Biology 119/Microbiology Final Exam Summer 2011

Transcription

1 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=

2 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

3 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 E or B A Nitrogen Fixation Ammonia Monooxygenase (AMO) D B Nitrogen Assimilation Dinitrogenase Reductase A C Dissimilatory Nitrate Reduction (Denitrification) Leghemoglobin A D Nitrification Glutamine Synthase B E 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 O 2 as the final electron acceptor. What happens to the other 4 electrons? They are used to reduce the O 2 used as substrate in the monooxygenase reaction. i.e. They end up in waters, but have not gone through electron transport.

4 3. [2 PARTS] A. The nitrogenase complex directly consumes (hydrolyses) ATPs for each molecule of N 2 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.

5 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. O 2 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 O 2. Yet there are several aerobic bacteria capable of fixing nitrogen because they have mechanisms to protect the nitrogenase complex from inactivation by O 2. So, at the cellular and organismal levels, nitrogen fixation occurs in both aerobic or anaerobic environments.

6 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). 2e- 2e- Luciferase enzyme emits Light O C R (+1) H FMNH 2 + O 2 oxygenase! 4 e - R O C (+3) O H! FMN + H 2 O

7 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

8 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.

9 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 H 2 O 2 Hydroxyl radical OH Superoxide Anion - O 2 Singlet State Oxygen 1 O 2 Hypochlorous Acid HOCl Nitric Oxide NO

10 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.

11 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 C H CH 3 Dodecanal (Luciferin) Siderophore (Enterobactin) Ribavirin (treatment for RNA viral infections)

12 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.