Characterizing and Classifying Viruses, Viroids, and Prions

Characteristics of Viruses Minuscule, acellular infectious agent having either DNA or RNA Causes many infections of humans, animals, plants, and bacteria Causes most of the diseases that plague the industrialized world 2

Characteristics of Viruses Cannot carry out any metabolic pathway Neither grow nor respond to the environment Cannot reproduce independently Recruit the cell’s metabolic pathways to increase their numbers No cytoplasmic membrane, cytosol, organelles (with one exception) Have extracellular and intracellular state 3

Characteristics of Viruses Extracellular State Called virion Protein coat (capsid) surrounding nucleic acid Nucleic acid and capsid also called nucleocapsid Some have phospholipid envelope Outermost layer provides protection and recognition sites for host cells Intracellular State Capsid removed Virus exists as nucleic acid 4

Figure 13.1 Virions-overview

Characteristics of Viruses Learning objective: Discuss viral genomes in terms of dsDNA, ssDNA, ssRNA, dsRNA, and number of segments of nucleic acid. Genetic Material of Viruses Show more variety in nature of their genomes than do cells Primary way scientists categorize and classify viruses May be DNA or RNA, but never both dsDNA, ssDNA, dsRNA, ssRNA Linear and segmented or single and circular Much smaller than genomes of cells 6

Figure 13.2 The relative sizes of genomes Partial genome of E. coli Viral genome

Characteristics of Viruses Learning objective: Explain how viruses are specific for their hot cells. Compare and contrast viruses of fungi, plants, animals, and bacteria. Hosts of Viruses Most viruses infect only particular host’s cells Affinity of viral surface proteins for proteins on host cell May be so specific they infect only particular kind of cell in a particular host Generalists – infect many kinds of cells in many different hosts 8

Figure 13.3 Hosts of viral infections-overview

Figure 13.4 Sizes of selected virions E. coli (bacterium) (1000 nm  3000 nm) Red blood cell (10,000 nm in diameter) Bacterial ribosomes (25 nm) Smallpox virus (200 nm  300 nm) Poliovirus (30 nm) Bacteriophage T4 (50 nm  225 nm) Bacteriophage MS2 (24 nm) Tobacco mosaic virus (15 nm  300 nm)

Characteristics of Viruses Learning objective: Discuss the structure and function of the function of the viral capsid. Capsid Morphology Capsids Provide protection for viral nucleic acid Means of attachment to host’s cells Composed of proteinaceous subunits called capsomeres Capsomere made of single or multiple types of proteins 11

Characteristics of Viruses Learning objective: List the characteristics by which viruses are classified. Viral Shapes Three basic shapes Helical Polyhedral Complex 12

Figure 13.5 The shapes of virions-overview

Figure 13.6 Bacteriophage T4-overview

Characteristics of Viruses The Viral Envelope Acquired from host cell during viral replication or release Envelope is portion of membrane system of host Composed of phospholipid bilayer and proteins Some proteins are virally coded glycoproteins (spikes) Envelope’s proteins and glycoproteins often play role in host recognition 15

Figure 13.7 Enveloped virion-overview

Table 13.2 Families of Human Viruses

Dependent on hosts’ organelles and enzymes to produce new virions Viral Replication Learning objective: Sketch and describe the five stages of the lytic replication cycle as it typically occurs in bacteriophages. Dependent on hosts’ organelles and enzymes to produce new virions Lytic replication Replication cycle usually results in death and lysis of host cell Stages of lytic replication cycle Attachment Entry Synthesis Assembly Release 18

Figure 13.8 The lytic replication cycle in bacteriophages-overview Attachment Bacteriophage genome Entry Tail sheath Outer membrane Peptidoglycan Cytoplasmic membrane Bacterial chromosome Entry Attachment Phage DNA Lytic replication cycle of bacteriophage Bacterial chromosome degraded Release Synthesis Phage proteins Assembly Assembly Base Tail Sheath DNA Capsid Mature head Tail fibers Mature virion

Figure 13.9 Pattern of virion abundance in lytic cycle Burst size Number of infective virions in medium (log scale) Release of virions by lysis Entry Synthesis and assembly Time (minutes) Attachment Burst time

Viral Replication Lysogeny Modified replication cycle Learning objective: Compare and contrast the glycogenic replication cycle of viruses with the lytic cycle and with latency. Lysogeny Modified replication cycle Infected host cells grow and reproduce normally for generations before they lyse Temperate phages Prophages – inactive phages Lysogenic conversion results when phages carry genes that alter phenotype of a bacterium 21

Figure 13.10 Bacteriophage lambda

Figure 13.11 The lysogenic replication cycle in bacteriophages: phage lambda and E. coli Attachment Entry Prophage in chromosome Lambda phage Lytic cycle Lysogeny Synthesis Release Replication of chromosome and virus; cell division Assembly Induction Further replications and cell divisions

Replication of Animal Viruses Viral Replication Learning objective: Explain the differences between bacteriophage replication and animal viral replication. Compare and contrast the replication and synthesis of DNA,-RNA,+RNA viruses. Compare and contrast the release of viral particles by lysis and budding. Replication of Animal Viruses Same basic replication pathway as bacteriophages Differences result from Presence of envelope around some viruses Eukaryotic nature of animal cells Lack of cell wall in animal cells 24

Replication of Animal Viruses Viral Replication Replication of Animal Viruses Attachment of animal viruses Chemical attraction Animal viruses do not have tails or tail fibers Have glycoprotein spikes or other attachment molecules that mediate attachment 25

Figure 13.12 Three mechanisms of entry of animal viruses-overview

Replication of Animal Viruses Viral Replication Replication of Animal Viruses Synthesis of animal viruses Requires different strategy depending on its nucleic acid DNA viruses often enter the nucleus RNA viruses often replicate in the cytoplasm Must consider How mRNA is synthesized What serves as template for nucleic acid replication 27

Figure 13.13 Synthesis of proteins and genomes in animal RNA viruses-overview

Replication of Animal Viruses Viral Replication Replication of Animal Viruses Assembly and release of animal viruses Most DNA viruses assemble in nucleus Most RNA viruses develop solely in cytoplasm Number of viruses produced depends on type of virus and size and initial health of host cell Enveloped viruses cause persistent infections Naked viruses are released by exocytosis or lysis 29

Figure 13.14 The process of budding in enveloped viruses Enveloped virion Budding of enveloped virus Viral glycoproteins Cytoplasmic membrane of host Viral capsid

Figure 13.15 Pattern of virion abundance in persistent infections Number of infective virions in medium Synthesis and assembly Release of virions Entry Time Attachment

Replication of Animal Viruses Viral Replication Replication of Animal Viruses Latency of animal viruses When animal viruses remain dormant in host cells May be prolonged for years with no viral activity Some latent viruses do not become incorporated into host chromosome Incorporation of provirus into host DNA is permanent 32

The Role of Viruses in Cancer Learning objective: Define the terms neoplasia , tumor, malignant ,cancer, and metastasis. Explain in simple terms how a cell may become cancerous, with special reference to the role of viruses. Animal’s genes dictate that some cells can no longer divide or are prevented from unlimited division Genes for cell division “turned off” or genes inhibiting division “turned on” Neoplasia Uncontrolled cell division in multicellular animal Mass of neoplastic cells is tumor Benign vs. malignant tumors Metastasis Cancers 33

Figure 13.16 The oncogene theory of the induction of cancer in humans Normal state: DNA Protooncogene Gene for repressor Represses mRNA Repressor Result: No cancer First “hit”: Virus inserts promoter DNA Oncogene Gene for repressor Represses mRNA Repressor Result: Still no cancer Second “hit”: Virus inserts into represssor gene DNA Oncogene No repressor protein because gene is segmented mRNA Protein Causes cell division Result: Cancer

The Role of Viruses in Cancer Environmental factors that contribute to the activation of oncogenes Ultraviolet light Radiation Carcinogens Viruses 35

The Role of Viruses in Cancer Viruses cause 20–25% of human cancers Some carry copies of oncogenes as part of their genomes Some promote oncogenes already present in host Some interfere with tumor repression Specific viruses are known to cause ~15% of human cancers Burkitt’s lymphoma Hodgkin’s disease Kaposi’s sarcoma Cervical cancer 36

Culturing Viruses in the Laboratory Learning objective: Describe some ethical and practical difficulties to overcome in culturing viruses. Describe three types of media used for culturing viruses. Culturing Viruses in Mature Organisms In bacteria In plants and animals Culturing Viruses in Embryonated Chicken Eggs Inexpensive, among the largest of cells, free of contaminating microbes, and contain a nourishing yolk Culturing Viruses in Cell (Tissue) Culture 37

Bacterial lawn Viral plaques Figure 13.17 Viral plaques in a lawn of bacterial growth on the surface of an agar plate Bacterial lawn Viral plaques

Injection into chorioallantoic membrane Figure 13.18 Inoculation sites for the culture of viruses in embryonated chicken eggs Air sac Injection into chorioallantoic membrane Injection into chorioallantois Injection into embryo Injection into amnion Injection into yolk sac

Culturing Viruses in the Laboratory Learning objective: Compare and contrast diploid cell culture and continuous cell culture. Culturing Viruses in Cell (Tissue) Culture Consists of cells isolated from an organism and grown on a medium or in a broth Two types of cell cultures Diploid cell cultures Continuous cell cultures 40

Figure 13.19 An example of cell culture

Some consider them complex pathogenic chemicals Are Viruses Alive? Some consider them complex pathogenic chemicals Others consider them the least complex living entities Use sophisticated methods to invade cells Have the ability to take control of their host cell Are able to replicate themselves 42

Other Parasitic Particles: Viroids and Prions Learning objective: Define and describe viroids. Compare and contrast viroids and viruses. Characteristics of Viroids Extremely small, circular pieces of RNA that are infectious and pathogenic in plants Similar to RNA viruses, but lack capsid May appear linear due to H bonding 43

Genome of bacteriophage T7 PSTV Figure 13.20 The RNA strand of the small potato spindle tuber viriod (PSTV) Genome of bacteriophage T7 PSTV

Figure 13.21 One effect of viroids on plants

Other Parasitic Particles: Viroids and Prions Learning objective: Define and describe prions, including their replication process. Compare and contrast prions and viruses. List four diseases caused by prions. Characteristics of Prions Proteinaceous infectious agents Cellular PrP protein Made by all mammals Normal structure with -helices called cellular PrP Prion PrP Disease-causing form with -pleated sheets called prion PrP Prion PrP changes shape of cellular PrP so it becomes prion PrP 46

Figure 13.22 The two stable, three-dimensional forms of prion protein (PrP)-overview

Other Parasitic Particles: Viroids and Prions Characteristics of Prions Normally, nearby proteins and polysaccharides force PrP into cellular shape PrP mutations result in formation of prion Pr 48

Other Parasitic Particles: Viroids and Prions Characteristics of Prions Prion diseases Fatal neurological degeneration, fibril deposits in brain, and loss of brain matter Large vacuoles form in brain Characteristic spongy appearance Spongiform encephalopathies Prions only destroyed by incineration or autoclaving in 1 N NaOH 49

Figure 13.23 The brain of a sheep with the prion disease called scrapie Vacuole