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any process through which gaseous CO2 is converted into primarily through photosynthesis; making a Carbon-carbon bond
an organism that uses methane as its primary electron donor and source of carbon for carbon fixation
are named for the unique way of getting energy: they convert hydrogen gas and carbon dioxide into methane gas anaerobically
pathway of nitrification
use of reduced nitrogen compounds (NH3) as electron donor in aerobic respiration
Sulfate-reducing bacteria use sulfate as an electron acceptor (anaerobic respiration), converting the sulfate to hydrogen sulfide
a complex of several proteins, pigments, and other cofactors assembled together to execute the primary energy conversion reactions of photosynthesis; give rise to electron transfer
Light harvesting complex
Used by plants and phototrophic bacteria to collect more of the incoming light than would be captured by the reaction center alone
electron does not return to RC, makes NADPH, requires external electron donor (H2S, H2)
3 main classes of soilborne pathogens
Endospore Forming Firmicutes
Metabolically diverse Proteobacteria
Soli fungi (often dimorphic)
Spore structure for B. anthracis
Inner part; core that houses chromosome and is tightly complexed to protective proteins
Next layer; cortex with thick layer of membrane and peptidoglycan
Outside layer; coat, a protein shell
Final layer; exosporium, another protein shell
3 modes of entry for B. anthracis
1. Cutaneous anthrax
2. Pulmonary anthrax
3. Gastrointestinal anthrax
What is the composition and role of the capsule in B. anthracis?
Made of polyglutamic acid, inhibits phagocytosis
A protease that cleaves proteins called MAP kinase kinases involved in signal transduction
How can Pseudomonas aeruginosa grow in so many different environments?
can use many different compounds as carbon/energy source via aerobic respiration
is an opportunistic pathogen
What are the main virulence factors for P. aeruginosa?
1. Type IV pilli mediate attachment to cell membranes
2. can secrete alginate and other EPS to form biofilm in host tissues
3. secretes toxins and degradative enzymes (protein synthesis inhibitor and proteases to degrade host tissues and antimicrobial proteins)
4. injects effectors via Type 3 secretion system
5. Produces siderophores for iron acquisition
What is the significance of biofilm formation on P. aeruginosa?
hinders access to phagocytes, limits diffusion of antibiotics and complement proteins to bacteria
What are factors needed for Y. pestis growth in human host?
Must survive inside macrophages and effect immune cells (Yops), Yersiniabactin (siderophore), F1 protein capsule (antiphagocytic), Psa (antiphagocytic) and Pla protein (degrades C3b and C5a and degrades clots)
Y. pestis infection that invades the lungs and eventually moves to bloodstream; can develop from bubonic or septicemic plague in primary infection then directly in secondarily infected patients
Life cycle of plasmodium
Sporozoites injected during bite and travel through blood to liver. Sporozoites develop in liver cell and multiplies to form the schizont which is made up of thousands of merozoites which bursts into the cytoplasm of the liver cell and enters the bloodstream to invade RBC, form vacuoles and replicate
Describe the basic process of liver infection of Plasmodium
Sporozoites travel through liver, glide over blood vessel lining and interact with heparan sulfate proteoglycan (HSPGs). They cross the endothelial barrier and migrate through liver cells. When reach the final cell, forms parasitophorous vacuoles, develop, multiply inside vacuole, and form schizant (thousands of merozoites) vacuole bursts and merozoites enter bloodstream
What is the significance of apical complex in RBC infection by Plasmodium
apical complex allows merozoites to rapidly invade RBC
What are 2 unique features of RBC that impact the ability of Plasmodium to grow and replicate inside RBC?
1. have no nucleus or ability to synthesize new proteins or lipids, cannot endocytose/exocytose
2. Do not present MHCI for antigen
How do the symptoms of uncomplicated malaria result from pathogen infection of RBC?
Destruction of RBC causes chills, fever, and sweats
How do the symptoms of severe malaria result from features associated with P. falciparum and its effects on RBC properties
Infected RBCs adhere to each other and uninfected RBCs and adhere to the lining of small blood vessels. This damages blood supply, tissues and organs. Decreased oxygen supply can lead to acidosis, brain infection, and severe anemia
DefinitionS of fermentation
1. Method to preserve fresh food via microbial production of preservatives
2. metabolic pathway using substrate level phosphorylation for ATP generation
3. growing microbes in large amounts
4. Incubating product for awhile until it changes (non microbial)
Sugar converted to lactic acid (glucose > pyruvate > lactic acid) net energy= 2 ATP/glucose
fermentation to ethanol and CO2 without lactic acid (used by bacteria and yeast)
yeast and lactic acid bacteria degrade the sugars and produce lactic acid and ethanol. the ethanol is used by acetic acid bacteria to make acetic acid. This product formation inhibits the growth of spoilage organisms.
Basic biology of Campylobacter jejuni
thermophile (42degreesC) survives well at 4degreesC not salt tolerant, sensitive to drying, pH, high O2, microaerophile (prefer 5% O2) capnophile (need increased CO2)
pathogens decorate their surface with molecules that mimic host cell surfaces, in Campylobacter involves recognition of LOS on the bacterium and similar sugars on human cells.
Basic biology of Listeria monocytogenes
Gram positive Firmicute (related to S. aureus), salt tolerant to 10% NaCl, acid tolerant to pH 4.5, Psychotroph (optimal growth 30-37degreesC, grows 1-45degreesC), Ubiquitous in the environment (found in water, soil, fresh and decaying plants, intestine of healthy animals)
2 different meanings of enteric pathogen
1. Causes disease in GI system
2. belonging to the Enterobacteriaceae
Probiotic E. coli
produces antimicrobials, exceptionally good colonist, no virulence factors, modulates immune system
EnteroPathogenic E. coli; developing countires, major cause of infant death, person-person spread possible
EnteroAggregative E. coli; children in developing countries; diarrhea with dehydration; growth retardation; chronic
disruption of intestional barrier function, water absorption and ion balance, causes diarrhea
EPEC inital attachment mechanism
Bacterium binds to host cell, T3SS is induced and injects effectors into host (Tir)
Intimin and Tir
adhesions of EPEC; Tir injected into host cell by T3SS and binds to intimin (bacterium outer membrane protein), induces cytoskeletal changes, produces pedestals and destroys normal microvilli structure
EPEC proteins; effacement of microvilli, mitochondrial dysfunction, affects ion transporters, affects tight junctions
AB toxin of Shinga toxin
B subunit= binds host glypolipds (kidney and intestine) A subunit= enters cell, cleaves RNA, kills cell
Attachment mechanism of EAEC
adhesions= Aggregative adherence fimbriae (AAF), forms biofilms, several toxins
What is different about Shigella?
Human only colonist, low infectious dose, spread person-person via fecal-oral, causes shigellosis: sever inflammation of colon with strong abdominal cramps, fever, and bloody/mucous stool
What is the effect of Shigella?
1. Taken up by M cells in colon: undergo phagocytosis, escape phagosome
2. Invade and kill macrophages: induce inflammation
3. Invade intestinal epithelial cells and replicate: induces inflammatory response, peptidoglycan released by shigella is recognized by PRRS, taken up by cells via T3SS, spreads cell-cell via actin-based motility
4. Neutrophils: arrive and eventually kill shigella, disrupt tight junctions, promote shigella access to underlying layer
What is the normal site of colonization for the ExPEC strains?
Colonize intestinal tract but don't cause disease there, if translocated to another location in body, has ability to cause disease if has appropriate virulence factors
-Urinary tract, blood, CNS
Not the same as GI pathovars
Moderately resistant microbes
protist cysts, some fungal spores, naked viruses, Mycobacterium, Staphylococcus, Pseudomonas
Least resistant microbes
most vegetative bacterial cells, some fungal spores, fungal and protist vegetative cells, and enveloped viruses
What are the main cellular targets for chemical control agents?
dissolve membranes, dentature proteins, modify (inactivate) proteins or DNA
chemical control agents
solubility in water or alcohol matters, must consider toxicity to non target organisms, presence of other organic material is important
selective toxicity in antimicrobial function
highly specific to one or very few targets in cell, target is present in microbe but NOT in host
How is MIC measured?
1. inoculate plate with liquid culture of test organism
2. antibiotic discs placed on surface of agar plate
3. incubate 24-48 hours
4. test organism shows susceptibility to some antibiotics indicated by inhibition of bacteria growth around discs
Steps of peptidogylcan synthesis
1. NAM is linked to peptide
2. special amino acid synthesis
3. transfer of NAM-peptide to bactoprenol carrier
4. addition of NAG to make PG subunit
5. transfer across membrane
6 & 7. incorporation into existing PG via transpeptidases and transglycosylases
8. Recycling of bactoprenol
Steps of cell wall disrupting antimicrobials
1. cycloserine: inhibits special amino acid synthesis (step 2)
2. Vancomycin: binds to peptide and inhibits addition to existing PG (steps 6&7)
3. Beta-lactams: inhibits transpeptidases (steps 6&7)
4. Bacitracin: inhibits recycling of bactoprenol (step 8)
How do antimicrobials that inhibit DNA replication work?
Quinolones inhibit DNA gyrase in bacteria, target bacterial RNA polymerase, target many steps of protein synthesis
What are some non-target effects of antimicrobials?
toxicity to host, allergies, alteration of microbiota (microbiota shift diseases)
What are the mechanisms of specific resistance to antimicrobials?
Intrinsic resistance- lack target, impermeable
Acquired resistance by mutation or horizontal gene transfer
Acquired resistance by mutation or horizontal gene transfer
1. reduced permeability of cell to antibiotic
2. inactivation of antibiotic
3. alteration of target
4. development of alternative pathway
5. Efflux of antibiotic out of cell (efflux pumps)
6. growth of biofilms helps cells resist killing
Resistance to Quinolones
1. change in target (gyrA or gyrB)
2. Decrease in OM permeability
3. Increase in efflux pump activity
4. drug modifying activity
What are the basic steps in cloning a piece of DNA?
1. prepare DNA purified DNA or PCR
2. select and prepare vector
3. digest DNA and vector with restriction enzymes
4. ligate DNA and vector
5. introduce to host and select clones
Describe the requirements for PolymeraseChainReaction
Relies on basic DNA biology
denaturation and rennaturation of DNA, complementary hybridization of DNA strands, microbial DNA polymerase
Uses a simple machine (thermal cycler)
1. create reaction mix (primers determine the DNA to be amplified)
2. Denaturation (raise temperature to denature with heat)
3. Primer annealing (cool to allow primer annealing)
4. Extension (polymerase extends primers and makes DNA)
What types of microbes produce polymerases useful for PCR?
Thermus aquaticus (Taq polymerase)
Hypothermophilic Archaea (produce vent polymerase)
Basic features of plasmids needed for good cloning vector
1. antibiotic resistance marker
2. restriction enzyme sites
3. origin of replication
What are two important features of how restriction enzymes recognize their target DNA site and how they cut the DNA?
1. Digest DNA at specific sequences- recognition sequences are usually palindromes of 6 bases in length, cutting DNA to leave staggered ends of single stranded DNA
2 insert genes into plasmid- identify a palindromic recognition site, attach same recognition site to the cDNA gene, add restriction endonuclease, sticky ends rest, insert gene into plasmid
Processing and activation of Bt toxin by insect
1. ingestion 2. alkaline pH of insects digestive tract causes release of protoxins 3. host proteases process into active toxin 4. specific receptor in insect gut (determines insect specificity) 5. death of insect larva
Retroviruses in gene therapy
1. insert RNA versions of normal allele into retrovirus
2. retrovirus infect bone marrow cells removed from patient and cultured
3. viral DNA carrying normal alleles inserts into chormosome
4. inject new cells back into patient
Listeria monocytogenes as antigen delivery system
1. cytoplasmic location allows entry o f antigens into MHCI antigen processing pathway, leads to priming of specific CD8+ T cell responses
2. attenuated Listeria expressing antigens may direct cellular immune response to area
Not directly involved in normal growth, development, or reproduction of an organism
antibiotics, anticancer agents, immunosuppressive drugs
Major roles of microbes in wastewater treatment
Primary= separate solids from liquids
Secondary= Microbes!! biological to remove organic material and pathogens
Tertiary= allows reentry of products into environment
biological oxygen demand, rough measure of available organic material used for aerobic respiration
why is proper floc formation important for wastewater treatment?
controlling biomass removal (microbes by EPS productions)
Why is microbial degradation of toxins important?
microbes can degrade insecticides, herbicides, and other toxins, some recalcitrant
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