Comprehensive Study Guide on Virology and Bacteriology and Virology
Course Logistics and Upcoming Assessments
Second Prelab: Due upon entering the classroom this coming Thursday. Students must print this out beforehand.
First Lab Exam (Thursday): Covers three specific topics:
Viruses.
Classification.
Bacteria.
Preparation Advice: The instructor suggests studying thoroughly for this first exam as it contains the least amount of information compared to future units.
Bacteria is the longest topic within this unit.
The Protozoa and Fungi unit is described as having more information and being trickier.
The Animals unit exam will contain significantly more information.
Project One: The entire next session will be dedicated to working on Project One.
Introduction to Virology
Zika Virus Structure: Represented by a capsular model showing various molecules. It features carbohydrate protrusions on the exterior that act as identification markers for hosts. These markers allow the virus to mask itself and appear as if it belongs in the host's body, slipping past cellular defenses undetected.
Significance in Biology: Viral research is the foundation for much of our knowledge regarding gene function, DNA, and RNA.
The first DNA genome ever sequenced and decoded was a viral genome.
Viruses are ideal for research due to their small size, the relative ease of culturing them, and their small amount of DNA compared to other organisms.
Host Interactions:
Viruses infect all types of living things, including specific bacteria, fungi, and protists.
Humans constantly ingest and breathe in virus particles through food and water.
Most viruses do not interact with the human body; they simply degrade or pass through if the person is not the specific host for that virus.
Human Viral Genome: Scientists have discovered viral DNA sequences within human chromosomes that do not belong to human genetics. These were incorporated into the human genome over millennia of exposure.
Numerical Data and Prevalence:
There are approximately bacteriophage particles on Earth.
A study in the Caribbean found approximately (8 billion) virus particles in a single liter of coastal ocean sediment.
A study of coleslaw from New York restaurants found approximately (100 million) virus particles per serving. These come from "cabbage loopers" (caterpillars) that host the viruses and leave them on the cabbage via waste. These viruses only interact with the caterpillar host and are harmless to humans.
Defining Life: Viruses are categorized as non-living entities because they do not meet all seven biological processes of life. However, they possess DNA or RNA and can reproduce, though they require a host cell's machinery to do so.
History of Virology
1800s Context: Microbiology was centered on learning about cells through microscopy and chemistry.
Tobacco Mosaic Disease: Observed by tobacco farmers in Europe; the disease caused spots and wrinkling in a patch-like pattern on crops.
Dr. Adolf Mayer: Contracted to study the disease; he initially hypothesized it was bacterial.
Dmitry Ivanovsky: Tested the bacterial hypothesis using a specialized filter designed to trap bacteria. He filtered sap from infected plants and rubbed the filtrate on healthy plants. The healthy plants became infected, proving the agent was smaller than bacteria. He theorized it might be a bacterial toxin.
Martinus Beijerinck: A Dutch scientist who attempted to culture the agent. When he failed to grow it using standard bacterial media, he concluded it was a unique biological agent. He utilized the Latin word "virus," meaning poison, to describe it.
Wendell Stanley (1935): Working after the invention of the electron microscope, Stanley was the first to see the virus. He observed it as a protein-wrapped cylinder coiling around nucleic acid, identified as the Tobacco Mosaic Virus (TMV).
Viral Structure and Classification
Core Components: All viruses consist of at least nucleic acid surrounded by a protein coat called a capsid.
The protein building blocks of the capsid are called capsomeres.
Virion: The term for a single, complete virus particle (it is not called a cell).
Size Exceptions: While most are smaller than bacteria, some large viruses exist, such as the cytomegalovirus.
Enveloped Viruses: Possess an additional outer layer (envelope) derived from the host cell's plasma membrane. This assists in fusion with new host cells and evading detection.
Examples: HIV (causes AIDS), Herpes, Smallpox, Influenza, Rabies.
Naked Viruses: Viruses lacking an outer envelope.
Examples: Warts, Polio, Parvo, Hepatitis A.
Bacteriophages: Viruses that specifically infect bacteria (often called "phages"). The name comes from "phage" meaning to eat, because they create clear zones in bacterial cultures on agar plates where they have hijacked and destroyed bacterial cells.
Viral Life Cycles and Infection
Bacteriophage vs. Animal Virus Entry:
Bacteriophages land on a cell and inject only their nucleic acid.
Animal viruses typically enter the host cell entirely.
Vectors: Arthropods (insects like mosquitoes or ticks) that transmit viruses to new hosts.
Latency: A dormant period in animal viruses (e.g., Herpes) where the virus remains hidden until triggered by stress or immunocompromise.
Zoonotic Viruses: Viruses obtained from animal hosts that jump to humans (e.g., COVID-19).
Lytic Cycle:
Derived from "lyse," meaning to break apart.
The virus replicates quickly and bursts the host cell to escape.
Viruses that solely use this mode are called virulent.
Lysogenic Cycle:
The viral DNA is incorporated into the host's DNA.
The combined DNA is called a prophage.
The bacteria continues to live and replicate, passing the viral DNA to all offspring.
The virus eventually "wakes up" and enters the lytic cycle.
Temperate Viruses: Viruses capable of utilizing both lytic and lysogenic modes.
Stages of the Life Cycle:
Adsorption (Attachment).
Entry (Penetration).
Integration (Transcribing/using host machinery).
Synthesis and Assembly (Producing/assembling viral components).
Release (Dispersal of new virions/"baby viruses").
Other Infectious Agents
Viroids: Small particles consisting of nucleic acid without a protein coat. They primarily infect plants (e.g., potato disease, coconut yellowing).
Prions: Infectious, mutated proteins that cause a domino effect of protein mutation in the host's brain.
Examples: Creutzfeldt-Jakob disease (humans), Scrapie (sheep), Mad Cow Disease (livestock).
Domain Bacteria and Archaea
Prokaryotes: Organisms lacking a nuclear membrane and membrane-bound organelles.
Three-Domain System: Developed by Carl Woese in the 1970s after sequencing ribosomal RNA.
Domain Archaea: Includes the oldest forms of life. Often extremophiles (living in boiling ocean vents, the salty Dead Sea, geysers, or acidic environments).
Mesophiles: Archaea living in moderate conditions.
Methanogens: Archaea that release methane gas as a byproduct; found in swamps, cow digestive tracts, and termites.
Domain Bacteria: Includes the "true" bacteria (Eubacteria).
Domain Eukarya: Includes plants, fungi, animals, and protists.
Human Interaction:
$Staphylococcus$ $epidermidis$ is common on human skin.
$Staphylococcus$ $aureus$ is carried by approximately 30% of people; it is usually harmless but can cause serious infections (e.g., MRSA—Methicillin-resistant $Staphylococcus$ $aureus$) in wounds or medical facilities.
Bacteria names often describe them: "Staphylo-" means clusters, "-coccus" means round, and "aureus" refers to gold (resembling Roman gold coins in culture).
Bacterial Ecology and Metabolism
Benefits:
$Rhizobium$ in soil fixes atmospheric nitrogen into fertilizer for plants.
Used in producing cheese, yogurt, sake, and enzymes.
Used in bioremediation to break down oil after spills (e.g., BP oil spill).
Genetically modified bacteria are used to manufacture medicines like insulin.
Nutritional Modes:
Phototrophs: Use photosynthesis for energy.
Chemoautotrophs: Get energy from inorganic chemicals and carbon from .
Photoheterotrophs: Get energy from sunlight and carbon from organic sources.
Chemoheterotrophs: Get energy and carbon from organic sources (similar to humans).
Oxygen Requirements:
Obligate Aerobes: Require oxygen to survive (e.g., $S.$ $epidermidis$).
Obligate Anaerobes: Oxygen is toxic to them.
Facultative Anaerobes: Can live with or without oxygen; they grow faster with oxygen using cellular respiration (e.g., $E.$ $coli$ in the gut).
Aerotolerant Anaerobes: Can survive in oxygen but do not use it for respiration.
Bacterial Morphology and Anatomy
Shapes:
Bacillus: Rod/capsule-shaped (e.g., $Lactobacillus$).
Coccus: Spherical (e.g., $Streptococcus$).
Spirillum: Fat spiral shape.
Spirochete: Long, skinny, corkscrew-shaped (e.g., $Treponema$ $pallidum$ causing syphilis; $Borrelia$ $burgdorferi$ causing Lyme disease).
Anatomy:
Nucleoid: Area containing the single chromosome of DNA.
Ribosomes: Protein-making factories.
Plasma Membrane: Semi-fluid medium separator.
Cell Wall: Structural support; most bacteria possess one.
Fimbriae: Short bristles for adhesion.
Conjugation Pilus (Sex Pilus): A long appendage used to transfer DNA (specifically plasmids) between cells. This is how antibiotic resistance often spreads.
Plasmids: Extra rings of DNA on the side of the nucleoid.
Mesosome: Infolding of the plasma membrane to increase surface area.
Binary Fission: The process of bacterial reproduction. The chromosome attaches to the cell wall, replicates, and the cell pinches into two. It is distinct from mitosis.
Medical Microbiology and Gram Staining
Bacterial Diseases: Anthrax, Botulism, Chlamydia ($Chlamydia$ $trachomatis$), Cholera, Dental Caries (cavities), Gonorrhea, Leprosy, Lyme disease, Peptic ulcers, Plague, Pneumonia, Tuberculosis, Typhus.
Gram Stain (Hans Christian Gram):
Gram-Positive: Thick peptidoglycan cell wall; retains crystal violet dye and appears purple (e.g., $Bacillus$ $anthracis$).
Gram-Negative: Thin cell wall with an additional outer membrane; loses purple dye during alcohol wash and takes up pink counterstain (pink/red) (e.g., $Pseudomonas$ $aeruginosa$, $E.$ $coli$).
Antibiotics: Biological or synthetic drugs used to kill or inhibit bacteria.
Alexander Fleming: Discovered Penicillin after a mold contamination in a bacterial dish inhibited growth.
Viral infections require antivirals, and fungal infections require antifungals; antibiotics do not work on them.
Resistance: Mutations are random errors in DNA (caused by copy errors, chemicals, or UV). They are not created "on purpose" by bacteria. If a random mutation provides resistance, that bacterium survives antibiotic treatment and reproduces.