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rhinovirus
single-stranded RNA viruses positive-sense RNA is directly translated into a polyprotein A protein encoded by the virus copes the single-stranded RNA Part of the Picornaviridae family TERM 2
Poliovirus
DEFINITION 2 Linear, ssRNA(+) genome, polyadenylated, composed of a single ORF encoding a polyprotein Viral genomic RNA has a viral protein (VPg) at its 5 end instead of a methylated nucleotide cap structure. The long UTR at the 5 end contains an internal ribosome entry site (IRES). The P1 region encodes the structural polypeptides. The P2 and P3 regions encode the nonstructural proteins associated with replication. The shorter 3 UTR is important in (-)strand synthesis. TERM 3
Vesicular stomatitis
virus
DEFINITION 3 Vesicular stomatitis Indiana virus (often still referred to as VSV) is a virus in the family Rhabdoviridae; the well-known Rabies virus belongs to the same family. TERM 4
sindbis virus
DEFINITION 4 Sindbis Virus is a member of the Togaviridae family, in the alphavirus subfamily. TERM 5
Nucleoprotein
DEFINITION 5 is any protein that is structurally associated with nucleic acid.
RNA-dependent RNA polymerase
or RNA replicase, is an enzyme () that catalyzes the replication of RNA from an RNA template. is an essential protein encoded in the genomes of all RNA-containing viruses with no DNA stage that have sense negative RNA It catalyses synthesis of the RNA strand complementary to a given RNA template TERM 7
RNA-dependent RNA poly mechanism
DEFINITION 7 Two-step mechanism: First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer- independent (de novo) primer-dependent mechanism that utilizes a viral protein genome-linked (VPg) primer. TERM 8
VPg
DEFINITION 8 VPg is a protein attached to the 5' end of RNA during RNA synthesis in a wide variety of viruses including Picornaviridae such as Foot-and-mouth disease and poliovirus. TERM 9
VP
DEFINITION 9 Vmw65, also known as VP16 or -TIF is a trans-acting protein that forms a complex with the host transcription factors Oct- 1 and HCF to induce immediate early gene transcription in the herpes simplex viruses. TERM 10
2Apro and
3Cpro/3CDpro
DEFINITION 10 protease which cleave the viral polypeptide.
Arenavirus
Is a genus of virus that infects rodents and occasionally humans: The virus contains a beaded nucleocapsid with two single- stranded RNA segments. The strands of RNA are considered negative sense, but encode genes in both directions and are thus ambisense The life cycle of the arena virus is restricted to the cell cytoplasm. TERM 17
Arenavirus
DEFINITION 17 Both segments are ambisense. The viral RNA dependent RNA polymerase (L) binds to a promoter on each encapsidated segment, and transcribes a messager RNA. Transcription is terminated by a strong hairpin sequence at the end of each gene. mRNAs are capped, probably by L protein during synthesis. TERM 18
Reovirus
DEFINITION 18 Has genomes consisting of segmented, double-stranded RNA (dsRNA). Has 5' cap but does not have poly(A) tail Has segments which are grouped into three categories corresponding to their size: L (large), M (medium) and S (small). Replication occurs exclusively in the cytoplasm virus encodes several proteins which are needed for replication and conversion of the dsRNA genome into (+)- RNAs. TERM 19
Rotavirus
DEFINITION 19 The dsRNA genome is never completely uncoated, to prevent activation of antiviral state by the cell in response of dsRNA. Rotavirus mRNAs have at their 3 end a consensus sequence (UGACC) The viral polymerase VP1 synthesizes a capped mRNA from each dsRNA segment. This capped mRNA is translocated to the cell cytoplasm where it is translated. TERM 20
Influenza virus
DEFINITION 20 Viral RNA polymerase (PB1, PB2 and PA) transcribes one mRNA from each genome segment. Transcription is primed by cap cleaved from cellular mRNAS by Cap snatching. mRNA are polyadenylated by the viral polymerase stuttering on a poly U track MP and NS mRNA can be spliced, giving rise to mRNA coding for M2 and NEP proteins PB1-F2 is translated from the +1 ORF of PB1 mRNA
Birnavirus
Virus penetrates into the cytoplasm. Transcription of the dsRNA genome by viral polymerase occurs inside the virion, so that dsRNA is never exposed to the cytoplasm. This plus-strand transcript is used as template for translation. TERM 22
Poliovirus gene expersion
DEFINITION 22 The virion RNA is infectious and serves as both the genome and viral messenger RNA. The IRES allows direct translation of the polyprotein. The polyprotein is initially processed by the viral protease(s) into various precursor and mature proteins to yield the structural proteins, replicase, VPg, and a number of proteins that modify the host cell, ultimately leading to cell lysis. TERM 23
quasispecies
DEFINITION 23 model is a description of the process of the evolution of certain self-replicating entities within the framework of physical chemistry. if the mutation rate is sufficiently high, selection acts on clouds of mutants rather than individual sequences. TERM 24
Recombination
DEFINITION 24 In the solid state physics of semiconductors, carrier generation and recombination are processes by which mobile charge carriers (electrons and electron holes) are created and eliminated. the exchange of nucleotide among different RNA virus TERM 25
Reassortment
DEFINITION 25 Reassortment is the mixing of the genetic material of a species into new combinations in different individuals. the exchanging of the entire RNA molecule between the viruses that are genetically related with segment genome Antigenic shift: is the process by which two or more different strains of a virus, or strains of two or more different viruses, combine to form a new subtype having a mixture of the surface antigens of the two or more original strain
RNAse H
The enzyme RNase H is a non-specific endonuclease and catalyzes the cleavage of RNA via a hydrolytic mechanism. TERM 32
Long terminal
repeat
DEFINITION 32 are sequences of DNA that repeat hundreds or thousands of times. TERM 33
Retroelement
DEFINITION 33 are genetic elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. TERM 34
Integrase
DEFINITION 34 an enzyme produced by a retrovirus (such as HIV) that enables its genetic material to be integrated into the DNA of the infected cell. TERM 35
RNA dependent DNA polymerase
DEFINITION 35 a reverse transcriptase, also known as RNA-dependent DNA polymerase, is a DNA polymerase enzyme that transcribes single- stranded RNA into single-stranded DNA. synthesizes a second strand of DNA complementary to the reverse-transcribed single-stranded cDNA after degrading the original mRNA with its RNaseH activity. Normal transcription involves the synthesis of RNA from DNA
DNA dependent DNA polymerase
is an enzyme that helps catalyze in the polymerization of deoxyribonucleotides into a DNA strand. TERM 37
Helicase
DEFINITION 37 are a class of enzymes vital to all living organisms. involve the separation of nucleic acid strands. often utilized to separate strands of a DNA double helix or a self-annealed RNA molecule using the energy from ATP hydrolysis TERM 38
parvovirus
DEFINITION 38 Parvoviruses are typically linear, non-segmented single- stranded DNA viruses The genome is replicated through rolling-hairpin mechanism Host proteins transcribe the genomes into mRNAs Some mRNAs are spliced allowing alternative forms of the protein to be produced Uncoating, and release of the viral genomic ssDNA into the nucleus. The ssDNA is converted into dsDNA by cellular proteins. TERM 39
parvovirus cont--
DEFINITION 39 viral mRNAs are transcribed when host cell enters S phase and translated to produce viral proteins. Replication occurs through rolling-hairpin mechanism, whith NS1 nickase binding covalently to the 5 genomic end. These newly synthesized ssDNA can either a) be converted to dsDNA and serve as a template for transcription/replication b) be encapsidated to form new virions that can budd out of the host cell. TERM 40
Papovavirus(SV40)
DEFINITION 40 Pa for papillomavirus, Po for polyomavirus, and Va for "vacuolating" (simian vacuolating virus 40 or SV40, which is now known to be part of the polyomavirus genus). DNA viruses containing double-stranded DNA
RNA polymerase
II
It catalyzes the transcription of DNA to synthesize precursors of mRNA (pre-mRNA) and most snRNA and microRNA TERM 47
RNA polymerase III
DEFINITION 47 transcribes DNA to synthesize ribosomal 5S rRNA, tRNA and other small RNAs. TERM 48
TATA box
DEFINITION 48 The TATA box is a DNA sequence (cis-regulatory element) found in the promoter region of genes in archaea and eukaryotes. it is the binding site of either general transcription factors or histones involves in the process of transcription by RNA polymerase. TERM 49
TFIId
DEFINITION 49 RNA polymerase II holoenzyme is a form of eukaryotic RNA polymerase II that is recruited to the promoters of protein-coding genes in living cells. It consists of RNA polymerase II, a subset of general transcription factors, and regulatory proteins known as SRB proteins. The transcription Factor II D (TFIID) complex, binds to the TATA box in the core promoter of the gene. TERM 50
TFIId cont--
DEFINITION 50 coordinates the activities of more than 70 polypeptides required for initiation of transcription by RNA polymerase II, binds to the core promoter to position the polymerase properly, serves as the scaffold for assembly of the remainder of the transcription complex, and acts as a channel for regulatory signals.
Co-activator
A coactivator is a protein that increases gene expression by binding to an activator which contains a DNA binding domain. such as TFIId and TERM 52
nuclear run-on transcription assay
DEFINITION 52 Infect the cells get the nuclei add the nuclei hybridize the RNA with M13 probe TERM 53
cdk
DEFINITION 53 Cyclin-dependent kinase 9 or CDK9 is a cyclin-dependent kinase associated with P-TEFb. component of the multiprotein complex TAK/P-TEFb, which is an elongation factor for RNA polymerase II- directed transcription TERM 54
P-TEFb
DEFINITION 54 Positive Transcription Elongation Factor b is the key factor regulating eukaryotic mRNA transcription at the level of elongation. The kinase activities of P-TEFb (the phosphorylation of serine 2 at RNA polymerase C-terminal repeats TERM 55
tat
DEFINITION 55 The tat protein is an RNA-binding protein Interacts with a short nucleotide sequence called TAR (trans- activation responsive) that lies within the 5' LTR region of HIV mRNA transcripts Binding of tat protein to the TAR sequence accelerates transcription of the provirus by cellular RNA polymerase II. The activity of the Tat protein increases the production of new virus particles by regulating the expression of several other genes.
tar
tar recognize sequence like RNA activate when close initiation site TERM 62
p-Tefb
DEFINITION 62 Positive Transcription Elongation Factor b is the key factor regulating eukaryotic mRNA transcription at the level of elongation. It is a cyclin dependent kinase, composed of Cdk9 and in humans one of three cyclins is also a required cellular cofactor for HIV-Tat TERM 63
Large T
DEFINITION 63 Activate late transcription TERM 64
VP
DEFINITION 64 also known as VP16 or -TIF is a trans-acting protein that forms a complex with the host transcription factors Oct-1 and HCF to induce immediate early gene transcription in the herpes simplex viruses. TERM 65
oct
DEFINITION 65 class 2, transcription factor 1 is a protein that in humans is encoded by the POU2F1 gene.
5' cap
The 5' cap is a specially altered nucleotide on the 5' end of precursor messenger RNA and some other primary RNA transcripts as found in eukaryotes. he process of 5' capping is vital to creating mature messenger RNA, which is then able to undergo translation. Capping ensures the messenger RNA's stability while it undergoes translation in the process of protein synthesis, TERM 67
Poly A binding protein
DEFINITION 67 Pol-binding protein (PAB or PABP) is a RNA-binding protein which binds to the poly(A) tail of mRNA. the mRNA encoding PABP contains in its 5' UTR an A-rich sequence which binds Poly(A)-binding protein This leads to repression of translation TERM 68
Polyadenylation
DEFINITION 68 Polyadenylation is the addition of a pol tail to an RNA molecule. it is a stretch of RNA that has only adenine bases. is part of the process that produces mature messenger RNA (mRNA) for translation polyadenylation can produce more than one transcript from a single gene, similar to alternative splicing. TERM 69
Alternate splicing
DEFINITION 69 Alternative splicing is a process by which the exons of the RNA produced by transcription of a gene (a primary gene transcript or pre-mRNA) are reconnected in multiple ways during RNA splicing. TERM 70
spliceosome
DEFINITION 70 A spliceosome is a complex of snRNA and protein subunits that removes introns from a transcribed pre-mRNA segment.
suppression of termination
(also referred to as stop codon readthrough) is an alternate mechanism of translation to produce a protein with an extended C-terminus. It is used as a regulatory strategy by a large number of plant, animal and prokaryot viruses (see table below).UAG amber and UGA opal codons are normally recognized by a release factor (eRF) instead of a tRNA, thereby stopping translation TERM 77
Ribosomal frameshifting
DEFINITION 77 allows alternative translation of a mRNA sequence by changing the open reading frame. Ribosomal frameshifting is promoted by a pseudoknot structure and slippery sequence (usually UUUAAAC) It is often required for translation of putative RNA- dependent RNA polymerase.
