BIOL310 Microbiology Spring 2015, Exam I study guide. Dr.

LaMontagne
Keywords: cocci, bacilli, spirilla, peptide, peptidoglycan, lipopolysaccharide (LPS), penicillin, hopanoid,
glycocalyx, virulence, endospore, germination, chemotaxis, CFU, MPN, chemostat, turbidostat,
generation time, halophile, acidophile, thermophile, thymine dimers, catalase, SOD, biofilm, quorum,
HSL, hydrophobic, hydrophilic, phospholipid, glycerol, saturated hydrocarbon, archaea, ribosomes,
nucleus/nucleoid, undulipodium, thylakoid, stoma, rubisco, ribosomes (rRNA copy), thallus, chitin,
heterotrophs, budding, YM shift, hyphae, coenocytic, septum, mycelium, diploid, haploid, autotrophs,
dimorphism, enthalpy, entropy, free energy, photoautotrophs, chemolithoautotrophs, respiration, NAD,
equilibrium constant, ATP, allosteric, feedback inhibition, cytochromes, ribose, glucose, fermentation,
acetyl-CoA, pyruvate
Describe the observations by Hooke (1665) and van Leeuwenhoek (1684) that lead to the discovery of
microorganisms and the experiments Needham (1745) and Pasteur (1864) conducted that refuted the
theory of spontaneous generation. Explain the significance of endosporulation in Needhams work.
Explain how Lister (1867) used phenolics to introduce antiseptic technique to surgery. List Kochs
postulates and discuss how these postulates relate to the Germ Theory of disease and discuss limitations
of these postulates in relation to normal microflora, yet-to-cultured bacteria, horizontal gene transfer and
opportunistic infections.
Estimate the age of the earth and when life and oxygenic photosynthesis first appeared. Explain the
importance of oxygenic photosynthesis in the development of complex macroorganisms (like you) in
terms of free energy. Sketch a phylogenetic tree of life as generated by sequencing of ribosomal genes
and identify branches for the domains (archaea, bacteria, eukarya). Include branches for animals, plants,
fungi, extreme halophiles and methanogens. Add branches for chloroplasts, cyanobacteria, mitochondria
and proteobacteria and discuss how that topology relates to the endosymbiotic theory of cellular
evolution. Contrast the domains in terms of cell walls (chitin, cellulose, peptidoglycan), ribosome size,
exons/introns, extremophiles, cellular size, reproduction (binary fission / budding / meiosis), membrane
bound organelles, cytoskeleton, chromosome (linear/circular; single/multiple), motility
(flagellum/undulipodium/cilia), membrane lipids, and hopanoids.
Explain the significance of bacterial size in terms of surface to volume ratio, nutritional requirement for
phosphate, protein localization and cytoskeleton. Provide five bacterial morphologies and explain the
clinical significance of pleomorphy, with reference to Legionella (James 1995) and fungi (Nickerson
2006). Contrast spirilla and spirochetes. Contrast gram positives and negatives in terms of: cell wall
thickness, outer membrane, teichoic acid, LPS, and endosporulation. How do these structure relate to
sensitivity to penicillin and lysozyme?
Identify the metabolism of fungi. Contrast coenocytic morphologies with hyphae divided by septum.
Explain what we mean by the YM shift and how that dimorphism relates to quorum sensing and
virulence. Compare sexual reproduction in fungi to that in animals. Contrast these mutualisms and
explain the ecological and economic significance: lichens, ectomycorrhizae, endomycorrhizae.
Provide a balanced equation for oxygenic photosynthesis that combines the light and dark reactions.
Break that equation down into two half reactions and identify where they occur in chloroplasts. Show
half reactions for the oxidation of ribose and methane too. Identify halogens and noble gasses on a
periodic table and relate those columns electronegativity, reduction/oxidation potential and to the
formation of ionic, covalent and hydrogen bonds in terms of protons, electrons and neutrons for the
elements C, N, H and O. Sketch the building blocks of life (sugars, fats, amino acids and nucleotides).
Label these functional groups - methyl, carboxyl, carbonyl, and amine - and the formation of the

BIOL 310, Microbiology, Draft Exam I study guide 2

polypeptides and triglycerides by dehydration synthesis. Sketch a saturated and unsaturated fats and
identify which is more fluid and which is more reduced. Identify the hydrophilic and phobic poles of a
phospholipid and explain the role of hopanoids and saturation in membrane stabilization and fluidity
(Kaimura 1992). Describe the role of membranes and ATP in homeostasis, using the terms hypertonic
and hypotonic as wells as and diffusion, facilitated diffusion and active transport. Identify these
structures found in some bacteria PHA, volutin, ribosomes, and magnetosomes as organic or
inorganic and explain their function. Contrast these cytoskeleton structure in eukaryotes in terms of
composition and function: microtubules, microfilaments and intermediate filaments. Contrast pili,
fimbriae, flagellum, cilia and undulipodium. Discuss the dual roles of pili in HGT and electron transfer.
Contrast these glycocalyx types: capsule, slime layer and biofilm. Explain the clinical significance of
capsules and biofilms and provide experimental evidence of the role quorum sensing plays in biofilm
formation (Davies 1998).
Discuss the four phases of bacterial growth in batch culture and contrast batch with chemostat culturing.
Explain the role of quorum sensing in batch culture (You 1998). Relate rRNA copy number
(Klappenbach et al. 2000) to the life strategy (r vs k) of microbes with reference to adaptability and
endosporulation. Compare estimates of microbial biomass by CFU, MPN, direct counts (microscopy,
Coulter counters, flow cytometry) and turbidity. Which of these would give the highest and lowest
counts for clinical and environmental samples. Differentiate selective from differential media and
defined from complex media. Classify bacteria in terms of utilization or tolerance of oxygen and how
that relates to SOD and catalase. Which of these are grown on reducing media? Describe the role cell
surface charge plays in the attachment of bacteria to surfaces and control of their growth. Explain the
shape of a Michaelis-Menten curve, as it relates to substrate utilization for growth in liquid culture, and
identify Km and Vmax. Contrast the Km for ammonium assimilation by oligotrophic and eutrophic
diatoms (Eppley 1969) and the Km for iron assimilation by virulent and toxic bacteria. Contrast
allosteric, covalent modification and competitive inhibition regulation of enzymes. Show these
regulations on a MM curve.
Contrast the terms sterilization/pasteurization/disinfection/sanitization. Explain how heat, radiation
(ionizing and UV), phenolics, halogens, alcohols and surfactants kill and/or control microbes. Provide
the minimal effective concentration of alcohol for sanitizing surfaces.
Contrast photoautotrophs, photoheterotrophs, chemolithotrophs, and chemoorganotrophs. Identify
systems where photoheterotrophs and chemolithotrophs appear important. Diagram change of free
energy in exergonic and endergonic reactions, indicate activation energy with and without a catalytic
enzyme. Predict the free energy change for a reaction from the reduction potential of the reactants and
the number of electrons exchanged. Practice with the Hindenburg, bacterial nanowire and aerobic
respiration examples. Contrast these compounds carry energy: ATP, NADH and cytochromes. Contrast
fermentation from aerobic and anerobic respiration in terms of electron acceptor and energy yield.
Sketch the reduction of pyruvate to lactic acid or to ethanol in fermentation. Contrast the energy yield of
glycolysis, fermentation and respiration. Sketch the structures of pyruvate and acetate and identify the
role of acetyl-CoA in oxaloacetate in linking glycolysis to the citric acid cycle. Explain how
ATPsynthase generates ATP using the proton motive force. Sketch the nitrogen cycle and identify
nitrogen fixing, anerobic respiration and chemolithoautotrophic steps.
Sketch a figure from the paper your team has selected and discuss it using the above language.