Lecture_11_and_12_Viruses___Eukaryotes__-__UPDATED

Learning Objectives

• Viruses & Eukaryotes

  • Describe and identify various virus forms, including symmetry types.

  • Describe methods for virus quantification.

  • List the steps of viral replication.

  • Describe and list the steps of the full viral life cycle (temperate, lytic, lysogenic).

  • List the possible consequences of viral infection in animal cells.

  • Describe and identify retroviruses, compare/contrast with typical viruses.

  • Define and describe structure of prions; describe epidemiology, examples of prion diseases, symptoms.

  • List cellular processes in mitochondrion, hydrogenosome, and chloroplast.

  • Identify key features of representative Eukaryote species.

  • Describe the epidemiology of flu and malaria; including transmission, internal pathways, and symptoms.

  • List key enzymes in viral and Eukaryotic processes, know their "job".

  • Identify phages; list life cycle steps and adaptations of bacteriophage T4.

  • Describe CRISPR technology.

  • Define positive and negative-strand RNA viruses.

  • Define terms like concatemer, terminal redundancy, circular permutation.

  • Describe slime molds; define quorum sensing.

General Properties of Viruses

• Virus: Genetic element that cannot replicate independently of a living (host) cell.

• Virus particle: Extracellular form that allows a virus to exist outside a host and facilitates transmission.

• Virion: Infectious virus particle consisting of the nucleic acid genome surrounded by a protein coat, with possible additional layers.

Viral Genomes

• Types of Viral Genomes: DNA or RNA genomes.

  • Typical classifications:

    • ssDNA: Some circular; most linear.

    • dsDNA: Double-stranded DNA viruses.

    • SSRNA: Single-stranded RNA viruses; includes retroviruses that reverse transcribe RNA into DNA.

    • dsRNA: Double-stranded RNA viruses.

Viral Classification

• Viruses can be grouped based on the hosts they infect.

• Taxonomy: Broadly classified based on genomic characteristics. Most viruses are smaller than prokaryotic cells (0.02 to 0.3 µm). Viral genomes are generally smaller than those of biological cells.

Structure of Viruses

• Capsid: Protein shell that surrounds the virus genome.

• Capsomer: Subunit of the capsid.

• Nucleocapsid: Complete complex of nucleic acid and protein packaged in the virion.

• Enveloped virus: Virus containing additional layers around the nucleocapsid, derived from the infected host cell’s membrane with embedded glycoproteins.

Nature of the Virion

• Symmetry of Nucleocapsids:

  • Helical symmetry: Rod-shaped viruses (e.g., tobacco mosaic virus).

  • Icosahedral symmetry: Spherical viruses with efficient arrangements of subunits in a closed shell.

Enveloped Viruses

• Membrane surrounding nucleocapsid; lipid bilayer with embedded proteins made by host cell machinery.

Complex Viruses

• Composed of several parts, each with separate shapes and symmetries; often seen in bacterial viruses with icosahedral heads and helical tails.

Essential Enzymes in Viruses

• Some virions contain enzymes crucial for infection:

  • Lysozyme: Helps breach host cell walls.

  • Nucleic acid polymerases (reverse transcriptase): Essential for replicating the viral genome.

  • Neuraminidases: Allow liberation of viruses from host cells by cleaving glycosidic bonds.

Quantification of Viruses

• Titer: Number of infectious units per volume of fluid.

• Plaque assay: Accurate method to measure virus infectivity by observing clear zones (plaques) on lawns of host cells resulting from viral infection.

General Features of Virus Replication

• Phases of Viral Replication:

  1. Attachment (adsorption) of the virus to host cell.

  2. Entry (penetration) of the virion.

  3. Synthesis of virus nucleic acid and proteins directed by the host cell.

  4. Assembly of capsids and packaging of viral genomes.

  5. Release of new virions via lysis.

Viral Life Cycle Overview

• Distinct phases of replication characterized by a one-step growth curve leading to cell lysis.

  • Key terms include eclipse (genome replication), maturation (packaging), and latent period (where detectable viral production ceases).

Viral Attachment and Penetration Mechanisms

• Attachment is highly specific; requires complementary receptors on the host cell. Bacteriophage T4 is a notable complex example that uses tail fibers to attach and penetrate E. coli cells.

Viral Defenses

• Eukaryotic organisms have mechanisms to diminish viral infections (e.g., immune responses, RNA interference). Bacteria utilize restriction-modification systems and CRISPR technology as defenses against viral infection.

Baltimore Classification of Viruses

• Viruses are classified based on genome type and replication strategies (e.g., dsDNA, ssRNA, etc.).

  • Examples include: Bacterial viruses (Lambda, T4), Animal viruses (Poliovirus, Influenza virus).

Retroviruses

• RNA viruses that replicate via a DNA intermediate and contain critical proteins such as reverse transcriptase and integrase. Their life cycle includes reverse transcription and integration into the host genome.

Prions

• Infectious proteins that cause transmissible spongiform encephalopathies in animals; misfolding of the prion protein leads to severe neurological symptoms.

• Mechanisms of prion disease include infectious, sporadic, and inherited forms.

Learning Objectives

Viruses & Eukaryotes

• Describe and identify various virus forms, including symmetry types such as helical, icosahedral, and complex structures that adapt for specific hosts.

• Describe methods for virus quantification, including techniques like plaque assays, tissue culture techniques, and qPCR to ascertain viral load and infectivity.

• List the steps of viral replication, detailing the phases: attachment, entry, synthesis, assembly, and release of new virions.

• Describe and list the steps of the full viral life cycle which includes both temperate (lysogenic and lytic) and lytic cycles across different environments and host interactions.

• List the possible consequences of viral infection in animal cells, including cytopathic effects, immune response evasion, and potential transformation leading to oncogenesis.

• Describe and identify retroviruses, such as HIV, comparing and contrasting with typical viruses regarding their unique replication strategies involving reverse transcription into DNA.

• Define and describe the structure of prions including their protein misfolding characteristics; describe epidemiology, symptoms, and examples of prion diseases like Creutzfeldt-Jakob Disease and Mad Cow Disease.

• List cellular processes in mitochondria, hydrogenosomes, and chloroplasts; detail their roles in ATP production, metabolic pathways, and unique features relevant to their organisms.

• Identify key features of representative Eukaryote species, emphasizing the biological diversity within eukaryotes such as plants, animals, fungi, and protists.

• Describe the epidemiology of flu and malaria; include transmission methods (vector-borne, airborne), internal pathways (tissue targeting), and the range of symptoms experienced by infected individuals.

• List key enzymes in viral and eukaryotic processes, knowing their specific functions in replication, metabolism, and biosynthesis, such as DNA/RNA polymerases and proteases.

• Identify phages with a focus on bacteriophage T4; list life cycle steps, adaptations for infection, and their ecological impact on bacterial populations.

• Describe CRISPR technology; outline its mechanism as a bacterial immunity system and its applications in genetic engineering and medicine.

• Define positive and negative-strand RNA viruses, exploring their replication strategies, structural differences, and implications for disease.

• Define terms like concatemer, terminal redundancy, circular permutation, offering explanations and examples relevant to viral genome structure.

• Describe slime molds and their characteristics, define quorum sensing and its role in behavior modulation within microbial communities.

General Properties of Viruses

• Virus: Genetic element that cannot replicate independently of a living (host) cell, requiring a host machinery to reproduce and express its genetic material.

• Virus particle: An extracellular form that allows a virus to exist outside a host and facilitates transmission to new hosts, providing an inert state relevant for survival.

• Virion: An infectious virus particle consisting of the nucleic acid genome surrounded by a protein coat, with possible additional layers (envelope) critical for infection and host recognition.

Viral Genomes

• Types of Viral Genomes: DNA or RNA genomes organized into various structures.

• Typical classifications:

  • ssDNA: Includes some circular forms; most are linear, faced with the challenge of replication.

  • dsDNA: Double-stranded DNA viruses, often exhibiting complex regulatory mechanisms.

  • SSRNA: Single-stranded RNA viruses, subdivided into positive-sense and negative-sense, including retroviruses that reverse transcribe RNA into DNA for integration into host genomes.

  • dsRNA: Double-stranded RNA viruses, often present in plant and animal pathogens.

Viral Classification

• Viruses can be grouped based on the hosts they infect; classifications include bacteriophages, plant viruses, and animal viruses.

• Taxonomy: Broadly classified based on genomic characteristics, revealing insights into evolutionary relationships; most viruses are significantly smaller than prokaryotic cells (0.02 to 0.3 µm).

Structure of Viruses

• Capsid: The protein shell that surrounds the virus genome, providing structural integrity and protection.

• Capsomer: Subunit of the capsid, arranged in precise patterns that determine the capsid's overall symmetry.

• Nucleocapsid: The complete complex of nucleic acid and protein packaged in the virion, critical for infection.

• Enveloped virus: Viruses that possess additional layers around the nucleocapsid, derived from the infected host cell’s membrane featuring embedded glycoproteins essential for host recognition and attachment.

Nature of the Virion

• Symmetry of Nucleocapsids:

  • Helical symmetry: Found in rod-shaped viruses like the tobacco mosaic virus.

  • Icosahedral symmetry: Common in spherical viruses, exhibiting efficient arrangements that minimize genetic material while maximizing structural stability.

Enveloped Viruses

• Membrane surrounding nucleocapsid; composed of lipid bilayer from the host cell’s membrane containing proteins essential for entry into new cells.

Complex Viruses

• Composed of multiple distinct parts, each with separate shapes and symmetries; often seen in bacteriophages demonstrating elaborate adaptations to infect specific bacterial hosts.

Essential Enzymes in Viruses

• Some virions contain enzymes crucial for infection such as:

  • Lysozyme: Facilitates breaching of bacterial cell walls enabling entry.

  • Nucleic acid polymerases (including reverse transcriptase): Essential for replicating the viral genome or converting RNA into DNA.

  • Neuraminidases: Enzymes that enable liberation of new virions from host cells by cleaving glycosidic bonds, aiding in the spread of infection.

Quantification of Viruses

• Titer: Represents the number of infectious units per volume of fluid, a critical measurement for virology studies.

• Plaque assay: An effective method to measure virus infectivity, whereby clear zones (plaques) are observed on lawns of host cells resulting from viral infection.

General Features of Virus Replication

• Phases of Viral Replication:

  1. Attachment (adsorption) to the host cell surface through specific receptor interactions.

  2. Entry (penetration) of the virion into the host cell.

  3. Synthesis of viral nucleic acid and proteins, directed by the host cellular machinery.

  4. Assembly of capsids and packaging of viral genomes into new virions.

  5. Release of new virions from the host cell via lysis or budding.

Viral Life Cycle Overview

• Involves distinct phases of replication characterized by a one-step growth curve leading to cell lysis; critical terms include:

  • Eclipse phase: Period of genome replication and protein synthesis when the virus cannot be detected.

  • Maturation phase: The process of packaging completed virions before release.

  • Latent period: Time frame during which detectable viral production is absent despite ongoing replication processes.

Viral Attachment and Penetration Mechanisms

• Attachment to host cells is highly specific, requiring complementary receptors on the cell surface; bacteriophage T4 provides a notable complex example that utilizes tail fibers to adhere to and penetrate E. coli cells.

Viral Defenses

• Eukaryotic organisms utilize various mechanisms, including immune responses and RNA interference, to mitigate viral infections. Bacteria utilize restriction-modification systems and CRISPR technology as sophisticated defenses against viral invaders.

Baltimore Classification of Viruses

• Classifies viruses based on genome type (DNA or RNA) and replication strategies, categorizing them into seven groups (e.g., dsDNA, ssRNA). Examples include bacterial viruses like Lambda and T4, as well as animal viruses like Poliovirus and Influenza virus.

Retroviruses

• RNA viruses that replicate through a DNA intermediate, containing vital proteins such as reverse transcriptase and integrase. Their life cycle involves reverse transcription of RNA into DNA, which is subsequently integrated into the host genome, affecting cellular functions and often leading to chronic infections.

Prions

• Infectious proteins responsible for transmissible spongiform encephalopathies in various animals; they induce misfolding of normal host proteins, leading to severe neurological symptoms such as ataxia and dementia in affected organisms. Mechanisms of prion disease encompass infectious, sporadic, and inherited forms, showcasing the unique challenges in treatment and prevention.

Learning Objectives

Viruses & Eukaryotes

• Describe and identify various virus forms, including symmetry types such as helical, icosahedral, and complex structures that adapt for specific hosts.

• Describe methods for virus quantification, including techniques like plaque assays, tissue culture techniques, and qPCR to ascertain viral load and infectivity.

• List the steps of viral replication, detailing the phases: attachment, entry, synthesis, assembly, and release of new virions.

• Describe and list the steps of the full viral life cycle which includes both temperate (lysogenic and lytic) and lytic cycles across different environments and host interactions.

• List the possible consequences of viral infection in animal cells, including cytopathic effects, immune response evasion, and potential transformation leading to oncogenesis.

• Describe and identify retroviruses, such as HIV, comparing and contrasting with typical viruses regarding their unique replication strategies involving reverse transcription into DNA.

• Define and describe the structure of prions including their protein misfolding characteristics; describe epidemiology, symptoms, and examples of prion diseases like Creutzfeldt-Jakob Disease and Mad Cow Disease.

• List cellular processes in mitochondria, hydrogenosomes, and chloroplasts; detail their roles in ATP production, metabolic pathways, and unique features relevant to their organisms.

• Identify key features of representative Eukaryote species, emphasizing the biological diversity within eukaryotes such as plants, animals, fungi, and protists.

• Describe the epidemiology of flu and malaria; include transmission methods (vector-borne, airborne), internal pathways (tissue targeting), and the range of symptoms experienced by infected individuals.

• List key enzymes in viral and eukaryotic processes, knowing their specific functions in replication, metabolism, and biosynthesis, such as DNA/RNA polymerases and proteases.

• Identify phages with a focus on bacteriophage T4; list life cycle steps, adaptations for infection, and their ecological impact on bacterial populations.

• Describe CRISPR technology; outline its mechanism as a bacterial immunity system and its applications in genetic engineering and medicine.

• Define positive and negative-strand RNA viruses, exploring their replication strategies, structural differences, and implications for disease.

• Define terms like concatemer, terminal redundancy, circular permutation, offering explanations and examples relevant to viral genome structure.

• Describe slime molds and their characteristics, define quorum sensing and its role in behavior modulation within microbial communities.

General Properties of Viruses

• Virus: Genetic element that cannot replicate independently of a living (host) cell, requiring a host machinery to reproduce and express its genetic material.

• Virus particle: An extracellular form that allows a virus to exist outside a host and facilitates transmission to new hosts, providing an inert state relevant for survival.

• Virion: An infectious virus particle consisting of the nucleic acid genome surrounded by a protein coat, with possible additional layers (envelope) critical for infection and host recognition.

Viral Genomes

• Types of Viral Genomes: DNA or RNA genomes organized into various structures.

• Typical classifications:

  • ssDNA: Includes some circular forms; most are linear, faced with the challenge of replication.

  • dsDNA: Double-stranded DNA viruses, often exhibiting complex regulatory mechanisms.

  • SSRNA: Single-stranded RNA viruses, subdivided into positive-sense and negative-sense, including retroviruses that reverse transcribe RNA into DNA for integration into host genomes.

  • dsRNA: Double-stranded RNA viruses, often present in plant and animal pathogens.

Viral Classification

• Viruses can be grouped based on the hosts they infect; classifications include bacteriophages, plant viruses, and animal viruses.

• Taxonomy: Broadly classified based on genomic characteristics, revealing insights into evolutionary relationships; most viruses are significantly smaller than prokaryotic cells (0.02 to 0.3 µm).

Structure of Viruses

• Capsid: The protein shell that surrounds the virus genome, providing structural integrity and protection.

• Capsomer: Subunit of the capsid, arranged in precise patterns that determine the capsid's overall symmetry.

• Nucleocapsid: The complete complex of nucleic acid and protein packaged in the virion, critical for infection.

• Enveloped virus: Viruses that possess additional layers around the nucleocapsid, derived from the infected host cell’s membrane featuring embedded glycoproteins essential for host recognition and attachment.

Nature of the Virion

• Symmetry of Nucleocapsids:

  • Helical symmetry: Found in rod-shaped viruses like the tobacco mosaic virus.

  • Icosahedral symmetry: Common in spherical viruses, exhibiting efficient arrangements that minimize genetic material while maximizing structural stability.

Enveloped Viruses

• Membrane surrounding nucleocapsid; composed of lipid bilayer from the host cell’s membrane containing proteins essential for entry into new cells.

Complex Viruses

• Composed of multiple distinct parts, each with separate shapes and symmetries; often seen in bacteriophages demonstrating elaborate adaptations to infect specific bacterial hosts.

Essential Enzymes in Viruses

• Some virions contain enzymes crucial for infection such as:

  • Lysozyme: Facilitates breaching of bacterial cell walls enabling entry.

  • Nucleic acid polymerases (including reverse transcriptase): Essential for replicating the viral genome or converting RNA into DNA.

  • Neuraminidases: Enzymes that enable liberation of new virions from host cells by cleaving glycosidic bonds, aiding in the spread of infection.

Quantification of Viruses

• Titer: Represents the number of infectious units per volume of fluid, a critical measurement for virology studies.

• Plaque assay: An effective method to measure virus infectivity, whereby clear zones (plaques) are observed on lawns of host cells resulting from viral infection.

General Features of Virus Replication

• Phases of Viral Replication:

  1. Attachment (adsorption) to the host cell surface through specific receptor interactions.

  2. Entry (penetration) of the virion into the host cell.

  3. Synthesis of viral nucleic acid and proteins, directed by the host cellular machinery.

  4. Assembly of capsids and packaging of viral genomes into new virions.

  5. Release of new virions from the host cell via lysis or budding.

Viral Life Cycle Overview

• Involves distinct phases of replication characterized by a one-step growth curve leading to cell lysis; critical terms include:

  • Eclipse phase: Period of genome replication and protein synthesis when the virus cannot be detected.

  • Maturation phase: The process of packaging completed virions before release.

  • Latent period: Time frame during which detectable viral production is absent despite ongoing replication processes.

Viral Attachment and Penetration Mechanisms

• Attachment to host cells is highly specific, requiring complementary receptors on the cell surface; bacteriophage T4 provides a notable complex example that utilizes tail fibers to adhere to and penetrate E. coli cells.

Viral Defenses

• Eukaryotic organisms utilize various mechanisms, including immune responses and RNA interference, to mitigate viral infections. Bacteria utilize restriction-modification systems and CRISPR technology as sophisticated defenses against viral invaders.

Baltimore Classification of Viruses

• Classifies viruses based on genome type (DNA or RNA) and replication strategies, categorizing them into seven groups (e.g., dsDNA, ssRNA). Examples include bacterial viruses like Lambda and T4, as well as animal viruses like Poliovirus and Influenza virus.

Retroviruses

• RNA viruses that replicate through a DNA intermediate, containing vital proteins such as reverse transcriptase and integrase. Their life cycle involves reverse transcription of RNA into DNA, which is subsequently integrated into the host genome, affecting cellular functions and often leading to chronic infections.

Prions

• Infectious proteins responsible for transmissible spongiform encephalopathies in various animals; they induce misfolding of normal host proteins, leading to severe neurological symptoms such as ataxia and dementia in affected organisms. Mechanisms of prion disease encompass infectious, sporadic, and inherited forms, showcasing the unique challenges in treatment and prevention.