micro exam 2 (class 12, 13, 14, 15)

what are the macro nutrients?

-nutrients needed in large amounts

-C, H, O, N, P

what are the micronutrients?

-nutrients needed in smaller amounts

-S, K, Mg, Ca, Fe

what are the trace elements?

-needed in very small amounts, often enzyme cofactors

-Co, Zn, Mo (molybdenum), Cu, Mn, Ni

what are the growth factors?

-organic molecules that a microbe cannot synthesize but are necessary for growth

-vitamins (folic acid, riboflavin, B12, vitamin K), amino acids, nucleotides

what is the minimal medium for E. Coli? (prob don’t need to know)

-see table from class 12 lecture

-E. Coli is capable of synthesizing all it requires from a single carbon source, glucose

what is complex media?

-complex media: contain yeast/meat/plant extracts/digest and the exact chemical composition isn’t known

-ex: brain heart infusion

what is a chemically defined medium?

-the chemical composition is known

-ex: minimal essential medium

what is MSA, mannitol salt agar?

-MSA is a selective medium for staphylococcus (genus grows on skin which is salty)

-has 7.5-10% NaCl, supports growth of salt loving bacteria like Staph while inhibiting gram negative bacteria

-differential medium

-mannitol fermenting staph cause pH change (phenol red → yellow) ex: S. aureus

what is a differential medium?

a differential medium can distinguish bacteria by change of color in colony/and or medium

what are the different types of carbon source microbes?

-autotroph (CO2)

-heterotroph (organic compounds in environment)

what are the different types of energy source microbes?

-phototroph (light)

-chemotroph (oxidation of inorganic or organic compounds)

what are the different types of electron source microbes?

-organotroph (organic compounds)

-lithotroph (inorganic, “rock eater”)

we saw a picture of cyanobacteria that were green growing on a rock crystal. what is their nutritional category?

-photolithoautotroph

-photo because green, litho because rock, auto because photosynthesizes and uses CO2

we looked at E. Coli which live in the gut. what is their nutritional category?

-chemoheteroorganotroph

-chemo because oxidizes compounds, hetero because uses organic compounds for energy (not CO2), organo because uses organic compounds as electron source, there is no light in the gut so couldn’t be photo

what is microbial growth defined as?

-microbial growth = increase in number of cells

how does microbial cell division occur by?

1. binary fission (in most bacteria)

2. budding (yeast or some bacteria like Caulobacter)

3. filamentous growth (fungi and actinomycetes bacteria)

how does binary fission happen? are planes of cell division specific to species?

-chromosome replication begins, one copy of origin moves toward other end of cell

-replication continues, one copy of origin now at each end of cell

-replication finishes, plasma membrane grows inward and new cell wall deposited

-two daughter cells result

*planes of cell division are species specific

what are some ways of measuring growth of a population of bacteria?

-change in bacterial cell number (direct cell count)

-change in turbidity or light scattering of the culture (indirect cell count)

-change in amount of a cellular component (indirect cell count)

how would you quantify a living bacteria? what is one way to count individual cells? how could you quantify growth in a liquid culture? (might not be tested on this)

-living bacteria: try a viable count to get the titer, directly count the colonies to quantify

-count individual cells with a hemocytometer

-liquid culture: spectrophotometer measure turbidity

what are the 4 stages of growth in culture?

1. lag phase

2. log (exponential) phase

3. stationary phase

4. death (decline) phase

what happens in the lag phase of bacterial growth?

-lag phase: synthesizing proteins/enzymes, preparing for growth an repairing cells damaged from the transfer to a new environment

what happens in the log phase of growth?

-log phase: exponential growth → cells are undergoing binary fission, population^number is increasing in size, constant growth + metabolic rate

what happens in the stationary phase of bacterial growth?

-stationary phase: waste increases, nutrients decrease and population^number growth stalls

-the number of new cells = number of dying cells, a switch to survival mode

-time for forming spores and producing antibodies, expression of virulence factors like toxins

what happens in the death phase of bacterial growth?

-death phase: waste increases even more, nutrients decrease even more as the cells die in great numbers more than they are dividing

-exponential decrease in viable cells

-cells are lysing and releasing nutrients

-the cells still dividing are called persistor cells which might not respond to antibiotics, are associated with chronic infections

if you were trying to test a bacterial culture for antibiotic sensitivity, what phase would you target?

-to test for antibiotic sensitivity, target the log phase where there is constant growth and metabolic activity, exponential growth

if you were trying to test for antibiotic production which stage of bacterial growth would you target?

-to test for antibiotic production target the stationary phase because this is when the bacteria have switched to survival mode

what are the different temperature preferences of bacteria and what optimal range exist for each temperature preference?

-psychrophile → grows only below 20C

-mesophile → optimal 20-45C

-thermophile → optimal 45-80C

-hyperthermophile → optimal above 80C

what are psychrotrophs?

-psychrotrophs have different growth rates in the psychro and meso temp ranges

-grow slowly at temps <20C

-are optimum in mesophile range

-ex: listeria monocytogenes

what are the characteristics of listeria (causes listeriosis)?

-gram positive

-rod shaped

-non-spore forming

-motile (temp dependent)

-catalase +, oxidase -

-beta hemolytic

-facultative anaerobe

where are some recent and ongoing outbreaks of listeria? what foods are involved?

-listeria outbreaks have occurred in rhode island, spain, south africa, other places in U.S

-foods like soft cheese, deli meats like Boar’s head, salmon, pasta

what are the symptoms of listeriosis? how long do symptoms last?

-nausea, vomiting, diarrhea

-24 hours -2 week gastrointestinal symptoms, but up to 70 days for symptoms to appear (long incubation period)

what are symptoms of severe listeriosis and who is at risk of dangerous listeriosis complications?

-severe infections: headache, stiff neck, convulsions, loss of balance, can be fatal

-if infection occurs during pregnancy, can be miscarriage, still birth, neonate death

what is a thioglycollate test?

-thyioglycollate test: contains reducing agent that lowers redox potential for the medium to negative level, suitable for anaerobic growth

-oxygen gradient in tube from high to low with a loose fitting cap

what is an obligate aerobe and what would its thyioglycollate tube look like?

-obligate aerobe: requires oxygen for growth and uses O2 as a final electron acceptor

-would be at top of tube near cap

what is an obligate anaerobe and what would its tube look like?

-obligate anaerobe: is killed/inhibited by oxygen, does anaerobic respiration with an alternative final electron acceptor, fermentation, methanogenesis

-may tolerate small % of O2 if produce catalase or superoxide dismutase

-would be at the bottom of the tube away from cap

what is a facultative anaerobe and what would its tube look like?

-can use O2 or grow anaerobically, does aerobic respiration when O2 is present and switches to fermentation or anaerobic when no O2

-spread throughout tube but more at the top of the tube near cap

what is an aerotolerant anaerobe and what would its tube look like?

-aerotolerant anaerobe: ignores O2, indifferent to oxygen

-uses fermentation and produces catalase and superoxide dismutase to detoxify reactive oxygen species

-spread throughout tube completely

what are reactive oxygen species (ROS)?

-ROS: highly unstable ions + molecules derived from partial reduction of oxygen that damage macromolecules/structure

-ex: peroxide (H2O2), hydroxyl radicals (OH*), superoxide (O2*, O2-), hypochlorite (OCl-)

what are the 3 main enzymes for dealing with toxic byproducts of the O2 lifestyle? how do they work?

1. catalase: converts H2O2 → O2 + H2O ( in lab we saw this with bubbles)

2. superoxide dismutase: breaks down superoxide

3. peroxidase: catalyzes oxidative reactions of peroxidase

what does the oxidase test do?

-oxidase test; tests for cytochrome c oxidase, a transmembrane protein used in aerobic respiration

what does an oxidase + result look like and mean? what about an oxidase - result?

-oxidase + = blue result → bacteria can use O2 for energy production with an electron transport chain

-oxidase - = no color change → no cytochrome c oxidase protein, the bacteria either can’t use O2 with the electron transport chain or use another cytochrome protein

go through the types of bacteria oxygen preferences one more time (answer is copied and pasted from class 14 slides)

Obligate aerobes → require O2 for growth

• Use O2 a final electron (e-) acceptor

• Produce catalase and superoxide dismutase to detoxify ROS

• Obligate anaerobes → killed or inhibited by O2

• Use anaerobic respiration (alternative final e- acceptor), fermentation,

methanogenesis.

• May tolerate small % of O2, if produce catalase or superoxide dismutase

• Facultative anaerobes → can use O2 or grow anaerobically

• Use aerobic respiration when O2 present

• Switch to fermentation or anaerobic respiration when no O2

• Aerotolerant anaerobes → ignore O2

• Use fermentation

• Produce catalase and superoxide dismutase to detoxify ROS

what are the characteristics of clostridium tetani?

-gram +

-rod shaped

-spore forming (tennis racket shape) spores infect wounds and cause tetanus

-obligate anaerobe

-motile

-catalase -, oxidase -

-alpha hemolytic intially, then beta

clostridium tetani is an obligate anaerobe and its spores infect wounds causing tetanus. how can an obligate anaerobe grow in a wound?

-clostridium tetani grows in damaged tissue that isn’t receiving adequate blood supply, deep wounds don’t get good blood supply so therefore no O2

what case study for tetanus did we discuss? what are some symptoms?

-6 year old wasn’t vaccinated, got tetanus on farm and was in hospital for 50+ days

-tetanus “lock-jaw”, jaw cramping

-muscle spasms and muscle stiffness, jerking, headache, fever

-complications include uncontrolled tightening of vocal chords, broken bones, difficulty breathing and possible death

what a recent tetanus outbreaks linked to?

-recent tetanus outbreaks linked to natural disasters and poor immunization rates

-ex: Indonesia outbreak following a tsunami

-cases in US are rising due to decreasing immunization rates

for this flashcard review notes from chapter 8 self study. what were big ideas?

-metabolism (catabolism and anabolism)

-auto-heterotroph

-electron carriers

-glycolysis (catabolism of glucose), Krebs cycle, aerobic respiration, fermentation, photosynthesis, calvin cycle

what are extremophiles?

-extremophiles: organisms that thrive in extreme conditions

-ex: pompeii worms

what did Carl Woese do? maybe look back at that assignment

-Carl Woese made a tree of life based on sequence similarity and discovered a new domain, archaea

-his ideas weren’t readily accepted

-Carl Woese wrote a letter to watson and crick

how do archaea differ from bacteria? think shape and cell wall/membrane, genome, metabolism

-archaea have more shapes (square or plate shaped)

-different structural features (archaellum instead of flagellum and hamus and cannulae for attachment)

-unique cell walls with a different version of peptidoglycan

-unique cell membranes (ether linked lipids instead of ester, phospholipid monolayer with branched side chains instead of bilayer)

-can have ‘s layer’ layer with glyco-proteins

-circular genomes more complex than bacteria, DNA wrapped with histones and a different RNA polymerase than bacteria

-use methionine instead of f-met as their first amino acid

-unique metabolism, don’t follow classic pathways like Krebs and glycolysis

-archaea don’t have nucleus or membrane bound organelles

what did Woese use for his sequence similarity tree?

-Woese used phylum proteobacteria based on 16S sequence similarity

-16S is a region of the 30S small subunit

-some were too long (23S) and some too short (5S)

what is the phylum proteobacteria? don’t need to know groups but they are mentioned in answer

-on top of the archaea discoveries, woese helped us recognize groups/phylum of gram negative vacteria called proteobactiera

-alpha proteo- nitrogen fixing

-beta proteo- arsenic resistance

-gamma proteo- human pathogens

-epsilon- gastric bacteria

eukaryotic and prokaryotic/archeae ribosomes are similar. what S do each use?

-prokaryote: 16S and 70S

-eukaryote: 18S and 80S

what is the benefit of 16S ribosomal RNA? where would you want primers to target?

-the 16S rRNA gene has highly conserved areas and variable regions

-you want primers to target conserved areas to bind, but then compare sequences in the variable areas

16S rRNA has sections that mutate quickly and ones that don’t, why is it important to design primers to detect highly conserved sequence?

-designing primers to detect highly conserved sequence will allow amplification of a wider array of bacterial species