Exam 3 Quizlet Flashcards
(260 cards)
1
Q
What kinds of symbiotic relationships do microbes form?
A
- Microbial cells outnumber human cells 10 to 1
- Microbes form a variety of symbiotic relationships with humans:
- commensalism, mutualism, parasitism
2
Q
In 2007, the National Institute of Health launched the ___ to better understand the symbiotic relationships that result in human health and disease
A
The Human Microbiome Project
3
Q
What is the human microbiome?
A
It is the collection of all the microorganisms living in association with the human body (also called the microbiota or microflora)
4
Q
Metagenomics
A
- Analysis of genetic material derived from microbial communities
- Can reveal diversity and metabolic potential of microbial communities
- Culture-independent (starts with genetic material from particular environment)
5
Q
A metagenomic approach
A
- Isolate genomic DNA
- PCR amplify SSUr RNA genes (16S rRNA in bacteria), clone and sequence
- Compare to database of known genes
6
Q
Immune system
A
- Widely distributed cells, tissues, organs
- Recognizes foreign substances that provoke immune response
- Antigens and antibodies
7
Q
Antigens (definition)
A
Foreign substances that provoke immune response
8
Q
Antibodies (definition)
A
Bind antigens, inactivate or eliminate (B-cells)
9
Q
Immunity (definition)
A
Ability to resist disease or infection
10
Q
Immunology (definition)
A
Studies how body defends against foreign invaders, harmful substances
11
Q
The immune system protects against what 4 classes of pathogen
A
Bacteria, viruses, fungi, and protists
12
Q
Pathogen: Bacteria (examples (genus, species), diseases)
A
- Salmonella trphimurium: food poisoning
- Mycobacterium tuberculosis: tuberculosis
13
Q
Pathogen: Viruses (examples, diseases)
A
- Influenza: flu
- HIV: AIDS
14
Q
Pathogen: Fungi (examples (genus, species), diseases)
A
- Cryptococcus neoformans: Cryptococcosis
- Candida albicans: thrush
15
Q
Pathogen: Protists (example (genus, species), diseases)
A
- Plasmodium falciparum: malaria
- Giardia: Giardiasis
16
Q
Immune system also participates in disease (examples)
A
- Allergy
- Autoimmunity
- Transplantation (tissue) rejection
- Graft-vs-Host-Disease
17
Q
Innate immunity
A
- Non-specific
- First line of defense
- Fast
- No memory
- Cells: macrophages, neutrophils, dendritic
- Components: anatomical features, complement, toll-like receptors, cytokines
18
Q
Innate immune response
A
Evolutionary ancient immune defense system comprised of anatomical barriers (skin, mucus membranes), cells (macrophages, neutrophils and dendritic), complement, toll-like receptors and cytokines
19
Q
Cells of the immune response
A
- Leukocytes (white blood cells)
- From pluripotent stem cells in bone marrow
- 5 major types
20
Q
Name the 5 major types of cells of the immune response
A
Basophils, eosinophils, neutrophils, monocytes, and lymphocytes
21
Q
Monocytes
A
Mature into macrophages or dendritic cells
22
Q
Lymphocytes (adaptive immune system)
A
T, B, and natural killer (NK) cells
23
Q
Macrophages (definition)
A
Phagocytes present in most tissues of the body. Derived from blood monocytes. Ingest and kill microbial pathogens, also capable of antigen presentation
24
Q
Macrophages
A
- From monocytes in blood
- Enter, reside in tissue
25
Name the 3 major function of macrophages
1. Phagocytic
2. Antigen presentation
3. Make cytokines and "chemokines" (signaling molecules)
26
Phagocytic
- Engulf and destroy pathogens
- Use reactive O2 and nitrogen species
- Hydrogen peroxide
- Nitric oxide
27
Phagocyte (definition)
Cell capable of ingesting and killing particulate material (e.g., microbes)
28
Phagocytosis (steps)
1. Pseudopodia surround food
2. Phagosome
3. Fuses with lysosome forms phagolysosome
4,5. Pathogen degraded
29
Reactive oxygen species such as hydrogen peroxide and reactive nitrogen species such as nitric oxide-
Microbicidal products produced in phagolysosomes of phagocytes to destroy phagocytosed microbes
30
Polymorphonuclear leukocytes (white blood cells)(definition)
Granulocytes, Phagocytes, most common are neutrophils: Produced in the bone marrow, circulate through the blood, live for only a few days. Capable of leaving the blood at sites of inflammation
31
Polymorphonuclear leukocytes (PMNs) (most common variety)
Neutrophils:
- Stain at neutral pH (Wright's stain)
- Circulate in blood, migrate to infection sites
- Function similar to macrophages
- Also a source of defensins (antimicrobial peptides)
- Multi-lobed nucleus
32
Dendritic cells (definition)
Phagocytic cells that bridge innate and adaptive immunity. Leave tissues in response to cytokines, migrate to lymph nodes to start the adaptive immune response
33
Dendritic cells
- Can also derive from monocytes
- In blood, skin, mucous membranes
- Phagocytic
- Migrate to lymph nodes - present antigens to lymphocytes
34
Name the 4 innate immune response components:
Anatomical features, complement, toll-like receptors, cytokines
35
Anatomical features: Mechanical (skin, gut, lungs, eyes/nose)
- Skin, gut, lungs, eyes/nose: epithelial cells joined by tight junctions
- Skin, gut: Longitudinal flow of air or fluid
- Lungs: Movement of mucus by cilia
- Eyes/nose: Tears, nasal cilia
36
Anatomical features: chemical (skin, gut, lungs, eyes/nose)
- Skin: Fatty acids
- Skin, gut, lungs: Antibacterial peptides
- Gut: Low pH, enzymes (pepsin)
- Lungs: NOTHING
- Eyes/nose: Enzymes in tears (lysozyme)
37
Anatomical features: microbiological (skin, gut, lungs, eyes/nose)
- Skin, gut: Normal flora (your microflora helps protect you)
38
Complement system (definition)
A set of serum proteins, which in the presence of microbial surfaces, cleave themselves into opsonins (C3b) that coat bacteria for phagocytosis, chemotactic factors (C5a) that attract neutrophils, or that kill certain bacteria directly by forming a membrane attack complex (C5-9)
39
The complement system
- >30 serum proteins (inactive state)
- Activated by enzymatic cleavage
- "Complements" activity of antibody (production of antibodies by B-cells)
40
Name the 3 functions of the complement system:
1. Opsonins - coat microbes for phagocytosis (C3b)
2. Chemotactic factors - PMN migration from blood to infection (C5a)
3. Membrane attack complex (plasma membrane or outer membrane of gram negative bacteria)(pore formed, leaks out, cell lysis)
41
Toll-like Receptors (TLRs)
- Pattern recognition receptors
- At least 10 distinct receptors in family
- Binds Pathogen-Associated Molecular Patterns (PAMPs)
42
Name 4 examples of the PAMPs
- TLR4 = LPS
- TLR2 = Peptidoglycan
- TLR3 = dsRNA
- TLR5 = Flagellin (protein that makes up the filament of the flagella)
43
Toll-like Receptor (TLR)(steps)
1. After the TLR binds PAMP, a signal transduction cascade is initiated
2. Cascade activates transcription factor NfkB that moves to nucleus (that promotes transcription of genes for cytokines and chemokines)
3. Genes for cytokines activated
4. Macrophage releases cytokines
44
Cytokines (definition)
Proteins released by cells of the immune system, influence cell activity. Protein signaling molecules
45
2 examples of Cytokines and description
1. Interleukins (IL) - stimulate cell growth, differentiation, proliferation
2. Tumor Necrosis Factor (TNF) - increases vascular permeability, permeability, induces fever, activates B and T cells
46
Tumor Necrosis Factor (TNF)(definition)
A cytokine made by phagocytes in response to Toll-like receptor signaling, which makes blood vessels sticky for neutrophils, also associated with fever production and activation of T and B cells
47
Chemokines (definition)
A type of cytokine, attract immune system cells to sites of infection
48
Chemokines
- A type of cytokine
| - Stimulate cell migration to infection sites
49
Name 2 examples of chemokines and description
1. Interferons - produced in response to viruses - block viral replication and assembly
2. Endogenous pyrogens - induce fever
- Circulate in brain -> induce neurons to make prostaglandins -> fever
50
fever and pain signaling steps
Bacteria trigger macrophages to release cytokines and chemokines -> vasodilation and increased vascular permeability cause redness, heat, and swelling -> inflammatory cells migrate into tissue, releasing inflammatory mediators that cause pain
51
Ecology and environmental microbiology
- Study behavior and activities of microbes in their environments
- Microbes are found in every environment on earth, and are integral to the biogeochemical cycles that shape the environment of earth and its ocean
- Elements flow in cycles, all nutrient cycles are linked and make life on earth possible
52
Biogeochemical cycling involves ___ that change chemical and physical characteristics of nutrients
Redox reactions
53
Carbon (reduced form, intermediate oxidation state forms, oxidized form)
- Reduced form: methane (CH4, -4)
- Intermediate forms: Carbon monoxide (CO, 2+)
- Oxidized form: Carbon dioxide (CO2, +4)
54
Nitrogen (reduced form, intermediate oxidation state forms, oxidized form)
- Reduced form: Ammonium (NH4+, -3; organic N, -3)
- Intermediate forms: Nitrogen gas (N2, 0), Nitrous oxide (N2O, +1), Nitrite (NO2-, +3)
- Oxidized form: Nitrate (NO3-, +5)
55
___ and ___ are greenhouse gases that trap heat within earth's atmosphere
Carbon dioxide (CO2) and methane (CH4)
56
Carbon cycling
- Oxidized: CO, CO2
- Reduced: organic matter, methane (CH4), glucose
- Photosynthesis fixes CO2 into biomass (calvin cycle)
- Microbes fix 1/2 of worlds C
- Produces O2 and organic compounds
- Organic compounds oxidized back to CO2 by respiration (glycolysis + TCA + ETC)
57
Carbon cycle steps
- Aerobic processes: reductive (CO2 fixation, Photo- and chemoautotrophy), oxidative and redox neutral (respiration and fermentation), oxidative (methano- and methylotrophy)
- Anaerobic process: reductive (methanogenesis)
- Fossil fuel/combustion & CO -> CO2
- CO2 -> reductive (CO2 fixation, photo- and chemoautotrophy) -> organic matter -> oxidative and redox neutral (respiration and fermentation) -> either CO2 or reductive (methanogenesis) -> CH4 -> oxidative (methano- and methylotrophy) -> CO2
58
Methanogens (anaerobic carbon cycling)
- Anaerobic archaea
- Energy reducing CO2 to CH4
- 1 billion tons CH4/yr
- Some in symbiosis with termites, ruminants
59
Methanotrophs (anaerobic carbon cycling)
- Aerobic, anaerobic archaea and bacteria
| - Methane as C source oxidized to CO2
60
The nitrogen cycle
Reduced Nitrogen (NH4+), electron donor -> NO2 (form of chemolithotrophy) -> oxidized nitrogen (NO3), electron acceptor -> atmospheric N2 (intermediate nitrogen) -> reduced nitrogen (NH4+)
61
Nitrification
NH4 -> NO2 -> NO3
- NH4 -> NO2 (Nitrosomonas)
- NO2 -> NO3 (Nitrobacter)
62
Denitrification
NO3 -> N2
| - Pseudomonas denitrificans
63
Nitrogen fixation
N2 -> NH4
| - Azotobacter
64
Symbioses
Association of 2 or more organisms
65
Name and describe the 2 types of physical associations
1. Ectosymbiont - organism on another
| 2. Endosymbiont - organism in another
66
Mutualism
Both benefit (often obligatory)
67
Name 3 types of mutualism relationships
1. Vibrio and squid
2. Photosynthetic algae (Protists) and coral
3. Tube worms and bacteria
68
Squid-bacterial relationship
- Hawaiian Bobtail squid and Vibrio fischeri
- Enzyme: Luciferase (luminescent)
- Vibrio fischeri uses quorum sensing to control light production; cells produce light only if they are at a high density
- The light from the Hawaiian Bobtail squid is caused by its relationship with the Vibrio
69
Signaling molecule (autoinducer)(AI)
- Diffusible: moves in and out of cells
- Low cell density, gradient favors movement (AI) out
- High cell density, gradient favors movement (AI) in and genes are activated
- LuxR: protein, transcription factor, binds autoinducer to the promoter region of the operon
- When the LuxR binds to the promoter region of the operon, then the luciferase enzyme can get made and genes are activated
- Benefit: protective niche (Vibrio), squid (protection from predators)
70
Quorum sensing - Vibrio fischeri
The AHL signaling molecule (AI) diffuses out of the cell; when cell density is high, AHL diffuses back into the cell, where it binds to and activates the transcriptional regulator LuxR. Active LuxR then stimulates transcription of the gene coding for AHL synthase (luxI), as well as the genes encoding proteins needed for light production
71
___ are photosynthetic algae that are Dinoflagellates
Zooxanthellae
72
Photosynthetic algae and coral
- Most corals obtain energy and nutrients from Zooxanthellae that live within the coral's tissue
- Zooxanthellae coral
- Coral bleaching: disruption and elimination of the Zooxanthellae
73
Tube worms and bacteria
O2, CO2, and H2S are absorbed through the gill plume and transported to the blood cells of the trophosome (packed with bacteria). H2S is bound to the worm's hemoglobin and carried to the endosymbiont bacteria. The bacteria oxidize the H2S and use some of the released energy to fix CO2, in the calvin cycle. Some of the reduced carbon compounds synthesized by the endosymbiont are translocated to the animal's tissues
74
Cooperation
Both benefit, not obligatory
75
Cooperation example
Azotobacter (N2) -- NH2 --> Cellulomonas (cellulose degrader) -- glucose --> Azotobacter (N2)
76
Commensalism
One benefits, other neutral
77
Commensalism example
- Skin or surface microbes (Staphylococcus epidermidis)
- Nitrosomonas and Nitrobacter
Ammonia -> Nitrite -> Nitrate (Nitrification)
- Bacteria (benefit), human (neutral)
- Nitrobacter (benefits), Nitrosomonas (neutral)
78
Predation
Predator attacks, usually kills prey
79
Name 2 examples (genus) of predation
1. Bdellovibrio - bacterial predator of other bacteria
| 2. Myxococcus - "wolf packs" prey on other bacteria
80
Parasitism
One benefits, other harmed (often coexist)
81
Name an example of paratism
Viruses and cells
82
Amensalism
Compound from one, negative effect on another
| - Antibiotic production by a bacteria and fungi
83
Fungi - general features
- Domain: Eukarya
- Kingdom: Fungi
- Size: single-celled yeast to 3-mile-wide honey mushroom
- Lack chlorophyll (non-photosynthetic)
- Plasma membranes
- Cell walls of chitin (polymer of NAG)
84
What are the 2 types of nutrition of Fungi?
1. Saprophytes - nutrients from dead matter
| 2. Absorptive - secrete enzymes, absorb nutrients
85
Fungi: the great decomposers
- Able to break down many complex organic compounds including cellulose
- Without fungi, dead plants and trees would accumulate to great depths
- Without fungal activity and resulting CO2 production - plant, and ultimately human life would cease
86
Mycology
The study of fungi
87
Mycoses
Diseases caused by fungi
88
Mycotoxicosis
- Poisoning by fungal toxin
- Alfatoxins - intercalate into DNA, carcinogens
- Ergot alkaloids - delusions, convulsions
89
___ and ___ produce mycotoxicosis (genus)
Aspergillus; Claviceps
90
Fungi: distribution
- Mostly terrestrial
- Can be part of human microflora
- Can be pathogens
- Can form associations (Lichens = fungi + cyanobacteria)
- Mycorrhizal fungi
91
__ are the combination of fungi and cyanobacteria
Lichens
92
Mycorrhizal fungi
With plant roots (mutualism)
93
Yeasts
- Unicellular fungi
| - Found in bread, found in wine
94
Function of yeasts in bread
- Ferment sugars in flour or added to dough
- Releases CO2 and ethanol, CO2 trapped in bubbles, results in dough expanding or rising
- Sourdough uses yeast in symbiosis with bacteria of the genus Lactobacillus
95
Function of yeasts in wine
- Ferment sugars in grape juice producing CO2 and ethanol
- Naturally occurring yeasts or modern methods of isolation and maintenance
- One yeast cell can ferment its own weight of glucose/hr, producing 15-18% by volume ethanol
96
Name 2 types of yeasts (genus and species)
1. Saccharomyces cerevisiae
| 2. Candida albicans
97
Saccharomyces cerevisiae (where is it found)
Bread, beer, wine
98
Candida albicans (where is it found)
- Microflora of mouth, vagina and intestinal tract
| - Opportunistic fungal pathogen
99
Molds
- Filamentous fungi
- Hyphae
- Mycelium (mass of hyphae)
100
Fungi: asexual reproduction
- Offspring genetically identical to parent
| - 3 mechanisms
101
Name the 3 mechanisms by which fungi can reproduce asexually
Binary fission, budding, spore production (conidiospores, sporangiospores -> the results of asexual reproduction)
- Aspergillus - conidiospores
102
Fungi: sexual reproduction
- Often under stress or limiting conditions
- Offspring genetically intermediate
- Haploid cells of opposite mating types fuse
- Pheromones: signal between types
- In yeast, mating types are designated a and alpha
- In other fungi, the hyphae meet and fuse
103
Fungi sexual reproduction (fusion)
- Hyphae are meeting and fusing
- Fusion can create a single hyphae with 2 distinct nuclei - dikaryon
- Nuclei can fuse forming diploid zygote
- Meiosis forms haploid spores
104
Rhizopus (common bread mold) sexual and asexual stages
- Sexual: zygospores
- Asexual: sporangiospores
- Requires compatible strains of opposite mating types. When the 2 mating strains are close, each produces a different hormone, called a pheromone, that causes their hyphae to form projections called progamtangia; these mature into gametangia. After fusion of the gametangia, the nuclei of the 2 gametes fuse, forming a zygote. The zygote then develops a thick, rough, black coat and becomes a dormant zygospore. Meiosis often occurs at the time of germination; the zygospore then splits open and produces a hypha that bears an asexual sporangium to begin the cycle again
105
Fungal divisions: name the SSrRNA and the number of divisions
- 18S rRNA analysis groups fungi into 8 subdivisions
106
Name 4 of the better known subdivisions of fungi:
Chytridiomycota, Zygomycota, Ascomycota, Basidiomycota
107
Chytridiomycota
- Simplest fungi
- Aquatic
- Motile flagellated zoospore
- Chytridiomycosis - massive frog deaths
108
Fungal subdivision:
- Simplest fungi
- Aquatic
- Motile flagellated zoospore
- Chytridiomycosis - massive frog deaths
Chytridiomycota
109
Zygomycota (name a genus)
- Sexual zygospores, asexual sporangiospores
| - Example: Rhizopus
110
Fungal subdivision:
- Sexual zygospores, asexual sporangiospores
(Name a genus)
Zygomycota
| Genus: Rhizopus
111
Rhizopus
- Bread mold
- Meat tenderizer, birth control agents
- Rice disease "seedling blight"
- an alpha-proteobacterium, Burkholderia found growing within the fungus produces the toxin
112
Fungal subdivision:
- Bread mold
- Meat tenderizer, birth control agents
- Rice disease "seedling blight"
- an alpha-proteobacterium, Burkholderia found growing within the fungus produces the toxin
Rhizopus
113
Ascomycota
- Sac fungi-ascus
| - Sexual ascospores, asexual conidiospores
114
Fungal subdivision:
- Sac fungi-ascus
- Sexual ascospores, asexual conidiospores
Ascomycota
115
Name 4 examples (genus) of Ascomycota
1. Saccharomyces
2. Aspergillus
3. Penicillin
4. Geomyces - white nose syndrome in bats (psychrophile)
116
Basidiomycota
- Club fungi
| - Basidium - bears sexual basidiospores
117
Fungal subdivision:
- Club fungi
- Basidium - bears sexual basidiospores
Basidiomycota
118
Name 2 examples of Basidiomycota (1 genus and species)
1. Mushrooms
| 2. Cryptococcus neoformans
119
Name the 2 genus of mushrooms
Agaricus and Amanita
120
Agaricus
Edible mushrooms
121
Amanita
- Includes death angle
- Amanitin - peptide toxin
- Targets RNA polymerase
122
Cryptococcus neoformans
- Pathogen in AIDS and other immunocompromised
- Basidiospores inhaled
- Source: pigeon droppings
- Infects lung and CNS
- Can cross the blood-brain barrier
- Virulence factors
- Capsule/polysaccharide
- Melanin type pigment production
123
Eukaryotic microorganisms
- Prominent members of ecosystems
- Useful as model systems and in industry
- Some are human and plant pathogens (among the 20 most frequent microbial causes of death world-wide, 6 are eukaryotic)
124
Name the 2 groups of eukaryotes.
Protists and Fungi
125
Common features of eukaryotic cells
- Sexual and asexual reproduction
- Meiosis, mitosis
- Membrane-bound nucleus
- Plasma membranes (lipid bilayers)
- Many have cell walls
- Membrane-enclosed organelles
126
Asexual reproduction
Binary fission or budding
127
Sexual reproduction
Sexual cells called gametes fuse to form diploid zygote
128
Endoplasmic Reticulum
Protein synthesis - ribosomes
129
Golgi apparatus
Chemical modification, packaging, secretion
130
Mitochondria
- Powerhouse of cell - ATP by electron transport and oxidative phosphorylation
- Site of TCA cycle (major generator of reducing power)
131
General features of Protists: (Domain? How many life forms? Unicellular or cellular? Examples? Where are they found? Are they parasitic? Are they motile? How do they reproduce?)
- Domain: Eukarya
- >60,000 different life forms
- Mostly unicellular
- Examples: Algae (photosynthetic), slime molds, and protozoa (chemoorganotrophic)
- Terrestrial or aquatic
- Some parasitic in humans, animals, and plants
- Motile (contain: cilia, flagella, pseudopodia)
- Reproduction: sexual and/or asexual
132
Importance of protists
- Important link in food chains
- Plankton in aquatic habitats
- Radiolarians, Diatoms, Foraminiferans
- Silica, calcium carbonate walls
- Reef formation, beach sand, limestone
133
Radiolarians
- Protozoa that produce intricate mineral skeletons
| - Have an internal skeleton made of siliceous materials (silica)
134
Diatoms
- The most common type of phytoplankton
| - Have a distinctive, 2-piece cell wall of silica called a frustule
135
Protozoa
Chemoorganotrophic
136
Algae
Photosynthetic
137
___ are protists with 2 types of nuclei
Ciliates
138
Name the 2 types of nuclei
Micronucleus and macronucleus
139
Micronucleus
"True nucleus", mitosis
140
Macronucleus
Thousands of short, linear chromosomes (genes for growth)
141
2 features of vacuoles:
1. Contractile
- Osmoregulatory
- Expel water
2. Phagocytic
- Food digestion
142
Endocystment
- Development into dormant stage - cyst
| - Protection, transmission
143
Excystment
Escape from cyst to metabolically active, motile form - trophozoite
144
Trophozoite
The escape from cyst to metabolically active, motile form
145
Metabolism
- Can be photosynthetic (oxygenic)
| - Also chemoorganoheterotrophs and mixotrophs (organic and inorganic)
146
Nutrition
- Solid nutrients by phagocytosis
| - Soluble nutrients by facilitated diffusion and active transport
147
Chlamydomonas (protists)
- Single-celled green algae
- Cell wall of cellulose
- Photosynthetic
- Motile
- Stigma (eyespot) role in phototaxis
- Sexual and asexual
148
Cellular slime molds (protists): Genus?
- Genus: Dictyostelium
| - Formation of a slug
149
Slug formation
1. Free-living amoeboid cells aggregate to form slug (signal = cAMP)
2. Motile slug (20,000 cells)
3. Fruiting body with spores
4. Spores germinate back to free-living amoeboid cells
- Nutrition depletion and stress can signal for initiation of fruting body
150
Giardia
- Protozoan parasite
- Human pathogen
- Cyst ingested
- Trophozoites attach to intestine
- Disrupts nutrient, water flow
- Animal reservoirs, human carriers
- Sucking disc (for attachment)
151
___ is the motile protist form of Giardia
Trophozoite
152
Naegleria fowleri
- Free-living, aquatic, amoeba
- Thermophile: warm, nutrient rich, fresh water
- 3 forms
153
Name the 3 forms of Naegleria fowleri:
1. Trophozoite (infectious)(enters nose, travels to brain)
2. Cyst
3. Flagellate
154
What disease is caused by Naegleria fowleri
Amebic meningoencephalitis
an infection of the brain by the free-living protist Naegleria fowleri, also known as the "brain-eating amoeba"
155
The Alveolata (group of protists) includes what 3 groups:
The Dinoflagellates, Ciliates, and the Apicomplexans
156
The Dinoflagellates (to whirl)
- Most commonly found in marine plankton
- Nutrition: photoautotrophy, heterotrophy, and mixotrophy
- Some are responsible for the phosphorescence seen in seawater
- Each cell bears 2 distinctively placed flagella: cause the cell to spin as it is propelled forward
- Have alveolar sacs lying just under the plasma membrane (armored with alveolar sacs)
- Have trichocysts (when attacked, they shoot out from the cell as a means of defense)
- Most are free-living
- Endosymbiotic dinoflagellates that live as undifferentiated cells occasionally send out motile cells called zooxanthellae
- Are responsible for toxic "red tides" that harm other organisms
157
Ciliates
- Chemoorganotrophic
- Employ many cilia for locomotion and feeding
- A few species have tentacles for the capture of prey
- Some can discharge toxic, threadlike darts called toxicysts, which are used in capturing prey
- Have the ability to quickly entrap many particles by the action of the cilia around the buccal cavity
- 2 types of nuclei: macronucleus, micronucleus
- Free-living, but symbiotic forms also exist
158
Aplicomplexans
- Are either intra- or inercellular parasites of animals
- Are important causes of human diseases
- Apical complex (located at the end of the cell)
- Calcium and enzyme release to penetrate host cells
- Apicoplasts - this makes them attractive targets for the development of drugs to inhibit the growth of pathogenic apicomplexans
- Both sexual and asexual reproduction
- The motile, infective stage is called the sporozoite
159
Name the 3 types of diseases of Apicomplexans:
Cryptosporidiosis, Toxoplasmosis, Malaria
160
Name the genus for Cryptosporidiosis
Cryptosporidium
161
Name the genus for Toxoplasmosis
Toxoplasma
162
Name the genus and species for Malaria
Plasmodium falciparum
163
Cryptosporidiosis (disease)
- Transmitted in contaminated water (feces from infected person or animal)
- Milwaukee 1993, 400,000 cases
- Oocysts ingested: small, chlorine resistant, stable
- Excystment to become trophozoites in intestine
164
Toxoplasmosis (disease)
- Oocysts from raw or undercooked meat, cat feces
- Mice are natural reservoir
- Cats also hosts, required to complete sexual cycle
- Ingested oocysts become tachyzoites - localize in neural and muscle tissue
- Can enter brain and can cross placenta
- Infection triggers permanent long-term behavior change in mice (mechanism unknown)
165
Malaria (disease)
- Caused by 4 species of Plasmodium
- Plasmodium falciparum
- Transmitted by bite of infected female Anopheles mosquito
- Sporozoite - motile form of parasite
- 300 million cases/year worldwide
166
Malaria (stages)
1. Sporozoites injected into human with saliva of mosquito
2. Within minutes, Sporozoite penetrates liver cell
- Erythrocytic cycle in blood
3. In liver, Sporozoites become Merozoites
4. Penetrates red blood cell; parasite forms knobs on red blood cells surface
5. Release more Merozoites
6. Merozoites reinvade red blood cells
7. Gametocytes taken into mosquito stomach with blood meal
8. Sexual (Gametocytes -> Sporozoites)(restarts cycle)
167
Malaria - clinical
- Periodic chills, fever
- Anemia
- Liver, spleen - hypertrophy
168
Malaria - control, prevention, treatment
- Mosquito control: wetland drainage, insecticides, bed netting
- Drugs: Chloroquine, malarone
169
Chloroquine
- Plasmodium degrades hemoglobin as a nutrient
- Releases toxic heme (iron rich component)
- Parasite polymerizes into non-toxic form
- Drug blocks polymerization
170
Malarone
A drug that blocks electron transport and pyrimidine synthesis in Plasmodium
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Adaptive (Specific) immune response
- Discriminates between self and non-self
- Has specificity and memory
- Slower than innate (during primary infection)
- Components: antibody, antigen receptors, Major Histocompatibility Complex (MHC)
- Main cells: B and T cells (lymphocytes)
- from stem cells in bone marrow
- B cells mature in bone marrow
- T cells mature in thymus
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Adaptive immune system (definition)
Immune system based on lymphocytes (T, B, and Natural Killer cells). Has specificity and memory, responsible for efficacy of vaccines
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The 2 branches of adaptive immunity
Humoral and cell-mediated
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Humoral branch of adaptive immunity
- Involves antibodies (made by B cells)
| - Defends against extracellular pathogens
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Cell-mediated branch of adaptive immunity
- Involves T cells
| - Largely defends against intracellular
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B lymphocytes (cells) (definition)
Generated and develop in the bone marrow. Use antibodies as antigen receptors. Naive B cells express their antibody molecules on the cell surface, activated B cells can secrete their antibodies. A mature, activated B cell is called a plasma cell
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While innate immune responses are often initiated at ___, adaptive immune responses are often initiated in ___ and ___
Sites of infection; lymphoid organs and tissues
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Primary lymphoid organs and tissues
- Where lymphocytes mature
| - Thymus, bone marrow
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Secondary lymphoid organs and tissues
- Where lymphocytes engage antigen
| - Spleen, lymph node
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B-cells
- Make antibodies (and also use them as receptors)
- Are antigen-presenting cells
- Activated by antigen and/or T cells
- Develop into: 1. plasma cells (activated by B cells) - produce and secrete antibodies; 2. memory cells
- B-cell activation by antigen and helper T cells -> antibody secretion by plasma cells
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Antigens (definition)
Substances capable of being recognized by antigen receptors. An antigen can have multiple epitopes - regions that can stimulate the production of, and combine with, specific antibodies
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Antigen receptors (definition)
Immunoglobulins for B cells, T cell receptors for T cells
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Antibodies (Immunoglobulin)
- Proteins made by B cells
- Defend against extracellular pathogens
- Attached to B cell surface or free in blood and tissues
- Bind antigens - neutralize or opsonize
- Affinity - strength that antibody binds antigen
- Epitopes - parts of an antigen that antibodies bind
- One antigen can have several epitopes, each can bind a different antibody
- 5 classes
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Name the 5 classes of antibodies (Immunoglobulin)
- IgM (one of the 1st classes made, first to appear), IgG (main in serum, most abundant), IgA (secretory Immunoglobulin. secretory antibody), IgE and IgD
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Antibody structure
- 2 identical heavy chains
- 2 identical light chains
- Di-sulfide bond holding the 2 identical heavy chains together and holding the heavy chain to the light chain
- Antigen binding site: between the heavy chain and light chain (Di-sulfide bond)
- Variable region - top part of heavy chain and light chain
- Constant region - The entire lower part of heavy chain and light chain
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Major mechanism for how our naive immune system is able to recognize millions of possible foreign antigens?
Rearrangement of antibody gene segments
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VDJ joining
- Forming a gene for the heavy chain of an antibody
- RAG genes - rearrangement proteins
- Takes place only in B cells
- DNA--V segments---D segments---J segments--- Constant region exons
1. D to J recombination
2. V to DJ recombination
3. Transcription, splicing
- mRNA--V segment---D segment---J segment--- Constant region exons (3) -AAA
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Clonal selection
- VDJ joining occurs as B cells develop in bone marrow - occurs before infection!
- Generates vast array of B cells, each preprogrammed to bind a specific antigen
- B cells travel to lymphoid organs and tissues
- Upon infection, antigen "selects" B cell with antibody that matches it
- B cell proliferates, forming clone of identical cells, each with antibody for the antigen
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Phylum Deinococcus - Thermus
Heat, radiation resistant
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The phylum Deinococcus - Thermus contains what 2 bacteria?
1. Thermus aquaticus
| 2. Deinococcus radiodurans
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Thermus aquaticus
- Grows at 70-75°C
- Source of Taq polymerase for PCR
- Thermophile
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Deinococcus radiodurans
- Deinococci are spherical or rod-shaped and non-motile
- Not thermophilic, but extremely resistant to radiation and desiccation
- Rapid DNA repair
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Phylum Cyanobacteria
- Oxygenic photosynthesis
- Primary producers in many ecosystems
- 2 photosystems (ATP and NADPH generated)
- Water as electron donor, produces oxygen (splits water)
- Uses calvin cycle to fix CO2
- Subcellular structures: thylakoid, carboxysomes, chlorophyll a/b
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The phylum Cyanobacteria contains what bacteria (genus)?
Anabaena
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Anabaena
- Gram-negative aquatic
| - Both oxygenic photosynthesis and Nitrogen fixation (N2 -> ammonia)
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Problem: The enzyme nitrogenase for N fixation is sensitive for O2 (Cyanobacteria, Anabaena). What is the solution?
Solution: differentiative vegetative cells into heterocyst cells devoid of O2
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How does this solution look? (phylum Cyanobacteria)
- Vegetative cells in a chain with a heterocyst cell in the middle
- Heterocyst cells contain: glutamate (N2->NH3-> glutamate)
- Vegetative cells contain: carbohydrates (CH2O)
- Vegetative cells generate carbohydrates from CO2 and release oxygen. These carbohydrates are fed to the heterocyst cell. The heterocyst cell generates glutamate and that is fed to the vegetative cells
- Vegetative cells use PSI and PSII Calvin Cycle
- Vegetative cell: a type of cell that can actively divide and give rise to new cells
- Heterocyst: Oxidizes the carbohydrates for electrons for the process of nitrogen fixation
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Phylum Chlamydiae
Obligate intracellular
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The phylum Chlamydiae contains what bacteria?
Chlamydia trachomatis (pathogen)
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Chlamydia trachomatis
- Gram-negative obligate intracellular
- Human and animal pathogens
- Causes #1 reported STD in U.S.
- Unique developmental cycle
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What are the 2 types of Chlamydia cells?
Elementary Body (EB) and Reticulate Body (RB)
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Elementary Body (EB)
A dormant cell type, infectious form, attaches, enters and develops into a reticulate body
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Reticulate Body (RB)
Reproductive, non-infectious, intracellular, develops back into EB-cell lysis
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Phylum Spirochaetes
- Flexible, helical shape
- Gram-negative
- Flagella within periplasm (axial filament, flagella rotation turns whole cell)
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The phylum Spirochaetes contains what 2 bacteria (pathogens)?
1. Treponema pallidum
| 2. Borrelia burgdorferi
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What disease is caused by Treponema pallidum?
Syphilis
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What disease is caused by Borrelia burgdorferi?
Lyme disease (ticks)
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Phylum Bacterioidetes
Obligate anaerobes
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The phylum Bacterioidetes contain what bacteria (genus)?
Bacteroides
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Bacteroides
- Anaerobic, gram-negative
- Major component of intestinal microflora
- Degrade complex, dietary polysaccharides
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Phylum Proteobacteria
- Largest group of bacteria
- Gram-negatives
- 5 major classes
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What are the 5 major classes of Proteobacteria?
Alpha, beta, gamma, delta, and epsilon
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Why are Proteobacteria considered to be diverse cell forms and metabolism?
- Heterotrophs, phototrophs, and lithotrophs
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Some alpha Proteobacteria are ____ meaning that they perform ___ photosynthesis. They use how many photosystems? Do they use chlorophyll?
- Photohetertrophs
- Anoxygenic photosynthesis
- Utilize a single photosystem
- Uses bacteriochlorophyll
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Name the bacteria (genus) is associated with photoheterotrophs alpha Protobacteria.
Rhodospirillum (anaerobic)
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Some alpha Proteobacteria are ___ meaning that they are organisms that live ___ ___ ___.
- Endosymbionts
| - Organisms that live in other organisms
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Name the 3 bacteria (genus) that are associated with endosymbionts alpha Protobacteria.
1. Rhizobium (root nodules, nitrogen fixing bacteria)
2. Agrobacterium (plant tumors, galls on plants)
3. Rickettsia (in plants, obligate intracellular bacteria)(Rocky mountain spotted fever, tick)
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Name another bacteria (genus) that is a alpha Protobacteria.
Caulobacter
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Caulobacter
- Gram-negative aquatic (fresh and marine) bacterium
- Dimorphic
- Cell division generates: 1) motile swarmer cells and 2) non-motile stalked cells
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Caulobacter life cycle
1. Motile Swarmer cell (can't replicate DNA
2. Flagella is lost/ejected
3. Stalk formed where the flagella use to be (can replicate its own DNA)
4. Begins to divide and a swarmer cell/flagella is formed
5. Separates: motile swarmer cell and a non-motile stalked cell
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Beta Proteobacteria
- Some are lithotrophs (use inorganic compounds as electron source)
- Nitrate, sulfur, iron oxidizers
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Name a bacteria (genus) that is a beta Proteobacteria.
Nitrosomonas
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Nitrosomonas
- Oxidizes ammonia to nitrite
| - 1st step of nitrification
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Name a bacteria that is an important human pathogen.
Neisseria meningitidis (gram-negative cocci)
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Gamma Proteobacteria includes ___ and ___
Enterics (associated with intestinal tract) and Non-Enterics
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Enteric gamma Proteobacteria
Facultative anaerobes, often motile rods
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Name 3 bacteria (genus) that are Enteric gamma Proteobacteria.
Escherichia coli, Salmonella, and Proteus
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Escherichia coli
Some strains normal inhabitants of intestine, others pathogenic (0157:H7)
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Salmonella
Food poisoning
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Proteus
Urinary tract infections
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Name 2 bacteria that are Non-Enteric gamma Proteobacteria.
Pseudomonas aeruginosa and Shewanella
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Pseudomonas aeruginosa
Opportunistic pathogen
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Shewanella
- Non-pathogen, aquatic and soil
| - Extracellular electron transport
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Name 2 bacteria (genus) that are delta Proteobacteria
Myxococcus and Bdellovibrio
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Myxococcus
- Gram-negative, social, soil bacteria
- Attack other bacteria in packs
- Gliding motility (no flagella)
- Nutrient limiting conditions, cells assemble into fruiting bodies (with dormant myxospores)
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Myxococcus fruiting body formation
1. Aggregate - stress, starvation signal aggregation
2. Fruiting body (with myxospores at top
3. Myxospore
4. Cells exit from spore state and return to vegetative cells where the cycle can restart again
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Bdellovibrio
- Parasitizes other bacteria
- Grows in periplasm
- Lyses host
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Epsilon Proteobacteria
- Smallest group of Proteobacteria
| - Gram-negative rods
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Name the 2 bacteria (genus) in epsilon Proteobacteria that cause disease in humans.
Campylobacter and Helicobacter
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Campylobacter
- Heterotrophs
- Contain both nonpathogens and species pathogenic
- Can cause a variety of conditions ranging from: septicemia (pathogens or other toxins in the blood) to enteritis (inflammation of the intestinal tract
- Development of Guillain-Barre syndrome (GBS), the most common form of flaccid paralysis
- Grastroenteritis - inflammation of the stomach and intestine with subsequent diarrhea
- Campylobacteria are transmitted to humans by contaminated food and water, contact with infected animals, or anal-oral sexual activity
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Helicobacter (H. pylori)
- Isolated from the stomachs and upper intestines of humans, dogs, cats, and other mammals
- Causes gastritis and peptic ulcer disease
- Obligate Microaerophile
- Spore formers
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Phylum Firmicutes
- Low-GC gram-positives
| - Includes pathogens and good bacteria
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Name are the 2 bacteria (genus) that are pathogens associated with the phylum Firmicutes. Name the 2 bacteria (genus) that are good bacteria that are associated with the phylum Firmicutes.
1. Staphylococcus (MRSA) and Streptococcus
| 2. Lactobacillus and Lactococcus (fermentation produce lactic acid)(found in probiotics, cheese, yogurt)
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Name the 2 major genera of the spore formers of the phylum Firmicutes.
1. Clostridium
| 2. Bacillus
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Name the 2 bacteria (genera Clostridium) associated with spore formers Firmicutes.
1. Clostridium difficile
| 2. Clostridium botulinum
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Clostridium difficile
Causes colitis (inflammation of colon)
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Clostridium botulinum
Makes a neurotoxin (Botox)
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Name the 3 bacteria (genera Bacillus) associated with spore formers Firmicutes.
1. Bacillus subtilis
2. Bacillus anthracis
3. Bacillus thuringiensis
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Bacillus subtillis
Non pathogenic
250
Bacillus anthracis
Pathogenic
251
Bacillus thuringiensis
Makes insecticidal toxin (Bt corn)
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Bacillus sporulation
- Adaptive response to starvation
- 8-10 hours to make a spore
- Mother cell, forespore
- Mother lysis, spore release
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___ is a dormant, stress resistant, but can germinate, becomes actively growing cell
1. Septum form asymmetrically
2. Mother cell engulfs forespore (covering forespore with another plasma membrane)
3. Then mother adds cortex of peptidoglycan and coat of protein and then lyses
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Sporulation requires gene expression at precise times and places
1. Sigma Factor cascade - A transcription factor that binds to RNA polymerase and causes it to turn on a different set of genes
2. Signal transduction cascade - sensor kinases sense starvation -> response regulators activate transcription of early sporulation genes
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Phylum Actinobacteria
- High G-C, gram-positive
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Name the 2 bacteria (genus) that are part of the phylum Actinobacteria.
1. Mycobacterium
| 2. Streptomyces
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Name the 2 species under the genus Mycobacterium
- Mycobacterium tuberculosis
| - Mycobacterium leprae
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Mycobacterium
- Acid-fast cells walls
| - Waxy lipids
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Streptomyces
- Form hyphae and mycelia
| - Source of many antibiotics
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Name a bacteria that is a beta Proteobacteria.
Nitrosomonas
