The World of Viruses A Classification Guide

Chapter 6 - - - - - What are viroids? - Viroids are small single-stranded, circular RNAs that are infectious pathogens. Unlike viruses, they have no protein coating. All known viroids are inhabitants of angiosperms, and most cause diseases, whose respective economic importance to humans varies widely. Only infect plants. Difference between virus and viroids - Viruses are composed of a nucleic acid (most plant viruses contain ribonucleic acid [RNA]) and are enclosed in a protein coat. The nucleic acid of a few plant viruses (Carnation etched ring virus, Dahlia mosaic virus) is deoxyribonucleic acid (DNA). Viroids consist of low molecular weight RNA that lacks a protein coat. Difference between viroid and virion - A viroid is an RNA molecule that only infects plants with no protein capsid with some potential catalytic ability that is replicated by host RNA polymerase. A virion is the infectious portion of a virus, they can be symmetrical or asymmetrical, infect more than just plants, and exist inside a protein coat/membrane, though a virion is the “infectious part of the virus” or the genome that enters the cell Prion: Infectious proteins, cause mad cow disease, no nucleic acid components, have an abnormal structure that alters the conformation of normal proteins How are viruses classified?: Through baltimore classification which is based on the genome composition, symmetry of the virus, the envelope, and the route they express their mRNA through Baltimore classification: a method of distinguishing viruses into different classes based on their genome composition and route they express their mRNA through. - Viral genome contains - DNA or RNA - Single or double stranded - Linear, circular, or segmented - Symmetry - Filamentous - Icosahedral - Asymmetrical - Envelope - From host - Not from host - Size (range from 30nm -270nm) (enterovirus-> mimivirus) - Host range (how closely related hosts are) - - - - - - - Baltimore Classification Group 1: Double stranded DNA, uses its own or host’s DNA pol for replication - Baltimore Classification Group 2: Single stranded DNA, requires DNA pol to form complementary strand - Baltimore Classification Group 3: Double stranded RNA, requires RNA-dependent RNA polymerase (RDRP) to make mRNA and genomic RNA - Examples of Baltimore Classification Group 3: reo and roto virus - Baltimore Classification Group 4: (+) Single stranded RNA, requires RDRP, (+) strand allows immediate translation - Examples of Baltimore Classification Group 4: Polio and Corona - Baltimore Classification Group 5: (-) single stranded RNA, requires RDRP, - examples of Baltimore Classification Group 5: Influenza - Baltimore Classification Group 6: Retrovirus, Packages its own reverse transcriptase to make dsDNA - Baltimore Classification Group 7: dsDNA pararetrovirus, requires plant host reverse transcriptase to make dsDNA RDRP: RNA-dependent RNA polymerase How is influenza able to become so genetically unique? - It is a segmented virus from multiple source species that can be be recombined to create great genetic diversity What is Ortholog - genes which evolved from a common ancestral gene by speciation that usually have retained a similar function in different species. What is Paralog - genes related by duplication within the genome and often they acquire a new function. How do bacteriophages get their genome inside the cell? - 4 possible routes, through LPS (if gram -), through cell surface proteins like OmpF and TolC, or through the flagella - Often only the genome is transferred into the cell through the cell envelope, and the phage capsid left outside the cell is referred to as a ghost - Ghost: the phage capsid left outside the cell, attached to its surface after delivering virus genome How will salmonella get rid of a bacterial infection? - It will turn off its genes that code for outer membrane proteins to prevent the virus from entering that way Why do we need bacteriophage in our gut How is Bacteriophage helpful for the immune system What is lytic and lysogenic and slow-release? - - - - Lytic cycle: Bacteria synthesizes capsid proteins based on available phage DNA, phage DNA is replicated and then packed into the capsids, cell is then lysed by phage, releasing viral progeny and killing the cell - Lysogenic cycle: phage DNA integrates itself into the bacterial chromosome and becomes a prophage at the ATT site using enzyme recombinase to perform site-specific recombination. Prophage is then replicated alongside chromosomal DNA prior to mitosis - Prophage:integrated phage DNA that replicates with host genome. Stress can induce its excision where the lytic cycle can then begin - Slow release: phage particles reproduce without destroying the host cell. Host cells grow slowly but do not die Site specific- recombination What is a positive strand? What is a negative strand? - Positive-strand RNA virus genomes are templates for both translation and replication, leading to interactions between host translation factors and RNA replication at multiple levels. All known positive-strand RNA viruses carry genes for an RNA-dependent RNA polymerase (RdRp) used in genome replication. - Negative-strand RNA virus: Also known as an antisense-strand RNA virus, a virus whose genetic information consists of a single strand of RNA that is the negative or antisense strand which does not encode mRNA (messenger RNA). How will a negative strand become a positive strand? Slow release, porins, between positive and negative strand What is bacterial defense? What is eclipse and latent period? What is difference between them? - Eclipse period: Period before any virus replication begins where virus readies cell machinery and gathers necessary nutrients - Latent period: Period where intercellular viruses are increasing but extracellular viruses are not because no cell lysis has occurred yet. - difference between latent period and eclipse period: In the latent period the virus can be reproducing and growing in number, those viruses just have not been released into the extracellular environment yet conversely the eclipse period is no virus replication is occurring at all and stops when the latent period begins. The latent period is the entire time leading up to extracellular virus release, including the eclipse period and after it. BacterioPhage? Why is it good for the gut? - Phages are implicated in the balance or imbalance of the intestinal microecology and can affect human health either directly, by preying on the ecological landscape of the bacterial hosts, or indirectly, by influencing the immune system or metabolic pathway - - - - Graph of Ellipse and Latent Icosahedral Viruses - polyhedral virus with 20 identical triangular faces made of 3 proteins from 1 gene. Has a fixed size and cannot extend Glycoprotein spikes: encoded by virus, lay on the envelope of viruses Question about CRISPR-CAS 9 - CRISPR-Cas9: uses splices from previously exposed bacteria (aka a spacer) to recognize foreign viral DNA/RNA and cut it next to the PAM sequence. Cas9 enzyme is the protein that cuts the sequence - spacer: DNA sequences from viruses the bacteria was previously exposed to that have been spliced and are used as a reference by CRISPR - crRNA: crispr array RNA that includes spacers that cas-9 uses as a reference to cut viral RNA/DNA Acr gene: (Anti-CRISPR Gene) prevents viral DNA from being cut, bacteriophages developed it as a response to CRISPR Transcytosis: When is lysogeny beneficial?: A beneficial bacteria can gain a toxin that allows it to outcompete a pathogenic bacteria. Ie it can be used to gain beneficial genes from the virus. What is tropism?: ability to infect a particular tissue type in host. What is a plaque? : on a lawn of cells, circles of white color caused by 1 virus that kills the bacteria turning them white virulency: ability to infect How to culture Bacteriophage? : add phages to bacterial broth and incubate, add this phage-bacteria mixture to molten top agar. This new solution is then poured over a set agar plate and plaques will form on the soft agar over night. Chapter 11 - How does bacteria prevent phage DNA integration? (Slide 6) - something about ATT site ATT site : where site specific recombination occurs by recombinase What side operon are genes CI, CII, CIII, and CRO? What functions do those genes control?: Right side, functional genes that control whether virus is lytic or lysogenic What side operon are genes E, D, J,K,Z,M? What do they encode for? : for structures like the tail proteins, tail tip proteins, capsid proteins, etc. On the left side. - Cos sequence : short for cohesive ends, a 200 bp long sequence that is cut by terminase when phage DNA was packaged, rejoin together when DNA enters new host cell to form circular genome - What are the three important functions of Terminase? : 1- make overhang, 2- cutting DNA at cos in rolling-circle replication 3- connect head w/ tail - Phage Lambda Infection of E coli (Slide 16) - Lytic and Lysogeny difference (switch why does it happen)how does it happen? Slide 16 - Lysogeny - Bacteriophage c1 and c2 gets together and gets integrated - Other genes are present crogene “do not wanna go to lysogeny wants to go to lytic” - Lysogeny tries to be quiet - When you expose bacteria into stress it converts from lysogenic or lytic - C1 and c2 gene - Diagram - 5 points - Cro gene, c1, c2, c3 what do they do - Image bacteria inside Cro gene - Cro gene goes for lytic cycle. - C2 and c1 hide inside the cell lysogeny and blocks lytic cycle and promotes lysogeny - Function of c3: block hflb - No more cro turned on lytic goes if c3 is on lysogenic cycles - C3 always supports c2 by preventing HFLB from cutting C2 - Why is there a switch between rolling replication and theta replication? : Rolling-circle replication occurs once 𝛳 is complete because it requires no proofreading and is thus faster. - Arian flu - What is a lambda phage and how is it packaged? : this phage binds E. Coli by contact between its tail fibers and maltose porin. The tail fibers of the phage change the maltose porin’s structure, allowing phage DNA to enter the cell. - How to prevent phage DNA from entering via porin? : Change binding site or close porin and take in alternative energy souce (in the case of λ porin, a sugar other than maltose) - Difference between antigenic shift and drift? - How does influenza come to human beings? - Have to have H1n1 in it Neura amindace: - remove yellow genes. Remove hiv: lentivirus - gag gene and pol Env gene Lenti viruses: textbook - Function of m channel - Helper plasmids what do they do - lentiviral therapy/hiv treatment - - - What does the enzyme terminase does - Cost to cost in connection terminate cut the cost new bacteriophage Why is bacterial circular - Cost to cost come together - (in slides) Why do we have circular chromosome and not straight (for protection) No terrace enzyme that’s why it’s circular What is integration site: att site Advantage of having rolling circle replication and theta replication : because it goes fast but theta replication synthesis happens . Theta replication: proofreading dna polymerase will check for signal goes slowly checking rolling surface is faster there is no proof reading Att site: What is integration site of bacteriophage into chromosome High hflb will cut all c2 and cro will be turned on a lot of sugars high nutrients high hlfb which will kill c2 which turns on cro Why when lot of bacteriophage inside tummy not take advantage and kill all the bacteria Use resources and integrate and slowly slowly replicate Where do they go for lysogeny and become stingy they use resources available Influenza what is genetic reinsortment - Bird virus monkey virus accumulate and come to human being - H1 n1 high transmission ability to human beings Genetic reinforcement HIV yellow genes - Remove yellow genes no more HIVGag gene enb gene What is qusasi species Lenty virus how to remove gene Tissue culture Chapter 7 - How bacteria chromosomes are kept in space with supercoiling When can we expect super coil to go for a relaxed position Gyrace and ciproflaxcin When do we have negative and positive supercoiling? Negative- when gene doesn’t get expressed Why is bacterial chromosome circular not linear? Bacteria doesn’t have telomere, doesn’t protect Okazaki fragments Slide 52 What is porin, parc, parm, What is clear cut between plasmid One sentence, what is the goal of meta genomic? DNA Sequencing, Horizontal gene Chapter 8 - The drugs (slide 17 and 20) - ciprofloxacin - Function of 17 and 32 - If you're a bacterium in high heat, what kind of event will occur? - You’re waiting for 32 prime to activate 17 prime - Antibiotics know their drug targets - Antibiotics must meet two fundamental criteria: - They must kill or retard the growth of a pathogen, and they must not harm the host. - Rifamycin B - Selectively binds to the bacterial RNA pol - Inhibits transcription initiation - Actinomycin D - Nonselectively binds to DNA - Inhibits transcription elongation - Binds to cancer cells - Streptomycin: inhibits 70S ribosome formation - Tetracycline: inhibits aminoacyl-tRNA binding to the A site - Chloramphenicol: inhibits peptidyltransferase - Puromycin: triggers peptidyltransferase prematurely - Erythromycin: causes abortive translocation - Fusidic acid: prevents translocation - Know about nucleic region and polar region - Polar region: physical binding done by NUSG - Pole side: transcription and translation - The Nucleoid Region harbors the organism's DNA and is pivotal for DNA replication, cellular division, and transcription, translating DNA into RNA for protein creation. - How is Hemlocyin being secreted? -Hemolysin is secreted to the extracellular milieu by type I secretion system. The export system consists of an ATP-binding cytoplasmic membrane protein, HlyB; a cytoplasmic membrane protein with a large periplasmic domain, HlyD; and an outer membrane protein not encoded within the hemolysin operon - How it Hemlocyin being transported by HLYABC? -Through type 1 secretion - ABC functions and why it’s being transported? -abc transporters are the simplest of the protein secretion systems and make up what is called the type I protein secretion. Type I protein moves certain proteins directly from the cytoplasm to the environment. Type 1 has 3 main components: an outer membrane channel, an abc protein at the inner membrane, a periplasmic protein lashed to the inner membrane. - Shaporin/ Chaperones proteins and functions? -Chaperones bind to and stabilize conformers of other proteins, and via cycles of regulated binding and release are able to facilitate the correct fate of their client protein and reduce protein aggregation. Chapter 9 - - Why are we turning on the genes When is bacteria choosing to go for non homologous enzymes - Translesion bypass synthesis - When you don’t have a non homologous plate How do i identify mutation in a cell - Slide #17 identify mutagen using bacterial guinea pigs is a test used for mutation analysis? - F’ F+ F- HFR - F- cells do not possess any form of a plasmid. F+ cells possess an F plasmid which is separate from the bacterial chromosome.F+ allows cells to initiate conjugation. Hfr cells possess a plasmid that replaces the bacterial chromosome entirely. F' cells possess an F' plasmid which contains plasmid DNA and some bacterial chromosomal DNA, - Conjugation requires the presence of special transferable plasmids. - These usually contain all the genes needed for pilus formation and DNA export. - A well-studied example in Escherichia coli is the fertility factor (F factor). Conjugation begins with contact between the donor cell, called the F+ cell, and a recipient F– cell. - The F-factor plasmid can integrate into the chromosome. - The cell is now designated Hfr, or high-frequency recombination strain. - An Hfr cell is capable of transferring parts of the chromosome into a recipient cell. - Genes are transferred in order. - The entire chromosome takes about 100 minutes to transfer. - How Crispr Works - CRISPR (clustered regularly interspaced short palindromic repeats) is an adaptive system. - An organism that manages to survive a phage attack captures a piece of the invader’s genome and wields it as a defense against future attack. - CRISPRs consist of repeats and spacers that do not encode proteins, but near them lie CRISPR-associated gene families that do encode proteins. - CRISPR is a primitive microbial immune system. - The function can be divided into three stages: spacer acquisition,crRNA processing, and effector stage. - Screen Assays - all mutants grow, but some show a different phenotype from wildtype. - Selection Assay - only mutants involved in the function of interestcan grow. - How bacteria loses a gene how bacteria gains a gene - In transformation, the recipient bacterium takes up extracellular donor DNA. In transduction, donor DNA packaged in a bacteriophage infects the recipient bacterium. In conjugation, the donor bacterium transfers DNA to the recipient by mating. - Transcription modification - Post-transcriptional modifications of pre-mRNA, such as capping, splicing, and polyadenylation, take place in the nucleus. After these modifications have been completed, the mature mRNA molecules have to be translocated into the cytoplasm, where protein synthesis occurs - How competent allies work Contains two replication origins for F factor: - – oriV: used in nonconjugating cells - – oriT: used during DNA transfer Chapter 9 How to identify mutation in gene What is competent cell? Bacteria is competent enough How bacteria gain and lose a gene? Transformation, transduction, conjunction Conjugation: sexual reproduction, makes plasma go inside NHEJ- Non homologous end joining Chapter. 12 What is CCR5 What is Pam, where is it present Slide 22; What is Cas 9 function Slide 11 Slide 4 Che Y- activation flagella swirl Che W- intermediate proteins Che A- Kinase adds phosphate to phosphorlate Che Z- phosphatase (kill phosphate) Che R- methylate (add methyl group) Che B- demethylase MCP Moving with purpose slide 11 Che Y- causes the tumble If Che-Y can’t phosphorylate there is no tumble, run Biofilm Slide 19