bio121 Flashcards
(181 cards)
1
Q
benefits of microbes
A
food materials
2
Q
problems w microbes
A
food spoilage , food borne diseases
3
Q
Examples of eukaryotes include?
A
fungi , animals , plants and some unicellular organisms
4
Q
are bacteria pro or euk
A
pro
5
Q
chracatersitics of arches
A
tRNA and ribosomal rna
no peptidoglycan wall- instead its large proteinaceous coat
linked lipids built from phytanyl chains
6
Q
properties of all cells
A
compartmentalisation
growth
evolution
7
Q
properties of some cells
A
motility
differentiation
communication
8
Q
What’s the ER for
A
protein glycosylation , membrane factory , lipids synthesis
9
Q
functions of cell membrane
A
separation of cell from environment
permeable barrier controls movement of molecules in or out of cell
site of respiration and photosynthesis
energy conservation
10
Q
mesophiles are ?
A
bacteria that grow the best at 20-40 degrees
many bacteria in our body are mesophiles
11
Q
thermophiles
A
grow best between 45-80 degrees
12
Q
hyperthermophiles
A
bacteria that grow best above 80 degrees
live in hot springs
13
Q
what’s a facultative aerobe?
A
grows better with oxygen but doesn’t need it
14
Q
pathogen
A
organism that causes disease , impairing or interfering with the normal physiological activities of the host
15
Q
Infection
A
Bacteria persist in host without necessarily causing tissue damage
16
Q
Disease
A
Overt damage to the host,parts of body cannot fulfil their normal functions
17
Q
What are the key events involved in the establishment of bacteria
A
The key events include bacterial entry, colonization, evasion of host defenses, and tissue damage.
18
Q
What factors contribute to bacterial colonization and tissue damage in a host?
A
Key factors include adhesins, toxins, and the ability to evade the immune system.
19
Q
What is the difference between pathogenicity and virulence
A
Pathogenicity refers to the ability of a pathogen to cause disease, while virulence is a measure of the severity of the disease caused by the pathogen.
20
Q
What are opportunistic pathogens?
A
Opportunistic pathogens are microorganisms that normally do not cause disease in a healthy host but can cause infections when the host’s immune system is compromised.
21
Q
What does pathogenicity refer to?
A
The ability of an organism to cause disease.
22
Q
What is the difference between infection and disease in the context of host-pathogen interactions?
A
Infection occurs when bacteria persist in a host without causing tissue damage, while disease involves overt damage to the host, impairing normal body functions.
23
Q
How does the concept of virulence relate to infection and disease?
A
Virulence refers to the degree of pathogenicity of a microorganism, influencing whether an infection leads to disease.
24
Q
What are Koch’s Postulates used for?
A
They are used to establish a causal relationship between a microbe and a disease.
25
What are the primary reservoirs for pathogens in humans?
Humans, livestock, and soil.
26
What are the different modes of pathogen transfer to hosts?
Direct transmission, airborne transmission, body contact, vector-borne transmission, and fomite transmission.
27
What are the two stages of bacterial adherence to host cells?
1. Association (non-specific forces) 2. Adhesion (specific bacterial adhesins and host receptors)
28
What is the significance of biofilms in bacterial colonization?
Biofilms can aggregate bacteria and may disperse to seed new sites of infection.
29
What is the role of Vibrio cholerae in adherence stages
Vibrio cholerae adheres to the brush border of rabbit villi.
30
What types of host receptors do bacteria interact with during biofilm formation?
Bacteria interact with host receptors like blood group antigens and extracellular matrix proteins such as fibronectin and collagen.
31
Bacteria interact with host receptors like blood group antigens and extracellular matrix proteins such as fibronectin and collagen.
Lytic compounds are substances that attack host tissues, facilitating bacterial invasion.
32
What structures do bacteria produce to resist phagocytosis?
Bacteria produce capsules and special surface proteins.
33
How do prokaryotes contribute to the success of pathogens?
Prokaryotes have structural and functional adaptations like fimbriae, flagella, and capsules that aid in their survival and pathogenicity.
34
What are the main differences between exotoxins and endotoxins?
Exotoxins are proteins secreted by living bacteria, while endotoxins are lipopolysaccharides found in the cell membrane of Gram-negative bacteria.
35
What are the three main forms of protists?
Ciliates, flagellates, and amoebae.
36
What is the function of the cytoskeleton in eukaryotic cells?
The cytoskeleton provides structural support and facilitates the trafficking of organelles within the cell.
37
How do flagellates exhibit mixotrophy under different light conditions?
In high light, they rely more on photosynthesis; in low light, they rely more on feeding.
38
Organellar Mixotrophy
Eats algal cells• Does not digest plastids(“Kleptoplastids”)• Plastids fix CO2• Plastids do not encodefor polymerases• Die and needreplenishing (so eatsmore)• Protist can live withoutthe plastids
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Cellular Mixotrophy
Eats algal cells• No digestion of algae• Algae fix CO2• Algae divide in cell• “Endosymbiosis”• Protist can livewithout the algae
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Ciliates
•Covered in cilia• Most developed protozoan• Cytostome (mouth)• Cytoproct (anus) • Two type of nucleus• Macronucleus• Micronuclei
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•Motile cilia
•9+2, dynein motor protein• Ciliates• Humans (bronchial and oviduct epithelium)
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•Non-motile cilium
•9+0, no dynein motor protein• ‘Primary cilium’ on all human cells
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Amoebae
One macronucleus
Most are aerobic
Most are heterotrophic
Some mixotrophic
Asexual reproduction only
No specific fission plane
Some move, some are stationary
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Naked amoebae
Amoeba proteus
Move by cytoplasmic streaming
Produce pseudopodia on surfaces
Feed by direct interception of prey
Raptorial feeding
No specific location for ingestion – can be anywhere
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3 cell forms of naked amebaoae
Trophozoites - the feeding form
Cysts – all produce a resting stage
• Floating form – stiffened pseudopodia for dispersal
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Shelled amoebae
Enclosed in a shell (‘test’)
Shell can be made of anything
Intrashellular cytoplasm within test
Project extrashellular cytoplasm to move and/or feed
Raptorial or diffusion feeding
Can produce cysts
47
Diffusion feeding in amoeba
Stationary predator captures prey with sticky extrashellular cytoplasm (‘axopodia’)
48
Leishmaniasis
blood infection by Flagellates e.g. Leishmania mexicana , the resoviour is dogs and is the sand fly vector , targets the liver and spleen tissue and is treatable
Aerobic, no cysts
49
Microbiology
The study of organisms too small to be seen clearly without magnification: viruses, prokaryotes (bacteria and archaea), and eukaryotes (protists, fungi, algae).
50
Beneficial Impacts of Microbes
Essential for food production (e.g., yogurt, cheese, wine), environmental cycles, and health.
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Harmful Impacts of Microbes
Cause infectious diseases like malaria, tuberculosis, cholera, and emerging diseases like COVID-19.
52
Microbial Populations
Microbes live mostly in mixed communities, interacting through competition and cooperation, greatly altering their environments.
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Estimated Microbial Cells on Earth
Estimated 5 × 10³⁰ microbial cells exist on Earth.
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Prokaryotic Cell Structure
Key features: no nucleus, cell membrane, cytoplasm, nucleoid, ribosomes, sometimes capsule, pili, and flagella.
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Examples of Prokaryotes
Bacteria and Archaea.
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Three Domains of Life
Bacteria: Prokaryotes with peptidoglycan cell walls. Archaea: Prokaryotes without peptidoglycan, unique lipids; thrive in extreme environments. Eukaryotes: Organisms with nucleus and membrane-bound organelles (animals, plants, fungi, protists).
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Typical Sizes of Microorganisms
Viruses: 0.01-0.2 μm, Bacteria: 0.2-5 μm, Yeasts: 5-10 μm, Algae: 10-100 μm, Protists: 50-1000 μm.
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Gram-positive Bacteria
Thick peptidoglycan layer, stains purple, susceptible to penicillin and lysozyme.
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Gram-negative Bacteria
Thin peptidoglycan, outer membrane, stains pink.
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Archaea Cell Walls
No peptidoglycan, various cell wall types.
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Capsules
Protect against desiccation and phagocytosis.
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Fimbriae
Short, hair-like structures for attachment.
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Pili
Longer structures used for DNA transfer (conjugation).
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Flagella
For motility; arrangements include monotrichous, amphitrichous, lophotrichous, peritrichous.
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Nucleoid
Region containing circular DNA.
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Plasmids
Extra-chromosomal DNA carrying beneficial genes (e.g., antibiotic resistance).
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Inclusions
Storage granules (e.g., glycogen, sulfur, magnetosomes for orientation).
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Endospores
Formed by some Gram-positive bacteria (e.g., Clostridium). Highly resistant structures enabling survival under extreme conditions (heat, drying, radiation).
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Calcium Dipicolinate
Contains calcium dipicolinate to dehydrate and protect DNA in endospores.
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halophiles
• grow in habitats with high salt concentration (sodium chloride)• Mild halophiles: grow with 1-6% NaCl• Moderate halophiles: grow with 7-15% NaCl• Extreme halophiles: grow with 15-30% NaCl
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Protists
Eukaryotic organisms, mostly unicellular, that are not classified as plants, animals, or fungi. They have a cytoskeleton and membrane-bound organelles.
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Size Range of Protists
Typically range from 5-200 µm. Some exceptions like large amoebae can reach up to 10 cm in size.
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Three Main Forms of Protists
Ciliates, flagellates, and amoebae.
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Major Modes of Nutrition in Protists
Photoautotrophic (e.g., algae with chloroplasts), heterotrophic (e.g., protozoa feeding on bacteria), and mixotrophic (combining photosynthesis and feeding).
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Differences between Prokaryotes and Protists
Protists have a nucleus, membranous organelles (e.g., mitochondria, Golgi apparatus), 80S ribosomes (70S in organelles), cilia (9+2 structure) and flagella, and larger cell size (>5 µm).
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Similarities between Protists and Bacteria
Both reproduce asexually (binary fission for bacteria, mitosis for protists) and have cytoplasmic ribosomes and can survive extreme conditions via cyst formation.
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Protist Cyst Formation
Cysts are protective, dormant forms that resist heat, drying, radiation, and can survive for up to 20 years, acting like bacterial endospores.
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Cell Walls in Protists
Some protists have cell walls (e.g., algae) made of cellulose or silica, while others (e.g., motile heterotrophs) lack cell walls, making them prone to osmosis.
79
Osmosis and Protists
Without a cell wall, water naturally moves into the cell (hypotonic environments), risking cell lysis unless mechanisms like contractile vacuoles are used.
80
Aerobic and Anaerobic Growth in Protists
Obligate aerobes need O₂, obligate anaerobes cannot tolerate O₂, facultative anaerobes grow with or without O₂, microaerophilic require low O₂, and aerotolerant anaerobes tolerate but don't use O₂.
81
Mitochondria and Hydrogenosomes
Mitochondria produce ATP via aerobic respiration (O₂), while hydrogenosomes evolved from mitochondria and allow ATP production under anaerobic conditions.
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Endosymbiont Theory
Mitochondria and chloroplasts evolved from free-living bacteria engulfed by a larger host cell, evidenced by circular DNA, 70S ribosomes, binary fission reproduction, and double membranes.
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Types of Mixotrophy in Protists
Organellar mixotrophy involves eating algae, digesting parts, and retaining plastids; cellular mixotrophy keeps algae alive inside; constitutive mixotrophy makes algae permanent organelles.
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Protist Movement Mechanisms
Cilia are hair-like structures for movement, flagella are long whip-like structures for swimming, and amoeboid movement occurs via pseudopodia extending and contracting.
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Medical and Ecological Impact of Protists
Protists can cause diseases (e.g., malaria, amoebic dysentery) and are ecologically important in marine food webs, carbon cycling, and as symbionts or parasites.
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Protists
Unicellular eukaryotes (not animals, plants, or fungi).
87
Classification of Protists
Classified into four eukaryote supergroups: Excavata, SAR, Archaeplastida, and Unikonta.
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Main Forms of Protists
Ciliates, flagellates, and amoebae—each with unique movement and feeding strategies.
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Modes of Nutrition among Protists
Autotrophy (photosynthesis), Heterotrophy (ingesting organic matter), Mixotrophy (combination of both).
90
Mixotrophy
Combining photosynthesis with feeding.
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Types of Mixotrophy in Protists
Organellar mixotrophy (retain plastids from prey), Cellular mixotrophy (harbor live prey), Constitutive mixotrophy (own plastids + raptorial feeding).
92
Cilia in Ciliates
Used for movement (beating back and forth) and feeding (direct prey to the cytostome via feeding currents and membranelles).
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Cytostome
A mouth structure in ciliates, surrounded by stiff cilia (membranelles) to filter prey into food vacuoles.
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Feeding in Suctorian Ciliates
Use microtubule tentacles ending in cytostomes, release toxins (extrusomes) to dissolve and suck out prey contents.
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Reproduction in Ciliates
Asexually via transverse binary fission (mitosis) and sexually via conjugation, involving meiosis, mitosis, and exchange of micronuclei.
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Structural Features of Flagellates
Possess one or more flagella (9+2 structure), typically have a macronucleus, reproduce by longitudinal binary fission, may be aerobic and use various nutrition modes.
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Raptorial vs Filter Feeding in Flagellates
Raptorial: Prey is actively captured via feeding currents (using flagella); ingested via pseudopodia. Filter feeding: Collar of microvilli (tentacles) filters prey, found in choanoflagellates.
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Choanoflagellates
Filter-feeding flagellates with a collar of microvilli, most closely related protists to animals.
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Photoautotrophic Flagellates
Called phytoflagellates, have their own plastids, perform photosynthesis, use flagella for movement toward light and nutrients.
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Examples of Phytoflagellates
Include genera like Euglena, Ceratium, Chlamydomonas.
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Eyespot (Stigma)
Organelle with carotenoid globules that shades a photoreceptor—used to detect light direction.
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Mixotrophic Flagellates
Ochromonas: Few plastids, prefers prey. Dinobryon: Plastids dominate, prefers photosynthesis.
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Feeding Study in Dinobryon divergens
Cells were fed prey at time zero, and prey/cell ratio measured after 30 minutes, examining effect of light and temperature on photosynthesis and ingestion.
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Fungi
A unique and highly diverse group of eukaryotic organisms, ranging from unicellular yeasts to massive multicellular fungi like Armillaria (>100 tons, 15,000 years old).
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Key defining characteristics of fungi
Eukaryotic, Cell wall (chitin + polysaccharides), Haploid nuclei, Heterotrophic (no chlorophyll), Cannot use CO₂ or fix N₂, Reproduce both sexually and asexually.
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Nutrient acquisition in fungi
Fungi are absorptive heterotrophs: Saprophytes: Feed on dead matter, Necrotrophs: Kill then consume hosts, Biotrophs: Feed on living hosts. Use a diverse array of carbon sources and occupy many ecological niches.
107
Differences between fungi and plants
Fungi are not photoautotrophs (no photosynthesis). Fungi digest externally and absorb nutrients. Typically filamentous; plants have box-like cells. Cell walls differ (chitin vs cellulose). Nuclear division occurs within an intact nucleus in fungi.
108
Historical view of fungi classification
Previously grouped with plants. Whittaker's Five Kingdom system (1969) recognized fungi as separate. Modern molecular methods show fungi are more closely related to animals.
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Main growth forms of fungi
Yeasts: Unicellular, reproduce by budding (e.g., S. cerevisiae). Filamentous fungi: Multicellular, composed of hyphae, form a mycelium. Dimorphic fungi: Switch between yeast and filamentous forms based on environmental cues (e.g., temperature).
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Mycelium and hyphae
Hyphae: Long, thread-like filaments with polarised tip growth. Mycelium: Interwoven mass of hyphae, forming the main fungal body.
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Yeast asexual reproduction
By budding, forming an identical daughter cell. Can aggregate into colonies or pseudohyphae.
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Filamentous fungi asexual reproduction
Via lightweight spores from aerial extensions of hyphae. Spores are haploid and enable rapid colonisation.
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Fungi sexual reproduction
Typically triggered by nutrient limitation. Involves fusion of compatible haploid nuclei → diploid zygote. Produces hardy sexual spores. Heterothallism: Requires two mating types (+/-). Homothallism: Self-fertilization.
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Major fungal phyla and species counts
Chytridiomycota: ~1,000, Zygomycota: ~1,000, Ascomycota: ~65,000, Basidiomycota: ~30,000, Deuteromycota (Fungi imperfecti): variable.
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Key features of Zygomycota
Aseptate hyphae. Asexual: sporangiospores. Sexual: zygospores. Mostly saprophytes, includes Glomus (important mycorrhizae).
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Characteristics of Ascomycota
Septate hyphae. Asexual: conidiospores. Sexual: ascospores (meiosis → mitosis). Includes model organisms and plant pathogens.
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Definition of Basidiomycota
Septate dikaryotic hyphae. Asexual reproduction is rare. Sexual: basidiospores produced in basidiocarps (fruiting bodies). Includes mushrooms, rusts, and wood decomposers.
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Deuteromycota (Fungi imperfecti)
Fungi with no known sexual cycle. Asexual spores: conidiospores, arthroconidia. Many are reclassified as ascomycetes using molecular tools. Include food spoilers and industrial fungi (e.g., Aspergillus niger).
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Mycoses
Fungal infections.
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Allergies
Immune responses to fungal allergens.
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Mycotoxins
Toxic compounds produced by fungi.
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True fungal pathogen
Capable of causing systemic infection in healthy hosts.
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Thermal dimorphism
A fungus exhibits filamentous growth <35°C, and yeast-like (or spherule) growth at 37°C.
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Histoplasma capsulatum
A fungus that exhibits thermal dimorphism.
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Coccidioides immitis
A fungus that exhibits thermal dimorphism.
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Histoplasma infection
Inhalation of spores → yeast conversion in lungs.
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Coccidioidomycosis
Caused by Coccidioides immitis in desert soils.
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Opportunistic fungal pathogen
Infects immunocompromised hosts.
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Candida albicans infection
Found in ~20% of healthy individuals.
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Aspergillosis
Caused by Aspergillus spp., mainly A. fumigatus.
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Dermatophytes
Fungi causing superficial infections in healthy individuals.
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Fungal infections concern
Rise in immunocompromised patients (e.g. organ transplants, HIV).
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Azoles
Inhibit ergosterol synthesis.
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Polyenes
Bind to ergosterol, disrupt membrane integrity.
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Phytopathogenic fungi
Two broad groups: pathogens of immature or compromised tissue and pathogens of mature, healthy tissue.
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Necrotrophic phytopathogens
Kill host cells using toxins and cell wall-degrading enzymes.
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Biotrophic phytopathogens
Do not kill host; maintain living tissue.
138
Haustorium
Specialized feeding structure formed by biotrophic fungi inside host cells.
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Virus
A minuscule, infectious, obligate intracellular parasite made up of genetic material (DNA or RNA) enclosed in a protein coat (capsid), sometimes surrounded by a lipid envelope derived from the host cell membrane.
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Virion
Extracellular infectious particle, used for transmission.
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Virus (intracellular)
Intracellular replicative form inside host cells.
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Bacterial multiplication
Via binary fission, producing two daughter cells.
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Viral replication
Hijacks host machinery to synthesize and assemble new virions; not by division.
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Helical capsid
Capsomers arranged spirally.
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Polyhedral (icosahedral) capsid
Spherical with 20 faces and 12 corners.
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Binal (complex) capsid
Mix of helical and polyhedral, or irregular forms.
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Functions of a viral capsid
Protects nucleic acid from enzymes, enables attachment to host cells, assists in membrane penetration or genome injection, may self-assemble under proper conditions.
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Naked virion
Composed of nucleocapsid only (e.g., poliovirus).
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Enveloped virion
Nucleocapsid enclosed within a host-derived lipid membrane, often with viral proteins embedded.
150
Organisms viruses can infect
Viruses infect all cellular life: Bacteria (e.g., bacteriophage T4), Protozoa, algae, fungi, Plants (e.g., tobacco mosaic virus), Animals, and even other viruses (e.g., virophages like Sputnik infect Mimivirus).
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Replication cycle of the lytic bacteriophage T4
Adsorption (attachment), Penetration (DNA injection), Replication (DNA/protein synthesis), Maturation (assembly), Release (lysis), Reinfection.
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Lytic phages
Destroy the host immediately.
153
Temperate phages
Integrate into host genome as prophages, replicating silently until stress (e.g., UV light) induces lysis.
154
Significance of bacteriophages in biomedicine
Phages regulate bacterial populations (e.g., 10 million on a human hand).
155
Quantification of bacteriophages
Quantified using plaque assays: molten agar with bacteria and phage is poured onto nutrient agar, and clear zones (plaques) are counted.
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Common ways viruses are named
Viruses may be named based on cytopathology, geographic origin, discoverers, disease caused, body site of isolation, cultural beliefs, host organism, or sometimes by multiple factors.
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Two main systems used to classify viruses
ICTV (International Committee on the Taxonomy of Viruses) and Baltimore Classification System.
158
Criteria used by ICTV for viral taxonomy
ICTV considers both phenotypic criteria (genome composition, capsid structure, envelope presence, host range, disease, etc.) and genotypic criteria (gene sequences, synteny, expression systems, phylogenetics).
159
Hierarchy of ICTV classification
As of 2020: 6 realms, 10 kingdoms, 17 phyla, 39 classes, 59 orders, 189 families, 2224 genera, and 9110 species.
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Classification of Monkeypox virus in ICTV system
Realm: Varidnaviria, Kingdom: Bamfordvirae, Phylum: Nucleocytoviricota, Class: Pokkesviricetes, Order: Chitovirales, Family: Poxviridae, Genus: Orthopoxvirus.
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Principle underlying the Baltimore classification system
All viruses must produce mRNA that can be read by host ribosomes.
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7 Baltimore groups based on genome types
Group I: dsDNA (e.g. Adenoviruses, Herpesviruses), Group IV: +ssRNA (e.g. Picornaviruses, Coronaviruses), Group VI: +ssRNA retroviruses (e.g. HIV), Group VII: DNA with reverse transcription (e.g. Hepatitis B).
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Four general modes of virus-cell interactions
Transformation into tumor cells, lytic infection (cell death and virus release), persistent infection (slow release, no death), latent infection (virus dormant, later reactivated).
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Key steps of the viral life cycle
Attachment, Uncoating, Replication (mRNA synthesis and genome replication), Biosynthesis (protein translation), Assembly, Exit (lysis for naked viruses, budding for enveloped viruses).
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How viruses enter cells and replicate
Entry: via receptor binding or direct genome injection (e.g. poliovirus). Replication: Synthesis of mRNA (mandatory for protein production) and replication of viral genome.
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Rhabdoviruses
Bullet-shaped virion (~170 nm), enveloped. -ssRNA genome with its own RNA-dependent RNA polymerase. Causes disease in a wide range of animals and humans.
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Rabies virus replication
Transmitted via saliva (commonly from dogs). Enters peripheral nervous system, travels to central nervous system. Reaches brain, causes encephalitis. Fatal in nearly all untreated cases.
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Furious Rabies
80-90% of cases, 100% mortality. Aggression, vocal changes, excessive salivation, death.
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Dumb Rabies
10-20% of cases, primarily paralytic. Lethargy, leads to death in ~3 days.
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Monkeypox virus
Group I dsDNA virus, first found in monkeys (1958), first human case in DRC (1970). Animal-to-human: bites, scratches, bushmeat. Human-to-human: direct skin contact or contaminated objects (e.g., bedding).
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Clades of Monkeypox virus
Clade I: Congo Basin / Central African. Clade II (IIa, IIb): West African. Clade I is more virulent. Both have caused recent outbreaks (e.g., 2022 UK case).
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Viroids
Smallest known pathogens, infect only plants. Naked circular RNA, no capsid, no proteins. Resistant to proteases and nucleases, replicate autonomously. Example: Potato Spindle Tuber Viroid.
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Obelisks
Novel viroid-like elements found in human oral and gut metatranscriptomes. Circular RNA (~1 kb) with predicted rod-like structure. Encode proteins called Oblins from a novel superfamily. No known similarity to any existing biological agents.
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Prions
Proteinaceous infectious agents without nucleic acids. Most likely mechanism: PrPsc converts normal PrPc to pathological form. Lead to spongiform encephalopathies: neurodegeneration and death.
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Scrapie
Affects sheep/goats, causes ataxia; no treatment.
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BSE (Mad Cow Disease)
Erratic behaviour; variant CJD in humans via contaminated beef. Subtypes: Classical, H-type, L-type BSE.
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Kuru
Fore tribe (PNG), from funerary cannibalism.
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sCJD
Sporadic Creutzfeldt-Jakob, most common.
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fCJD
Inherited genetic mutation.
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vCJD
From eating BSE-contaminated beef.
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iCJD
Accidental transmission during surgery or medical treatment.
