Biology 119/Microbiology
Final Exam
Summer 2011
Name: _____KEY______________________
Each of the 11 questions is valued at 10 points. We will drop the question with
the lowest score. Maximum possible on the exam is therefore 100 points.
TOTAL SCORE=
1.
[2 PARTS]
A.
The existence of anoxic (anaerobic) microenvironments on the contemporary aerobic
earth generally is associated with the following 4 circumstances:
1.
Physical barriers to exchange with atmosphere.
2. Dark.
3. Presence of organic carbon.
4. Presence of organisms capable of aerobic respiration.
B.
Each of the 5 tubes of thioglycollate medium has been inoculated with a pure culture of a
specific bacterial species. Which tubes represent the growth characteristics you expect for:
an aerotolerant anaerobe A
an obligate aerobe E
2.
[2 PARTS]
A.
Each of the proteins listed in the column on the left is involved with one of the
biochemical processes in the nitrogen cycle listed in the column on the right.
Use the correct letter to match each protein with the correct biochemical process.
HINT: The choices may be used more than once, or not at all.
Nitrate Reductase
Ammonia Monooxygenase (AMO)
Dinitrogenase Reductase
Leghemoglobin
Glutamine Synthase
E or B
D
A
A
B
A
B
C
D
E
Nitrogen Fixation
Nitrogen Assimilation
Dissimilatory Nitrate Reduction (Denitrification)
Nitrification
Assimilatory Nitrate Reduction
B.
The oxidation of ammonia to nitrite yields a total of 6 electrons. In the metabolism of
nitrosofying bacteria only 2 of these 6 electrons move through an electron transport chain to O2
as the final electron acceptor. What happens to the other 4 electrons?
They are used to reduce the O2 used as substrate in the monooxygenase reaction.
i.e. They end up in waters, but have not gone through electron transport.
3.
[2 PARTS]
A.
The nitrogenase complex directly consumes (hydrolyses) 16-24 ATPs for each molecule
of N2 that it reduces to ammonia. Yet even this large input underestimates the total energetic
investment in nitrogen fixation.
Briefly explain why merely counting the ATPs consumed underestimates the overall energetic
cost of nitrogen fixation.
The 8 electrons used to reduce N2 (and H+) are derived from pyruvate oxidation. These
electrons would otherwise have been available to electron transport, contributing to ATP
yield by chemisosmosis.
B.
In filamentous cyanobacteria (such as Anabena) certain cells differentiate into specialized
cells called heterocysts.
i. What is the function of heterocysts?
Nitrogen fixation/protect nitrogenase from oxygen inhibition
ii. What specific modifications allow heterocysts to carry out this function?
Repression of photosystem II; i.e. no oxygen evolution
Thick walls limit diffusion of oxygen.
4. For each process below, does it occur in
a. primarily aerobic environments
b. primarily anaerobic environments
c. either aerobic or anaerobic environments.
Explain why this is the case.
a. Nitrification
Nitrification is strictly an aerobic process. O2 is the terminal electron acceptor for
electron transport in these organisms, and is also required as substrate for the
ammonia monooxygenase reaction.
b. Nitrogen Fixation
Nitrogen Fixation is anaerobic at the molecular level because the nitrogenase complex
is inactivated by O2. Yet there are several aerobic bacteria capable of fixing nitrogen
because they have mechanisms to protect the nitrogenase complex from inactivation
by O2. So, at the cellular and organismal levels, nitrogen fixation occurs in both
aerobic or anaerobic environments.
5.
[2 PARTS]
A. Briefly explain the difference between bioluminescence and phosphorescence.
Bioluminescence is the emission of light by a biochemical reaction.
Phosphorescence is emission of light from a molecule excited by absorption of light
energy (i.e. fluorescence).
B.
Give a general description of the biochemical reaction involved in bacterial
bioluminescence.
This means that you should provide a balanced overall reaction showing substrates, products,
and the enzyme involved.
Indicate the specific molecule that actually emits light (by an arrow, or by drawing a circle around
it).
Luciferase enzyme emits Light
2e-
O
R C H
FMNH2 + O2
! 4 e-
(+1)
!
O
R C OH
oxygenase
2e-
(+3)
FMN + H2O
6.
[2 PARTS]
A.
In the acetone-butanol fermentation, acetyl CoA may be converted to either acetate
(acetic acid) or to ethanol.
i. What is the benefit derived from producing ethanol?
Oxidizes NADH; restoring redox balance.
ii. What is the benefit derived from producing acetate?
ATP production
B.
Compare the energetic efficiency homolactic fermentation, the ethanolic fermentation and
the acetone-butanol fermentation in terms of the number of ATP produced per glucose.
homolactic 2 ATP/glucose
alcoholic 2 ATP/glucose
acetone-butanol 3 ATP/glucose
7. Describe the mode of action (at the molecular level) of either diptheria AB exotoxin or tetanus
AB exotoxin.
Diptheria: Inactivation of EF2 inhibits protein synthesis.
TETANUS TOXIN: Prevents release of glycne neurotransmitter from inhibitory neuron.
Irreversible muscle contraction/spastic paralysis.
8.
[2 PARTS]
A.
List 4 "barriers" to infection (physical or chemical) to infectious organisms.
Epidermis (fatty acid secretion)
Mucocilliary Elevator
Enzymes (Lysozyme)
Normal Bacterial Flora (Gnotobiotic mice)
Gastric Acidity
Hypoferremic response, transferrin, lacotoferrin
Behaviour (Public Health Regulations and Monitoring/Sanitary
Infrastructure/Vaccination/Custom)
Innate and Adaptive (Acquired) Immunity (see Chap. 29)
etc.
B. List 4 forms of toxic oxygen produced in phagolysosomes.
Any 4 of the following:
Hydrogen Peroxide
Hydroxyl radical
Superoxide Anion
Singlet State Oxygen
Hypochlorous Acid
Nitric Oxide
H 2O 2
•OH
O 21
O2
HOCl
NO
9.
[2 PARTS]
A.
Cells of the innate immune system use Pathogen Associated Molecular Pattern
(PAMP) recognition proteins to detect the presence of certain molecules that indicate the
presence of an infection. The molecules are chemically diverse, and are referred to as Pattern
Recognition Molecules (PRMs).
HINT: PAMP recognition proteins are sometimes referred to as "Toll-like Receptors"
List 4 different types of PRM that are detected by PAMPs of the innate immune system.
Any 4 of the following:
Lipoproteins in Mycobacterial Cell Walls
Gram-Positive Peptidoglycan
Fungal Zymosan
dsRNA
Flagellin
unmethylated CpG oligodeoxyribonucleotdes
B.
Briefly describe 3 factors that contribute to the high incidence, and unusual severity, of
Health Care Associated Infections (= nosocomial infections).
Any 3:
Bacteria involved in nosocomial infections are more likely to be antibiotic resistant than
strains of the same organism outside a health care setting.
Patients often have compromised immune system or are at hoigh risk of infection due to
pre-existing disease conditions.
Patients are often compromised by catheters, IV drips, surgical incisions, etc. that
provide a route of entry.
Pateinets are exposed to other patients with infectious diseases either directly or
indirectly by the clinical staff.
10.
Identify each of the 5 chemical structures below by name, or by function if you do not
know the name..
______________LACTIC ACID__________________
Acyl Homoserine Lactone "Autoinducer"
O
CH2
CH3
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
C
H
CH2
Dodecanal (Luciferin)
Siderophore (Enterobactin) Ribavirin (treatment for RNA viral infections)
11.
[2 PARTS]
A.
Two of the seven classes of viruses use reverse transcriptases in their genomic
replication cycles.
i. Which two classes are they? VI VII
ii. How do these 2 classes differ from each other?
Class VI has ssRNA in virion.
Class VII has dsDNA in virion.
iii. Give one virus as an example of each class.
___VI HIV etc.___ ____VII HEPADNAVIRUS (Hepatitis B)__________
B.
Expression of the hantavirus genome in an infected host cell leads to the production of 6
different proteins. These 6 proteins have 3 general functions, or roles in hantavirus replication.
What are the 3 general roles of the hantavirus-specific proteins?
i. RNA REPLICASE-Genomic replication.
ii. Nucleocapsid assembly and structure
iii. G1 G2 Glycoproteins in envelope.