Virus Lecture Notes PDF

Announcements NO class this Friday (Feb. 23) I will provide an online synthesis day recording that covers Ch. 6 and all of Ch. 13 next Tues/Wed Semester Project (So Many Scientists!) Time Full assignment under Assignments tomorrow (Counts for 100 points!) Written report due 11:59pm on Friday, April...

Announcements NO class this Friday (Feb. 23) I will provide an online synthesis day recording that covers Ch. 6 and all of Ch. 13 next Tues/Wed Semester Project (So Many Scientists!) Time Full assignment under Assignments tomorrow (Counts for 100 points!) Written report due 11:59pm on Friday, April 26th (4-6 pages, DS) Goal: Research an approved microbiologist and read an approved peerreviewed research manuscript by this scientist. You will then write a report on the scientists’ background, research topic, and their contribution to that research topic followed by a discussion of one of their scientific works. I’ve provided a list of possibilities, but feel free to choose your own! (Just get it approved by me first) 1 CHAPTER 6.1 – 6.4 Viruses Copyright © 2024 by W. W. Norton & Company, Inc. Learning Objectives 1. Know the basic structures of virus 2. Understand that the synthesis of viral genetic material and proteins is dependent on host cells and these processes are different among viruses 3. Compare and contrast lytic and lysogenic replication cycles 3 Introduction § Viruses are everywhere, in all ecosystems, and all cellular organisms are infected by them. 4 Introduction § Viruses are everywhere, in all ecosystems, and all cellular organisms are infected by them. § Some viruses generate serious diseases in humans, including Zika fever, influenza, and AIDS. 5 Introduction § Some viruses fill essential, beneficial niches, particularly in marine ecosystems and the human gut, where they cycle nutrients and improve health. 6 6.1 Viruses in Ecosystems § A virus is a noncellular particle that infects a host cell and directs it to produce progeny particles (more viruses). § The virus particle, or virion, generally consists of a viral genome (DNA or RNA) contained within a protein capsid. 7 Viruses Infect Specific Hosts Bacteriophages (or phages) are viruses that infect bacteria. 8 Viruses Infect Specific Hosts Bacteriophages (or phages) are viruses that infect bacteria. Their replication is observed as a plaque of lysed cells on a lawn of bacteria growing in a Petri dish. 9 Integrated Viral Genomes § Viruses can replicate and lyse cells or integrate their genome into the host genome and be “dormant” § A bacteriophage that integrates its genome into its bacterial host’s genome is called a prophage. Lytic Cycle Environmental Cues Lysogenic Cycle 10 Ecological Roles of Viruses § Acute viruses rapidly kill their hosts and thus act as predators to limit host population density. Host death recycles nutrients back to the community. Surviving hosts have undergone selection for resistance. 11 Ecological Roles of Viruses § Persistent viruses remain in hosts where they may evolve traits that confer positive benefits in a virus-host mutualism. The virions express wasp genes in the caterpillar, where they prevent the encapsulation process that would otherwise wall off the wasp egg and kill it. 12 6.2 Virus Structure § A virion possesses a genome of either DNA or RNA. The precise configuration of the genome varies with virus type. § The protein capsid packages the viral genome and delivers it into the host cell. 13 6.2 Virus Structure § A virion possesses a genome of either DNA or RNA. The precise configuration of the genome varies with virus type. § The protein capsid packages the viral genome and delivers it into the host cell. Different viruses make different types of capsids. Capsid types are either symmetrical or asymmetrical. 14 Symmetrical Virions § Icosahedral viruses Are polyhedral with 20 identical triangular faces Have a structure that exhibits rotational symmetry 15 Symmetrical Virions § In some icosahedral viruses, the capsid is enclosed in an envelope that is derived from the cell membrane of the host organism. The envelope contains glycoprotein spikes, which are encoded by the virus. 16 Tailed Viruses § Tailed viruses have complex multipart structures that often include elaborate delivery devices. § For example, the bacteriophage T4 has an icosahedral “head” that is attached to a helical “neck,” baseplate, and tail fibers. 17 Viroids § Viroids are RNA molecules that infect plants. They have no protein capsid. They are replicated by host RNA polymerase. 18 Prions § Prions are infectious proteins. They have no nucleic acid component. They have an abnormal structure that alters the conformation of other normal proteins. 19 6.3 Viral Genomes and Classification § Viral genomes can be: DNA or RNA Single- or double-stranded (ss or ds) Linear, circular, or segmented § Viral genome features are used as the basis of virus classification. 20 Viral Genomes: Small or Large § Small viruses commonly have a small genome, encoding fewer than ten genes. The genes may actually overlap in sequence. § Many small viral genomes consist of RNA. 21 Viral Genomes: Small or Large § The “giant viruses” have genomes of double-stranded DNA comprising 300–2,500 genes. § The mimivirus, which infects amoebas, is as large as some bacteria. It can become infected by smaller viruses called virophages. 22 Viral Genomes: Small or Large § Giant viruses have genomes that specify a surprisingly large number of enzymes with housekeeping cell functions. Suggest that a virus evolved from a parasitic cell 23 The International Committee on Taxonomy of Viruses § The International Committee on Taxonomy of Viruses (ICTV) devised a working classification system for viruses based on several criteria: Genome composition Capsid symmetry Envelope Size of the virion Host range 24 The Baltimore Virus Classification § In 1971, David Baltimore proposed that the classes of viruses be distinguished by two main criteria. Genome composition (RNA or DNA) Route to express messenger RNA 25 mRNA Translation to Amino Acids 26 Expressing mRNA (sense vs. antisense nucleic acid strands) Sense strand (or positive strand) contains the code needed for the protein Anti-sense strand (or negative strand) is complementary to the sense strand Sense Strand If you wanted to get an mRNA version of the sense strand, what would you need to do? Anti-Sense Strand 27 Expressing mRNA (sense vs. antisense nucleic acid strands) Sense strand (or positive strand) contains the code needed for the protein Anti-sense strand (or negative strand) is complementary to the sense strand AND serves as the template to create the mRNA Sense Strand Anti-Sense Strand 28 The Baltimore Virus Classification 29 The Baltimore Virus Classification 30 Molecular Evolution of Viruses § The relatedness of different viruses can be measured by comparing their genome sequences – just like other organisms! § What can this tell us about the virus? 31 6.4 Bacteriophages § Viruses display a remarkable diversity of ways to replicate within a host cell. § Let’s discuss the key modes of bacteriophage replication, and their consequences for host cells. § Do bacteria have defenses for bacteriophages? 32 Bacteriophages Infect a Host Cell by Cell-surface Receptors § To commence an infection cycle, bacteriophages need to contact and attach to the surface of an appropriate host cell. § Viruses target specific, key proteins of their host. 33 Bacteriophages Infect a Host Cell 34 Bacteriophages Infect a Host Cell § Bacteriophages exhibit two different types of replication cycles: 1. Lytic cycle 2. Lysogenic cycle 35 Bacteriophages Infect a Host Cell § Bacteriophages exhibit two different types of replication cycles: 1. Lytic cycle 2. Lysogenic cycle § The “decision” of which replication cycle to utilize is dictated by environmental cues that either activate or repress transcription of genes for virus replication. In general, events that threaten host cell survival trigger a lytic burst. Why do you think that is? 36 The lytic replication cycle requires... 1. Host recognition and attachment 2. Genome entry 3. Assembly of phages 4. Exit and transmission 37 Bacteriophages Infect a Host Cell § A temperate phage can infect and lyse cells like a virulent phage, but it also has the unique ability to integrate its genome as a prophage. § The phage is said to “lysogenize” the host, leading to a state called lysogeny. Bacteriophage is not replicating. The phage can reactivate to become lytic. 38 39 Bacterial Defenses § Bacteria have evolved several forms of defense against bacteriophage infection: Genetic resistance – Restriction endonucleases – Altered receptor proteins Cleave viral DNA lacking methylation CRISPR integration of phage DNA sequences – Clustered regularly interspaced short palindromic repeats – A bacterial immune system 40 CRISPR Defense of a Bacterial Cell and anti-CRISPR Counter-defense 41 CRISPR Defense of a Bacterial Cell and anti-CRISPR Counter-defense 42 CRISPR Defense of a Bacterial Cell and anti-CRISPR Counter-defense 43 CRISPR Defense of a Bacterial Cell and anti-CRISPR Counter-defense 44 CRISPR Defense of a Bacterial Cell and anti-CRISPR Counter-defense CRISPR-Cas complex binds and cleaves phage DNA 45 CRISPR Defense of a Bacterial Cell and anti-CRISPR Counter-defense Acr inhibits CRISPR-Cas binding 46