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Define taxonomy and related terms: classification, nomenclature, identification, taxon, and character.
What is the difference between a species and a strain? What is meant by morphotype, serotype,
biotype, and phage-type?
What is the primary literary source of prokaryote taxonomy?
What are the four major types of phenetic characters? Describe each with examples.
Which major groups of biomolecules did we discuss as providing molecular characters?
What is Phylogenetic (Phyletic) Classification? Some genes change very slowly over evolutionary
time and thereby make for good molecular chronometers. What are the attributes of molecular
chronometers and why do the 16SrRNA gene (16SrDNA) of prokaryotes and the 18SrRNA gene of
eukaryotes fulfill these attributes?
What are the steps in producing a cladogram (phylogenetic tree diagram)?
Be able to recognize examples of each type of positive and negative interactions between microbial
populations.
Understand the hydrothermal vent ecosystem (vent location, sulfide source, both free-living and Riftia
spp endosymbiont chemolithoautotrophs).
Know the aerobic and anaerobic transformations of the Carbon Cycle.
Understand the general function of the rumen microbial ecosystem for the cow. What anaerobic
microbial processes take place and where do the different byproducts end up?
Understand the complexity of the soil community; its patchiness; and gradients in nutrients and supply
of oxygen or other electron acceptors.
What are source of organic matter for the soil community? How does the distribution of bacteria
change with proximity to these sources?
Know the basic relationships between plants and microbe for mycorrhizae and root nodules. Which
microbes and mutual benefits are involved in each relationship?
Understand physical and biological processes in the basic steps in sewage treatment (preliminary,
primary secondary (aerobic and anaerobic), tertiary. What’s the difference between a biofilm and a
floc? What’s a coliform and why do we test for it during wastewater treatment? How can bacteria be
involved in tertiary treatment for P and N removal?
The first line of defense involves your body’s physical barriers and associated mechanical and
chemical defenses. Be able to describe details of these for skin, eyes, ears, as well as major mucous
membrane regions of the gastrointestinal, genitourinary (male & female) and respiratory tracks.
Be able to match characteristics of major leukocytes: neutrophils, basophils, eosinophils, macrophage,
dendritic cells, natural killer cells, B cells, and T cells. Know their origin and role in non-specific or
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specific resistance. What specifically is the difference between granulocytes and agranulocytes.
What’s the specific difference between wandering and fixed macrophage?
Which are the phagocytic leukocytes? Be able to diagram, label and describe major steps in
phagocytosis. What is meant by opsonization?
What are the details of the fever (pyrogenic) response, including endotoxins, phagocytes, interleukin-1,
and the hypothalamus. How does the body heat up? When and how does it cool back down?
Know the major steps, cells types, and chemical involvement in the inflammatory (pyogenic) response:
* How are mast cells involved (what and where are they)?
* Know major inflammatory mediators and the role of kalikrein and bradykinin.
* What is meant by vasodilation, edema, and the pain response? Know the chemical, cellular,
and or tissue level events leading to all three of these inflammation events.
* How does chemical stimulation of capillary endothelial cells and chemotaxis relate to
phagocyte attack at the infected tissue site? What’s margination and emigration?
* When does the inflammation subside?
Know the three major roles of complement system proteins in non-specific resistance. Why is C3
protein important? How is the complement system activated by “classic “and “alternate” pathways?
Specifically, be able to explain which complement proteins, or protein subunits (e.g. C5a) are involved
in inflammation, opsonization and cytolysis. What is the membrane attack complex (MAC)?
What are interferons (specifically alpha and betta) and their role in preventing the spread of viral
infections? Which cells produce the interferons and which produce antiviral proteins (AVP)? What is
the role and mechainsm of AVPs?
Know where in the human body lymphocytes come from and where they mature into either B cells or
T cells. Focus on helper and cytotoxic T cells, as well as plasma and memory B cells. Which of these
lymphocyte types are involved in the cell-mediated versus antibody-mediated (Humeral) immune
response.
Understand the interaction between antigen and antibody. Which part of the antibody structure (light
and heavy chain variable regions) interacts with which part of an antigen (epitope)?
Be able to recognize unique characteristics of structure and/or function of the five different Ig types.
Given examples of how someone acquired immunity, be able to categorize it as passive or active and
as natural or artificial.
Define the basic structure of an antibody (immunoglobin) protein structure.
Define antigen and the antigen-antibody specific interaction. What’s a hapten?
Define in general terms the five classes of antibodies.
Know the four types of acquired immunity. Be able to label a given scenario as one of the four.
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Where do B cells come from? What is the role of B cells in humoral immunity (memory and
plasma); what activates the process?
Understand the difference between T-dependent and T-independent antigens, and how the former
represents organization between cellular-mediated and humoral immunity.
Explain why a second exposure to the same antigen elicits a more rapid and intense immune response.
Describe six beneficial functions of antibodies; recall three are interrelated to the classic activation
pathway of the complement system.
What are the details of antibody dependent cell-mediated cytotoxicity (ADCC)? Which other
leukocytes are involved? Under what circumstances would this most likely occur?
What are the T cells (helper and cytotoxic) and where do they come from?
What is the major histocompatibility complex (MHC); which cells do which classes bind to?
Describe the chemical (cytokine) signaling between T helper, T cytotoxic and B cells.
Describe the events in cytotoxicity of T cell .
Appreciate the interconnectedness of the humoral and cell-mediated responses and how this interaction
can be enhanced by non-specific resistance, like complement system).
Plasma membrane: lipid structure; which fatty acids characteristics influence lipid membrane fluidity
and stability. What fatty acid characteristics would most likely exist for a psychrophile versus a
thermophile.
Explain the four major physiological categories (Nutrition Types) based on energy, electrons and
carbon sources.
What is meant by open versus closed culture systems? What are the four phases of growth in a batch
(closed) culture? Understand what is happening in each phases of the “growth curve”. When growth
is balanced versus unbalanced; what’s that mean?
What happens in anabolism versus catabolism? Which requires energy and electrons for reductive
synthesis? Which yields energy and electrons from oxidative degradation?
What is the difference between competitive versus non-competitive inhibition of enzyme activity.
What happens to the substrate affinity of an allosteric enzyme when a negative effector (= noncompetitive inhibitor) is bound; when a positive effector (activator) is bound?
How can metabolic pathways be organized; how are metabolic pathways controlled? What is feed
back inhibition versus feed forward activation? What is the role of pathway end-products versus
substrates, respectively, in controlling pathway reaction rate and expression of pathway operons by
repression versus induction, respectively?
Electron Transport Chain: How is energy released from reduced electron carriers (NADH, FADH) and
what work is performed with it? What is the proton motive force, and how does it relate to ATP
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Synthase? Why do we call ATP synthesis of this type oxidative phosphorylation (what’s oxidized;
what’s phosphorylated)?
What is basic meaning of genetic recombination? Give a basic description of the three possible
mechanisms of genetic exchange in bacteria: natural transformation, conjugation, and transduction.
What is a high frequency of recombination (Hfr) strain and how can it form an F’ (i.e. “F prime”)
strain versus a recombinant F- strain?