extends tRNA primer from 3' OH, copying + ssRNA to 5' end, generating - DNA complementary to U5 and R of 5' end (strong stop DNA)
PBS
-primer binding site
-18 nt
-5'
-tRNA binds and acts as primer for reverse transcriptase
"strong stop DNA"
-- DNA strand complementary to U5 and R of 5' end RNA
-3-400 nt
-abundant a few hours after RT initiation
First jump in reverse transcription
-strong stop DNA dissociates from RNA template through circular mechanism and hybridises to R sequence on 3' end
-RT elongates DNA from 5' to 3'
RNAaseH activity and ppt
-RNAaseH degrades most RNA except small region at 3' end called ppt and tRNA
-DNA overhang and tRNA primer left
-RT uses DNA dependant polymerase activity to begin synthesising second strand DNA from U5 to PBS as RNAase H degrades rest of template
-elongation finished, ppt and tRNAdegraded by RNAaseH activity
Retroviral genomes
-all have 3 main coding regions: gag, pol, env
-UTRs
-3' Poly A tail
-methyl 5' cap
-some contain additional coding regions, number proteins increases with complexity virus (HIV)
gag
-group specific antigen
-codes for antigenic molecules recognised by immune response, distinct between viruses
-codes for structural proteins: matrix, capsid, nucleocapsid proteins
pol
-codes for enzymatic activity: reverse transcriptase, integrase, protease
env
-codes for surface and transmembrane glycoproteins in envelope
UTRs
-regulatory regions
-R: repeat unit important for process of reverse transcription
U3: unique to 3' end, important for regulation of integrated proviral DNA
U5: unique to 5' end, important for regulation of integrated proviral DNA
3' Poly A tail
-part of viral RNA, very similar to cellular mRNA
methyl 5' cap
-part of viral RNA, very similar to cellular mRNA
Reverse Transcriptase
-heterodimeric protein, 66 and 51 kDa polypeptides
-right hand as polymerase activity (groove region where RNA or DNA sits)
-thumb portion has RNAase H enzymatic activity
-DNA dependent polymerase,RNA dependant polymerase activity as well
-no proofreading, high mutations, 10 mistakes/10 000bp
RNAase H enzymatic activity
-degrade RNA in RNA-DNA hybrids
-part of reverse transcriptase enzyme
Reverse Transcription
1. tRNA binds PBS and elongation
2. first jump
3. RNAase H activity and ppt
4. second jump and ds completion
tRNA to PBS and elongation of reverse transcription
-prepackaged cellular tRNA packaged in core binds to PBS and acts as primer for reverse transcriptase, which extends primer
-RT extends tRNA primer from 3' OH, copying + ssRNA to 5' end, generating - DNA complementary to U5 and R of 5' end (strong stop DNA)
PBS
-primer binding site
-18 nt
-5'
-tRNA binds and acts as primer for reverse transcriptase
"strong stop DNA"
-- DNA strand complementary to U5 and R of 5' end RNA
-3-400 nt
-abundant a few hours after RT initiation
First jump in reverse transcription
-strong stop DNA dissociates from RNA template through circular mechanism and hybridises to R sequence on 3' end
-RT elongates DNA from 5' to 3'
RNAaseH activity and ppt
-RNAaseH degrades most RNA except small region at 3' end called ppt and tRNA
-RT uses DNA dependant polymerase activity to begin synthesising second strand DNA
-elongation finished, ppt and tRNAdegraded by RNAaseH activity
ppt
-polypurine tract
-at 3' end RNA + of retrovirus
-initially resistant to degradation by RNAase H activity
-acts as RNA primer for synthesis U3, R, U5 and PBS fragments on 5' end
Second Jump and ds completion in reverse transcription
-DNA strands dissociate and re-hybridise at comlementary PBS region of 1st DNA strand by circular mechanism
-DNA dependant DNA polymerase activity of RT elongates both strands from 3' end
-new molecule has LTR repeat on either end
LTR
-either end newly synthesised DNA
-important for transcriptional regulation and integration
-aka UTR
-all regulatory sequences allowing for capping, transcription, cleaving and polyadenylation present after integration
-provirus ready to undergo alternate splicing
-3' end LTR promotes provirus
-5' LTR influences downstream genes to provirus
-independant and can operate without transcription factors so provirus can operate regardless of where inserted
-more complex retroviruses, simple LTR promoter not enough, so more complex LTR inserted into host DNA
-can also determine which cells are best suited for integration (component retroviral specificity)
Integrase
-inserts fragments DNA by opening OH groups on either end of DNA
-nucleotides excised are replaced based on insert's template
-gives direct repeats on either side insert, even though proviral DNA was originally inverted repeats
Promoter occlusion
-process that blocks 5' LTR of provirus
MMTV
-mouse mammary tumour virus
-U3 region binds hormone as transcription factor (LTR complex promoter)
-works perfectly in mammary glands which secrete hormones
T-cell leukemia virus
-U3 region has binding sites for proteins expressed solely in activated T-cells and macrophages (LTR complex promoter)
Alternative splicing
-amount determines use of RNA
-proviral synthesises mRNA which can be used for viral portein or genomic RNA
Single spliced RNA
-splicing out ost of gag and pol, leaving env
-env migrates to cytoplasm (by cap and polyA use) to be translated to envelope proteins
psi sequence
-51 nt
-next to gag sequence
-when spliced, so are gag and pol
Double spliced RNA
-in more complex viruses (HIV)
-for Tax and Rex proteins
Translatoin termination sequence
-ensure gag sequence sole production 90% of time
-end of gag region
-1/20 times sequence recognised by termination tRNA which suppresses it allowing for translation pol
-allows for more efficient translation, even if unbalanced
Termination tRNA
-recognises translation termination sequence at end gag region and suppresses it
-allows for translation pol
Protease enzyme
-cleaves integrase and reverse transcriptase from nucleocapsid
-activates viral core
-if inactive, new virus buds, but can't infect new cells