Chapter 5 Lecture Notes on Viruses and Prions PDF

CHAPTER 5 LECTURE NOTES Chapter 5 Lecture Notes Viruses and Prions 1. Discovery of viruses: scientists discovered that a disease in tobacco plant was caused by a virus, an animal virus causes foot-and-mouth d...

CHAPTER 5 LECTURE NOTES Chapter 5 Lecture Notes Viruses and Prions 1. Discovery of viruses: scientists discovered that a disease in tobacco plant was caused by a virus, an animal virus causes foot-and-mouth disease in cattle, and bodily fluids that were filtered to remove bacteria remained infectious indicating there were infectious agents smaller than bacteria 2. Role of viruses in evolution: infect cells and influence their genetic makeup, 8% of the human and 10-20% of bacterial genome contains viral sequences 3. Properties of viruses a. Obligate intracellular parasites: cannot multiply unless they invade a host cell and instruct its machinery to make and release new viruses since they lack enzymes for most metabolic processes and machinery for protein synthesis b. Infect: bacteria, algae, fungi, protozoa, plants, and animals, ubiquitous in nature and have had a major impact on development of biological life c. Classification and naming: based on hosts and diseases they cause, their structure and chemical composition, and similarities in genetic makeup, the Internal Committee of the Taxonomy of Viruses classifies and categorizes viruses d. Size: 20nm to 1,000nm diameter, almost all require an electron microscope to visualize e. Describing viruses: active/inactive instead of alive/dead since they are non-living and unable to multiply independent from a host f. Attachment to host cells: molecules on virus surfaces provides high specificity for host cell attachment g. Viral structure: capsid, nucleic acids, may have one or two enzymes, may have an envelope, not a cell and do not independently fulfill the characteristics of life i. Capsid: protein shell that surrounds nucleic acid 1. Nucleocapsid: capsid together with nucleic acids 2. Capsomeres: identical protein subunits that spontaneously self-assemble into the finished capsid 3. Three types: helical (hollow cylinders), icosahedral (3D, vary in number of capsomeres), and complex (never enveloped) ii. Envelope: covering external to the capsid that is usually a modified piece of the host's cell membrane from budding 1. Naked viruses consist only of a nucleocapsid 2. Enveloped viruses can bud from the cell membrane, nuclear envelope, or the endoplasmic reticulum, and are pleomorphic due to the flexibility the envelope confers iii. Spikes: project from the nucleocapsid or the envelope and allow viruses to dock onto host cells iv. Virion: fully formed virus that is able to establish an infection in a host cell v. Nucleic acids: DNA or RNA, not both 1. Only possess genes needed to invade host cells and redirect their activity 2. DNA: double- or single-stranded 3. RNA: double- or more often single-stranded a. Positive-sense RNA: ready for immediate translation 15 CHAPTER 5 LECTURE NOTES b. Negative-sense RNA: used as a template to make mRNA before translation c. Segmented: individual genes exist on separate pieces of RNA d. Retroviruses: possess enzymes to create DNA from their RNA 4. Baltimore Classification System: describes how each type of virus makes mRNA TYPES OF VIRAL STRATEGY EXAMPLE GENOMES Class I dsDNA dsDNA → mRNA Herpes simplex (herpes) Class II ssDNA ssDNA → dsDNA → mRNA Parvovirus B19 (skin rash) Class III dsRNA dsRNA → mRNA Rotavirus (gastroenteritis) Class IV (+) (+) ssRNA → (-) ssRNA → mRNA Poliovirus (polio) ssRNA Class V (-) (-) ssRNA → mRNA Influenza virus ssRNA (influenza) Class VI ssRNA- ssRNA-RT → DNA/RNA → HIV (AIDS) RT dsDNA → mRNA Class VII dsDNA-RT → mRNA Hepatitis B virus dsDNA-RT (Hepatitis B) vi. Other components 1. Enzymes a. Polymerases: synthesize DNA and RNA b. Replicases: copy RNA c. Reverse transcriptase: synthesizes DNA from RNA d. Most viruses lack the genes for synthesis of metabolic enzymes 2. Taking components from host cell a. Arenaviruses: take host ribosomes b. Retroviruses: use host tRNA molecules h. Multiplication cycles of animal viruses: dictate the way the virus is transmitted, what it does to the host, immune responses, human measures to control viral infections, vary in length i. Adsorption 1. Virus encounters susceptible host cell and adsorbs specifically to receptors on the cell membrane that are usually proteins the cell requires for normal function 2. Glycoprotein spikes on the envelope or on the capsid of a naked virus binds to the receptors on the membrane 3. Host range: range of cells that a virus can infect 16 CHAPTER 5 LECTURE NOTES a. Restricted: Hepatitis B, only infects liver cells of humans b. Moderate: Poliovirus, infects intestinal and nerve cells of primates c. Broad: rabies, infects various cells of mammals d. Cells that lack compatible virus receptors are resistant to adsorption and invasion by that virus e. Tropisms: specificities of viruses for certain tissues ii. Penetration and uncoating 1. Virus or its nucleic acid penetrates the host cell membrane a. Endocytosis: entire virus is engulfed by the cell and enclosed in a vacuole or vesicle, enzymes in the vacuole may break down the capsid, freeing the nucleic acid b. Fusion: viral envelope fuses with cell membrane, nucleocapsid enters cell, nucleic acids uncoated iii. Synthesis 1. Replication and protein production a. DNA viruses: enter nucleus for replication and assembly b. RNA viruses: enter cytoplasm for replication and assembly c. Retroviruses: copies its RNA into DNA, complex life cycle 2. Example 1: +ssRNA viruses a. +ssRNA serves as mRNA and is translated into viral proteins, especially those useful for further viral replication b. +ssRNA is replicated into -ssRNA, becoming the template for the creation of many new +ssRNAs that are used as the viral genomes of new viruses, additional +ssRNAs are synthesized and used for late-stage mRNAs c. Some viruses are equipped with the necessary enzymes for synthesis of viral components, others utilize those of the host 17 CHAPTER 5 LECTURE NOTES d. Proteins for the capsid, spikes, and viral enzymes are synthesized on the host's ribosomes using its amino acids 3. Example 2: DNA viruses a. Early phase i. Viral DNA enters nucleus and genes are transcribed into mRNA ii. mRNA moves into cytoplasm to be translated into viral protein/enzymes needed to replicate the viral DNA iii. Host cell's DNA polymerase is involved b. Late phase i. Parts of viral genome are transcribed and translated into proteins required to form the capsid and other structures ii. New viral genomes and capsids are assembled iii. Mature viruses are released by budding or cell disintegration iv. Assembly 1. Mature viruses are constructed from the growing pool of parts 2. Capsid is first laid down as an empty shell that will serve as the receptable for the nucleic acid 3. Viral spikes are inserted into the host's cell membrane so they can be picked up as the virus buds off with its envelope v. Release 1. Nonenveloped and complex viruses: reach maturation in nucleus or cytoplasm and are released when the cell lyses or ruptures 2. Enveloped viruses: liberated by budding from the membranes of the cytoplasm, nucleus, endoplasmic reticulum, or vesicles a. Nucleocapsid binds to the membrane, which will curve completely around it and form a small pouch b. The pouch will pinch off and release the virus with its envelope 3. The number of viruses released by infected cells varies and is controlled by: the size of the virus and the health of the host cell a. Poxvirus-infected cell: may release 3,000-4,000 virions b. Poliovirus-infected cell: may release up to 100,000 virions c. With large numbers of virions released by some infected cells, there is potential for rapid viral proliferation as the released viruses encounter susceptible cells 18  CHAPTER 5 LECTURE NOTES 4. Damage to host cell a. Cytopathic effects (CPEs): virus-induced damage to the cell that alters the cell's microscopic appearance i. Types of CPEs 1. Gross changes in shape and size 2. Development of intracellular changes 3. Inclusion bodies: compacted masses of viruses or damaged cell organelles in the nucleus and cytoplasm 4. Syncytia: fusion of multiple damaged host cells into single large cells containing multiple nuclei b. Accumulated damage from a viral infection kills most host cells 5. Persistent infections a. Carrier relationship: some cells harbor the virus and are not immediately lysed, this can last from a few weeks to the remainder of the host's life, and can remain latent in the cytoplasm b. Provirus: viral DNA becomes incorporated into the DNA of the host, measles virus in brain cells occasionally causing progressive damage c. Chronic latent state: latent viruses periodically become activated under the influence of various stimuli, herpes simplex and herpes zoster viruses (chickenpox and shingles) 6. Viruses and cancer a. Estimation that 20% of cancers are caused by oncoviruses b. Transformation: effect of oncogenic (cancer-causing) viruses on host cells c. Some viruses carry genes that directly cause cancers, other viruses produce proteins that induce a loss of growth regulation, leading to cancer d. Some retroviruses viral oncogenes incorporate into host cell DNA and produce proteins that lead to uncontrolled cell growth, other retroviruses viral genes affect expression of host oncogene leading to uncontrolled cell growth e. DNA tumor viruses viral genes directly produce proteins that lead to uncontrolled cell growth f. Transformed cells demonstrate i. Increased rate of growth ii. Changes in their chromosomes iii. Changes in cell surface molecules iv. Capacity to divide indefinitely g. Examples of mammalian oncoviruses capable of initiating tumors i. Papillomaviruses: cervical cancer ii. Herpesviruses: Burkitt's lymphoma 19  CHAPTER 5 LECTURE NOTES iii. Hepatitis B virus: liver cancer iv. HTLV-1: leukemia/lymphoma 7. Viruses infecting bacteria a. Bacteriophage: virus that infects bacteria i. Most contain double-stranded DNA, some contain RNA ii. Each bacterial species is parasitized by various specific bacteriophages iii. May cause the bacteria they infect to become more pathogenic to humans iv. Virophage: recently discovered, virus that parasitizes other larger viruses that are also within a host cell v. T-Even Bacteriophage 1. Infect Escherichia coli 2. Structure: icosahedral capsid containing DNA, central tube surrounded by a sheath, collar, base plate, tail pins, and fibers b. Temperate phage: undergo adsorption and penetration, the viral genome will either continue with the lytic cycle or become a prophage in the lysogenic cycle, do not undergo replication or release immediately i. Lytic cycle: adsorption → penetration/genetic material injected into cell → duplication of phage components and replication of virus genetic material → assembly of new virus → maturation → lysis of weakened cell → release of viruses ii. Lysogenic cycle: Viral DNA enters an inactive prophage state that is inserted into the bacterial chromosome and copied during bacterial cell division 1. Lysogeny: a condition in which the host chromosome carries bacteriophage DNA 2. Induction: prophage in a lysogenic cell becomes activated and progresses directly into lytic cycle/viral replication 3. Lysogenic conversion: when a bacterium acquires new genes/traits from its temperate phage, causing toxin and enzyme production the bacterium would not otherwise be able to carry out a. Corynebacterium diphtheriae: diphtheria toxin b. Vibrio cholerae: cholera toxin c. Clostridium botulinum: botulinum toxin 20  CHAPTER 5 LECTURE NOTES 8. Detection of viral growth in cell/tissue culture (in vitro) a. Cells/tissue cultures are cultivated in sterile chambers with special media that contains nutrients for the cells to survive, cells form a monolayer that supports viral multiplication, allows for close inspection of culture for signs of infection b. Viral growth can be detected by observing degeneration and lysis of infected cells i. Plaques: where virus-infected cells have been destroyed, clear well-defined patches in the cell sheet of tissue culture, visible manifestation of CPEs 9. Detection/counting of bacteriophages a. Plaques: where virus-infected cells have been destroyed and released viruses radiate to adjacent host cells, clear macroscopic space that corresponds to area of dead cells 10. Prions a. Misfolded proteins, no nucleic acid b. Deposited as long protein fibrils in the brain tissue of humans and animals c. Creutzfeldt-Jakob disease (CJD): affects CNS, causes degeneration and death i. Genetic mutation ii. Sporadic CJD iii. Acquired CJD (medical instruments, organ transplants, consuming infected meat) d. Bovine spongiform encephalopathy (BSE): "mad cow disease," these prions can be transmitted to humans 11. Satellite viruses: dependent on other viruses for replication a. Adeno-associated virus (AAV): originally thought it could only replicate in cells infected with adenovirus, but can also infect cells that are infected with other viruses b. Delta agent: naked circle of RNA, expressed only in presence of hepatitis B virus, worsens the severity of liver damage 12. Viroids: virus-like agents that parasitize plants a. Smaller size than average virus b. Naked strands of RNA, lack a capsid or other coating c. Significant pathogens in economically important plants such as tomatoes, cucumbers and potatoes 13. Treatment of animal viral infections a. Antibiotics designed to treat bacterial infections have no effect on viruses b. Difficult to find drugs that will affect viruses without damaging host cells c. Almost all licensed antiviral drugs target a step of the viral life cycle i. Integrase inhibitor class of HIV drugs: interrupts the ability of HIV genetic information to incorporate into the host cell DNA ii. Paxlovid for COVID-19: inhibits a packaging enzyme d. Easier to develop vaccines to prevent viral diseases 21