Chapter 19
Chapter 19: Viruses
Learning Objectives
Characteristics of Viruses
A virus is an infectious particle consisting of genes packaged in a protein coat.
Structure Challenge: Viruses are much simpler in structure than prokaryotic cells.
Metabolic Limitations: Viruses cannot reproduce or carry out metabolism outside of a host cell, placing them in a category that straddles life-forms and chemicals, often referred to as "borrowed life".
COVID-19 Inquiry: Discussion on the origins of the COVID-19 virus.
Concept 19.1: Structure of Viruses
Composition: A virus consists of a nucleic acid surrounded by a protein coat.
Historical Context: Viruses were detected indirectly long before they were actually seen.
First Discovery: The Tobacco mosaic disease (TMV), which stunts growth and causes a mosaic coloration in tobacco plants, was one of the first indications of viral infection.
Early Hypotheses: In the late 1800s, the assumption was that unusually small bacteria were responsible for TMV. Later studies revealed that the infectious agent lacked bacterial characteristics (e.g., inability to grow on nutrient media).
Wendell Stanley's Confirmation (1935): Confirmed TMV as an infectious particle by crystallization.
Structural Components of Viruses
Non-Cellular Nature: Viruses are not cells and technically not alive.
Nucleic Acid Types: Viral genomes may consist of either double-stranded or single-stranded DNA, or double-stranded or single-stranded RNA.
Classification: Viruses are classified as DNA viruses or RNA viruses based on their genetic material.
Genome Structure: The viral genome can be a single linear or circular molecule of nucleic acid and contains between 3 to 2,000 genes.
Capsids and Envelopes
Capsid Definition: A capsid is the protein shell surrounding the viral genome.
Building Blocks: Capsids are constructed from protein subunits called capsomeres.
Structural Variability: Capsids can take on various structures referred to as either helical or icosahedral viruses.
Accessory Structures
Some viruses possess accessory structures aiding in host infection.
Viral Envelopes: Derived from host cell membranes, these envelopes surround capsids and contain both viral and host cell molecules.
Bacteriophages (Phages): Viruses that infect bacteria possess an elongated capsid head enclosing their DNA, along with a protein tail piece that attaches to hosts and injects viral DNA.
Concept 19.2: Viral Replication in Host Cells
Obligate Intracellular Parasites: Viruses can only replicate within a host cell.
Host Range: Each virus has a host range, meaning a limited number of host cells it can infect.
Cross-Species Transmission (CST): This is a rare phenomenon where viruses jump from one species to another.
Entry Process: Viral genomes enter host cells in various ways, initiating the host to manufacture viral proteins.
Host Utilization: Viruses utilize host supplies including enzymes, ribosomes, tRNAs, amino acids, ATP, and other molecules to facilitate replication.
Self-Assembly: Following manufacture, viral nucleic acids and capsomeres self-assemble into new viral particles.
Replicative Cycles of Phages
Understanding Phages: The best-understood viruses, phages have two reproductive mechanisms:
Lytic Cycle: Culminates in the death of the host cell and induces lysis to release new phages.
Lysogenic Cycle: Replicates the phage genome without killing the host. The viral DNA integrates into the host chromosome, known as prophage. Host cell division copies the integrated DNA, passing it to daughter cells. Environmental triggers can switch the virus back to lytic mode.
Bacterial Defenses Against Phages
Defense Mechanisms: Bacteria employ defenses against phages, favoring mutants with surface proteins that phages cannot recognize.
Restriction Enzymes (RE): Bacteria utilize restriction enzymes that cleave foreign DNA at specific sequences.
Example: The restriction enzyme AhaIII cuts at 5’-TTT▼AAA-3’. The symbol '▼' indicates the cut location.
Protection Mechanisms: Bacterial DNA is protected as it is methylated to prevent restriction enzyme activity.
Restriction Enzymes and Recognition Sequences
Function of RE: Restriction enzymes act as molecular scissors that cut double-stranded DNA at specified sequences.
Palindrome Recognition: They recognize palindromic sequences, such as "Madam, I’m Adam", indicating that the sequence reads the same forward and backward.
Clarification on Palindromes: Not all DNA sequences are palindromic; a distinction exists between complementary and palindromic sequences.
Examples of Recognition Sequences
Alul: Cuts at 5'-AG▼CT-3'.
Tagl: Cuts at 5'-T▼CGA-3'.
Hpal: Cuts at 5'-GTT AAC-3'.
EcoRI: Cuts at 5’–ATT▼AAT–3’.
Replicative Cycles of Animal Viruses
Classification Variables: Two key variables classify animal viruses:
Type of genome (RNA or DNA, single-stranded or double-stranded).
Presence of a membranous envelope.
Many animal viruses possess both envelopes and RNA genomes.
Viral Envelopes: Often derived from the host cell’s plasma membrane as capsids exit; some utilize the nuclear envelope or Golgi apparatus membrane.
Viral Genetic Material
Diversity in Animal Viruses: The broadest variety of RNA genomes is found in viruses that infect animals.
Retroviruses: Utilize reverse transcriptase to convert their RNA genome into DNA. HIV (human immunodeficiency virus) is a notable retrovirus that causes AIDS. The integrated viral DNA within the host is termed a provirus, which differs from a prophage as it remains a permanent resident of the cell.
Classes of Animal Viruses
Class I: Double-Stranded DNA (dsDNA)
Examples: Adenovirus (No), Papillomavirus (No), Polyomavirus (No), Herpesvirus (Yes), Poxvirus (Yes).
Class II: Single-Stranded DNA (ssDNA)
Example: Parvovirus (No).
Class III: Double-Stranded RNA (dsRNA)
Example: Reovirus (No).
Class IV: Single-Stranded RNA (ssRNA); Serves as mRNA
Examples: Picornavirus (No), Coronavirus (Yes), Flavivirus (Yes), Togavirus (Yes).
Class V: ssRNA; Serves as Template for mRNA Synthesis
Example: Ebola virus (Yes).
Evolution of Viruses
Evolutionary Perspective: Viruses do not fit traditional definitions of living organisms due to their reliance on host cells for replication.
Origins Theory: Many theorize they evolved as fragments of cellular nucleic acid, with candidates for their genomes including plasmids and transposons.
Viral Size: The largest known virus, Megavirus chilensis, has a 1.3 MB dsDNA genome and a capsid size of 440nm.
Evolution Debate: Ongoing debate exists regarding whether viruses evolved before or after cells.
Concept 19.3: Pathogen Presence in Animals and Plants
Impact of Viruses: Viruses are significant pathogens affecting human health, agriculture, and livestock.
Prions: Smaller infectious proteins causing diseases in plants and animals such as mad cow disease and Creutzfeldt-Jakob disease.
Mechanisms of Damage: Viruses may cause damage by releasing hydrolytic enzymes from lysosomes, inducing infected cells to produce toxins, or via toxic envelope proteins.
Vaccines and Treatment Strategies
Vaccine Definition: Harmless derivatives of pathogens that trigger the immune response against disease-causing microbes.
Flu Vaccine Misnomer: It is incorrect to claim flu shots cause flu; they do not induce the disease.
Efficacy of Vaccines: Vaccines, such as flu vaccines, are not 100% effective but significantly reduce risks.
Antiviral Treatments: Work by inhibiting viral DNA synthesis and assembly rather than curing infections. Example includes Valacyclovir for cold sores.
Vaccines and Autism: No scientific connection between vaccines and autism has been established.
Emerging Viruses
Definition: Emerging viruses are those that become newly apparent in populations.
Examples: Ebola virus, chikungunya virus, and the Zika virus (discovered in 2015).
Infectious Disease Transmission Terms
Epidemic: A widespread occurrence of an infectious disease at a specific time in a community (e.g., H1N1 outbreak in 2009).
Pandemic: Global epidemic (e.g., Black Death, Spanish flu, and HIV/AIDS).
Endemic: A disease present continuously in a specific region, such as malaria in Africa.
Sporadic: Isolated cases that occur infrequently, such as tetanus and typhoid fever in the U.S.
Viral Disease Mechanisms in Plants
More than 2,000 plant viral diseases have been identified, contributing to issues like leaf spots, stunted growth, and damaged flowers.
Viral Spread Routes:
Vertical Transmission: Inheriting the virus from a parent.
Horizontal Transmission: Virus entering through damaged cell walls.
Prions: Proteins as Infectious Agents
Prion Definition: Infectious proteins leading to degenerative diseases such as scrapie in sheep, mad cow disease, and Creutzfeldt-Jakob disease in humans.
Prion Mechanism: Misfolded prions induce normal proteins to adopt an abnormal structure, creating aggregates that harm cellular function.
Potential Implications: Prions may also play a role in other neurodegenerative diseases like Alzheimer’s and Parkinson’s disease.