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74 Cards in this Set
- Front
- Back
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HIV infected macrophage
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-cell has very large vacuoles filled with virus partciles, followed by release and cell death
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Retroviruses
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-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 |
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Oncoretroviruses
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-group of retroviruses
-cause cancer -acquire host sequences and present them as oncogenes -cause activation or inactivation different genes -similarily act as transposable elements |
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Lenti viruses
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-group of retroviruses
-chronic disease causer -mild to severe immunodefiencies |
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Spuma viruses
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-group of retroviruses
-infect and accumulate in vacuoles, giving foamy look -foamy viruses -no known pathology -co-exist with host |
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HERV
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"-group of retroviruses"
-human endogenous retroviruses -no known pathology -ancestral relics retroviruses |
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Inner Core retroviruses
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-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 |
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Lipid Bilayer retroviruses
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-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 |
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Attachment retroviruses
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-receptor to glycoprotein provides specificity
-receptors used by viruses usually involved in cellular metabolism -specificity provides level at which restriction viral infection can occur |
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Murine and Feline Leukemia Viruses
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-recognise different amino acid transporters as receptors
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Reverse Transcription retroviruses
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-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 |
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Apo3G and TRIM5
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-used by cell to restrict viral replication by altering its RNA structure
-proteins |
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Integration retroviruses
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-integrase catalyses integration proviral DNA into host in random location
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Production viral proteins and new virions of retroviruses
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-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 |
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Late stage maturation retroviruses
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-virion buds, then viral protease produces mature and infections virion
-protease important target for drug development |
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Retroviral genomes
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-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) |
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gag
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-group specific antigen
-codes for antigenic molecules recognised by immune response, distinct between viruses -codes for structural proteins: matrix, capsid, nucleocapsid proteins |
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pol
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-codes for enzymatic activity: reverse transcriptase, integrase, protease
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env
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-codes for surface and transmembrane glycoproteins in envelope
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UTRs
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-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 |
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3' Poly A tail
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-part of viral RNA, very similar to cellular mRNA
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methyl 5' cap
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-part of viral RNA, very similar to cellular mRNA
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Reverse Transcriptase
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-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 |
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RNAase H enzymatic activity
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-degrade RNA in RNA-DNA hybrids
-part of reverse transcriptase enzyme |
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Reverse Transcription
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1. tRNA binds PBS and elongation
2. first jump 3. RNAase H activity and ppt 4. second jump and ds completion |
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tRNA to PBS and elongation of reverse transcription
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-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) |
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PBS
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-primer binding site
-18 nt -5' -tRNA binds and acts as primer for reverse transcriptase |
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"strong stop DNA"
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-- DNA strand complementary to U5 and R of 5' end RNA
-3-400 nt -abundant a few hours after RT initiation |
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First jump in reverse transcription
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-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' |
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RNAaseH activity and ppt
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-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 |
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Retroviral genomes
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-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) |
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gag
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-group specific antigen
-codes for antigenic molecules recognised by immune response, distinct between viruses -codes for structural proteins: matrix, capsid, nucleocapsid proteins |
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pol
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-codes for enzymatic activity: reverse transcriptase, integrase, protease
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env
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-codes for surface and transmembrane glycoproteins in envelope
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UTRs
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-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 |
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3' Poly A tail
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-part of viral RNA, very similar to cellular mRNA
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methyl 5' cap
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-part of viral RNA, very similar to cellular mRNA
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Reverse Transcriptase
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-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 |
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RNAase H enzymatic activity
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-degrade RNA in RNA-DNA hybrids
-part of reverse transcriptase enzyme |
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Reverse Transcription
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1. tRNA binds PBS and elongation
2. first jump 3. RNAase H activity and ppt 4. second jump and ds completion |
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tRNA to PBS and elongation of reverse transcription
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-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) |
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PBS
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-primer binding site
-18 nt -5' -tRNA binds and acts as primer for reverse transcriptase |
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"strong stop DNA"
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-- DNA strand complementary to U5 and R of 5' end RNA
-3-400 nt -abundant a few hours after RT initiation |
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First jump in reverse transcription
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-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' |
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RNAaseH activity and ppt
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-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 |
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Retroviral genomes
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-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) |
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|
gag
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-group specific antigen
-codes for antigenic molecules recognised by immune response, distinct between viruses -codes for structural proteins: matrix, capsid, nucleocapsid proteins |
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pol
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-codes for enzymatic activity: reverse transcriptase, integrase, protease
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env
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-codes for surface and transmembrane glycoproteins in envelope
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UTRs
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-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 |
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3' Poly A tail
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-part of viral RNA, very similar to cellular mRNA
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methyl 5' cap
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-part of viral RNA, very similar to cellular mRNA
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Reverse Transcriptase
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-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 |
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RNAase H enzymatic activity
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-degrade RNA in RNA-DNA hybrids
-part of reverse transcriptase enzyme |
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Reverse Transcription
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1. tRNA binds PBS and elongation
2. first jump 3. RNAase H activity and ppt 4. second jump and ds completion |
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tRNA to PBS and elongation of reverse transcription
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-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) |
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PBS
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-primer binding site
-18 nt -5' -tRNA binds and acts as primer for reverse transcriptase |
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"strong stop DNA"
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-- DNA strand complementary to U5 and R of 5' end RNA
-3-400 nt -abundant a few hours after RT initiation |
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First jump in reverse transcription
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-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' |
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RNAaseH activity and ppt
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-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 |
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ppt
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-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 |
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Second Jump and ds completion in reverse transcription
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-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 |
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LTR
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-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) |
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Integrase
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-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 |
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Promoter occlusion
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-process that blocks 5' LTR of provirus
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MMTV
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-mouse mammary tumour virus
-U3 region binds hormone as transcription factor (LTR complex promoter) -works perfectly in mammary glands which secrete hormones |
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T-cell leukemia virus
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-U3 region has binding sites for proteins expressed solely in activated T-cells and macrophages (LTR complex promoter)
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Alternative splicing
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-amount determines use of RNA
-proviral synthesises mRNA which can be used for viral portein or genomic RNA |
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Single spliced RNA
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-splicing out ost of gag and pol, leaving env
-env migrates to cytoplasm (by cap and polyA use) to be translated to envelope proteins |
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psi sequence
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-51 nt
-next to gag sequence -when spliced, so are gag and pol |
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Double spliced RNA
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-in more complex viruses (HIV)
-for Tax and Rex proteins |
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Translatoin termination sequence
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-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 |
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Termination tRNA
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-recognises translation termination sequence at end gag region and suppresses it
-allows for translation pol |
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Protease enzyme
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-cleaves integrase and reverse transcriptase from nucleocapsid
-activates viral core -if inactive, new virus buds, but can't infect new cells |
