Microbiology Test #2 Review Questions
More questions will be added after Tuesday’s lecture (when I know what I covered)
Definitions:
1. Be able to define and give the significance of the following terms:
a. stromatolite
b. serpentinization
c. LUCA
d. chemolithotroph
e. autotroph
f. phototroph
g. endosymbiosis
h. horizontal gene transfer
i. molecular clock
j. FISH
k. FAME
l. Ribotyping
m. DNA-DNA hybridization
n. Multilocus sequence typing
o. Multigene analysis
p. Ecotypes
q. promoter
r. Shine-Delgarno sequence
s.  factors
t. helix-turn-helix
u. enzyme repression
v. repressor
w. inducer
x. corepressor
y. negative supercoil
z. positive supercoil
aa. nucleosome
bb. class I topoisomerase
cc. class II topoisomerase
dd. plasmid
ee. insertion sequences
ff. transposons
gg. oriC
hh. regulon
ii. operon
jj. catabolite repression
kk. two-component regulatory system
ll. Quorum sensing
mm.
Anti-sense RNA
nn. Riboswitches
oo. Anoxygenic photosynthesis
pp. Chlorosome
qq. Reaction center
rr. Antenna pigments
ss. Carotenoid
tt. Phycobilin
uu. Reverse Electron Transport
vv. Photophosphorylation
ww.
syntrophy
Microbial evolution and systematics:
1. Be able to discuss the subsurface hypothesis. What were the conditions in
that environment? What was the source of the chemicals that gave rise to the
earliest organic molecules, and how did serpentinization probably cause
their formation?
2. What was the first informational/catalytic biomolecule?
3. Be able to discuss major events in the evolution of microbial life, in
particular:
a. The most probable metabolic strategies of the earliest microbes
b. The origin of an ‘oxic’ earth
4. What is LUCA, and when did it arise?
5. Be able to describe the hydrogen hypothesis. What are its strengths and
weaknesses?
6. Why do microbes evolve so much more rapidly than humans?
7. Describe how you would go about determining if a new bacterial isolate is a
new species or not. Use and describe a variety of different types of analysis –
at least 2 genetics and at least 2 physiological/morphological to help you
draw your conclusions.
8. Why is defining a species so difficult in bacteria?
Bacterial and Archaeal Genetics:
1. Be able to describe how prokaryotic chromosomes are structured and
condensed. What is the role of topoisomerases in this process?
2. How do operons help microbes respond rapidly to their environments?
3. What are plasmids? What types of genes to they contain (list and describe 4
different types).
4. Discuss similarities and differences between the molecular biology of
Bacteria and Archaea. Give three genomic similarities, three genomic
differences. Do the same for gene expression (transcription and translation).
5. Be able to describe and discuss one example of:
a. Enzyme repression
b. Enzyme induction
c. Enzyme activation
6.
7.
8.
9.
d. Catabolite repression
e. A process controlled by a two-component regulatory system
Be able to describe how flagellar rotation is controlled by the presence of
repellants and attractants. Be sure to include the roles of MCP’s, CheA,W,R
and B.
What is the stringent response and how does amino acid starvation lead to
the production of alarmones? What do these alarmones do?
Be able to discuss the interplay of RpoH and DnaK in the heat shock
response.
Be able to discuss the cascade of activated  factors that lead to sporulation
in Bacillus.
Phototrophy and Chemolithotrophy
2. Why do phototrophs have so many different light-activated pigments? Be
able to give 4 examples of different types of pigments, and tell what they do.
3. How do the photosynthetic membranes of prokaryotes differ from those in
eukaryotes?
4. Be able to draw/discuss the structure and function of a chlorosome.
5. Be able to compare and contrast the basic pattern of electron
excitation/transfer in purple bacteria, green sulfur bacteria and
cyanobacteria. You do not need to know pigment names, the
names/numbers of electron transfer molecules or specific wavelengths used.
However, you do need to know how ATP is generated in each case, and how
the reducing power for NAD(P)H is generated (where in the system the
electrons enter, what molecule(s) donate the electrons, and what is produced
as a result of that donation).
6. Be able to discuss how the E0’ values of electron donors and receptors
determine how much energy is theoretically generated during electron
transfer.
7. Be able to compare and contrast your two favorite forms of
chemolithotrophy (if you choose sulfur oxidation as one, you need only know
one of the pathways…and you may not use another sulfur pathway as your
second form of chemolithotrophy). In particular, discuss how ATP is
generated, how the reducing power for NADH is generated, how (in general)
CO2 is fixed (Calvin Cycle or some other mechanism?), any important
enzymes involved in the process and their location(s) in the cell, and the
ecology of the microbes that perform the process (where they live, what
impact they have on the environment).
8. Be able to place hydrogen oxidation, sulfur oxidation, nitrogen oxidation and
iron oxidation in correct order regarding their potential energy generation.
9. Some of these chemolithotrophic processes can be performed anaerobically.
Give two examples, and tell the final electron acceptors involved in each.
10. What is an annammoxosome, and what is its role in a bacterial call? Be able
to describe the biochemical reactions in anaerobic ammonia oxidation.
11. Be able to describe the biochemical reactions and electron flow in nitrogen
fixation.
12. Nitrogen fixation is an energetically expensive process. Be able to discuss
how it is regulated at both the genetic and the enzymatic levels.
Catabolism of Organic Compounds – Coming as soon as I know how far I got….