BIOL 238 Review 2009

This page provides review questions for BIOL 238 (Spring 2009). Answers may be posted by students.

Chapter 7

1. What are the relative advantages and limitations of bidirectional replication versus rolling circle replication? What kind of genetic entities are likely to favor one over the other?

2. What kinds of mutant phenotypes reveal aspect of the mechanism of DNA replication and cell division? Explain two specific examples.

3. Explain how it's possible for the replisome to replicate the leading and lagging strands simultaneously.

4. During resolution of a catenane, how might a major mutation occur affecting the entire genome? How do you think this mutation is prevented?

5. During rapid growth, why would a bacterial cell die if the antibiotic drug “forms a physical barrier in front of the DNA replication complex.”?

6. What are the relative advantages and limitations of bidirectional versus rolling-circle replication of DNA? Explain in terms of different genome sizes, types, and cell situation when replication occurs.

7. When you sequence a genome, how do you know where the base pairs in the genome are located since the DNA used to sequence the genome is in fragments?

Chapter 8

1. Explain how a biochemical experiment can demonstrate the specific protein targeted by a new antibiotic that impairs transcription.

2. If Mycoplasma genitalium cannot synthesize its own amino acids, does it have extensive/multiple protein channels (ABC pumps) to let amino acids pass its membrane? If proteins are made of amino acids, though, how did the first M. genitalium’s protein channels come into existence?

3. In tRNA, there are "unusual" bases not found in mRNA How are these bases generated? Do you think they arise from a recently-evolved aspect of tRNA, or do you think they are an ancient phenomenon of the original RNA world? Explain.

4. What kinds of pharmaceutical agents could you design to act on gene promoters? Explain using protein and/or RNA molecules.

5. Why do you think bacterial cells absorb protein and nucleic acids that are exported by other bacteria?

6. How could you sequence the genome of an unculturable microbe?

Chapter 9 and 10

1. In the process of conjugation, how are genes moved? Are genes moved individually or in groups? Could part of a gene be moved?

2. How are microbial species defined? What is the role of vertical phylogeny; and the role of horizontal gene exchange? Explain why species definition is a problem.

3. Why is competence factor exported out of the cell to bind to ComD externally in transformation of Streptococcus? Why doesn't the molecule bind internally? Doesn't exporting CF waste energy?

4. If a spontaneous mutation occurs to form an apurinic site, transcription and replication are hindered, but what actually happens when the replisome gets to the hole where the base should be?

5. Explain how a DNA sequence inverts during phase variation. Would you expect it to revert at the same rate? Why or why not?

6. Explain the different propagation strategies available to a replicative transposon. What are various ways the transposon could spread within a cell? Among organisms?

7. Explain how the ara operon works, and how it differs from the lac operon.

8. Explain how different mechanisms acting at different levels on DNA and RNA can modulate gene expression over a range of time scales, from multiple generations to within a few seconds.

9. Explain the roles of thermodynamic and kinetic effects in attenuation control of the trp operon.

Wozniak lecture on Biofilms

1. What do bacterial biofilms have in common with multicellular organisms? How do they differ?

2. What are the advantages to bacteria of biofilm formation? What properties do biofilms confer?

3. Where in the body do biofilms form infections? Why?

4. Explain the basis of "twitching motility." Compare and contrast twitching with flagellar motility. How does twitching motility promote biofilm development?

5. How does the ara promoter work (pBAD)? How was pBAD used to test the role of the psl operon in bioflim development?

6. How was it proved that psl encodes PSL polysaccharide? How does PSL compare in structure with alginate?

Chapter 13

1. ATP and NADH are both energy carriers: What are the advantages of using one over the other?

2. When cells need to make glucose (gluconeogenesis), they "reverse glycolysis" because most steps are reversible. However, there are a couple of steps that are not reversible. How do you think they get reversed for gluconeogenesis?

3. There are 3 main pathways to form pyruvate- EMP, ED and PPS. How and why might a cell switch among these?

4. Explain why most soil bacteria grow using energy-yielding reactions with very small delta-G.

5. Why are glucose catabolism pathways ubiquitous, despite the fact that most bacterial habitats never provide glucose? Explain several reasons.

6. In glycolysis, explain why bacteria have to return the hydrogens from NADH back onto pyruvate to make fermentation products. Why can't NAD+ serve as a terminal electron acceptor, like O₂?

7. Why do environmental factors regulate catabolism? Give examples. Why are amino acids decarboxylated at low pH, and under anaerobiosis?

8. Why does catabolism of benzene derivatives yield less energy than sugar catabolism? Why is benzene-derivative catabolism nevertheless widespread among soil bacteria?

Chapter 14

1. Explain how bacteria and archaea switch among various electron acceptors depending on environmental conditions.

2. Explain how cell processes such as ATP synthesis can be powered by either the transmembrane pH difference or by the charge difference across the membrane. Which form of energy is likely to be used at low external pH? At high external pH?

3. For phototrophy, discuss the relative advantages and limitations of using PS I versus PS II.

4. What environments favor oxygenic photosynthesis, versus sulfur phototrophy and photoorganotrophy? Explain.

5. Explain why certain lithotrophs acidify their environments, to more extreme levels than fermentation. What are some practical consequences for human industry?

6. Is it surprising that an organism may switch between lithotrophy and organotrophy? What enzymes would have to be replaced, and what enzymes could be used in common for both kinds of metabolism?

7. What kind of environments favor methanogenesis? Why are methanogens widespread, despite the low delta-G of their energy-yielding metabolism?

Chapter 15

1. Why does biosynthesis need both ATP and NADPH? Why couldn't biosynthetic pathways use just ATP, or just NADPH?

2. Compare and contrast fatty acid biosynthesis and amino acid biosynthesis. Which pathway requires more reduction? Which requires a greater number of different enzymes? Why?

3. What forms of nitrogen are available to microbes for assimilation? When fertilizer is spread on farmland to nourish crops, what problem is caused by microbes?

The only form of nitrogen that microbes can directly assimilate into biomass is ammonium ion (NH4+ protonated from NH3). While there are other forms of nitrogen available in the environment, these other forms have to be reduced to ammonia before they can be assimilated. What are the other oxidized forms that bacteria and plants take up and reduce to ammonia and ammonium ion? What about N from reduced organic compounds?

When fertilizer is spread on farmland to nourish crops, lithotrophic microbes cause a problem by oxidizing ammonia fertilizer to nitrates and nitrites. Plants can take up the nitrates and reduce them (with energy input), but a large excess runs into streams and water supplies. These high concentrations of nitrates in water form nitrites that can combine with hemoglobin (in the blood) to create a form of hemoglobin that is not able to take up oxygen. This is a problem for babies trying to breathe.

4. How are the pathways of amino acid biosynthesis organized? What common routes flow from which core pathways?

5. How and why do bacteria make "secondary products"? What are their functions?

6. How can we manipulate bacterial secondary product formation to develop new pharmaceutical agents?

Species to know for Test

For each species, state one or two broader categories of organism (such as gram-positive endospore-forming bacteria), the type of genome, type(s) of metabolism, habitat, and disease caused (if any).

Aeromonas hydrophila

Broader Categories: Gram-negative, anaerobic Genome: Genes that contribute to its toxicity are cytotoxic enterotoxin gene (act), heat labile enterotoxins (Alt), and heat-stable cytotonic enterotoxins (Ast). Metabolism: Heterotrophic, ferments glucose, digests gelatin, hemoglobin, and elastin. Habitat: Exists in aerobic and anaerobic environments: aquatic environments, fish guts, food, human bloodstream and organs. Disease: Causes many diseases in fish and amphibians, since it exists in aquatic environments. Can cause disease in humans, such as septiticemia, meningitis, pneumonia, and gastroenteritis.

Anabaena sp.

Broader Categories: Barrel-shaped cells. Filamentous cyanobacteria (blue-green algae) found as plankton. Genome: 1 circular chromosome with 5368 protein-coding regions and 6 plasmids (from sequenced PCC 7120 strain). Metabolism: Photoautotrophic, perform oxygenic photosynthesis. Form heterocysts (specialized nitrogen-fixing cells that convert nitrogen to ammonia) during nitrogen starvation. Habitat: Freshwater and damp soil. Form symbiotic relationships with certain plants. Disease: Produce neurotoxins, such as anatoxins (neuromuscular poisons), that are harmful to wildlife and farm animals.

Aspergillus sp.

Broader Categories: Over 185 species of this genus Genome: Largely incomplete Metabolism: Highly aerobic. Pathogenic species obtain nutrients from host, while non-pathogenic species obtain nutrients from soil, wood, and plant detritus. Habitat: Grow as molds in oxygen-rich environments and carbon-sources. Some species are capable of living in nutrient-depleted environments as well. Disease: About 20 species are pathogenic in humans and animals. Aspergillus fumigatus and Aspergillus flavus cause invasive pulmonary aspergillosis and is often fatal.

Bacillus anthracis

Broader Categories: Gram-positive, rod-shaped, form endo-spores and biofilms Genome: 1 circular chromosome with over 5 million b.p. 2 circular plasmids made of d.s. DNA: pxO1 and pxO2 encode main virulent factors. Metabolism: Facultative anaerobe and must grow in medium with essential nutrients including C and N sources. Upon nutrient deprivation, endospores form (requires oxygen to form) and can live in inhospitable envrionments for many years. Can grow into vegetative cells in aqueous environment with adequate nutrients. Habitat: Live in soils world-wide and is the main habitat. Disease: Anthrax disease. Infectious endospores harms host by producing toxins in the body of humans and animals. The slimy capsule enables it to resist phagocytosis. 3 main forms of the disease: cutaneous, pulmonary, and gastrointestinal. Can cause death in 2-48 hours.

Bacillus subtilis

Broader Categories: Gram-positive, rod-shaped, form stress-resistant endospores Genome: 1 circular chromosome with 4100 genes coding for proteins. Metabolism: Can grow in aerobic and anaerobic conditions. Uses fermentation and nitrate ammonification to make ATP in the absence of oxygen. Habitat: Soil and vegetation at mesophilic temperatures. Disease: Non-pathogenic. Responsible for spoilage of food, since contamination often results in decomposition, but it rarely causes food-poisoning.

Bacillus thuringiensis

Broader Categories: Gram-positive, spore-forming, rod-shaped Genome: 1 circular chromosome with 5.2-5.8 Megabases. Contains many plasmids. Metabolism: Facultative anaerobe (makes ATP by aerobic respiration if oxygen is present, but can switch to fermentation). Habitat: Soil. It is used in 90% of pesticides. Fends off insects by producing crystal proteins (Cry proteins). Disease: Species-specific, non-pathogenic to humans, making it an environmentally-friendly insecticide. Cry toxin grows and sporulates in alkaline gut o finsect, which aids in its ability to infect the insect gut. The gut breaks down and the insect eventually dies.

Bacteroides thetaiotaomicron

Broader Categories: Gram-negative, anaerobic, human-bacterial symbiosis model Genome: 1 circular chromosome made of d.s. DNA, consists of 4776 proein-coding genes, 90% of which are essential in the binding and import of various polysaccharides. Metabolism: Starch (all 3 forms) is primary carbohydrate used as its source of C and Energy. Polysaccharides bind to the cell surface before undergoing hydrolysis. Habitat: Adult intestine-allows humans to degrade plant polysaccharides Disease: Serious infections include intra-abdominal sepsis and bacteremia. It is resistant to many antimicrobial agents.

Borrelia burgdorferi

Broader Categories: Sprial-shaped with 2 flagella Genome: A linear chromosome with 910,725 b.p. with 853 genes. 17 linear and circular plasmids. Metabolism: Require specific nutritional requirements making it difficult to culture in vitro. Habitat: Live extracellularly and adapts to various host animals (tick, rodents, birds) by regulating various lipoproteins on thier surface. Disease: Lyme disease and recurring fever.

Chlamydia sp.

Broader Categories: Gram-negative, aerobic, coccoid or rod-shaped Genome: C. trachomatis-1,042,519 b.p. with 894 protein-coding sequences (70 genes are not homologous to sequences on the C. pneumoniae genome). C. pneumoniae- 1,230,230 b.p. (186 genes are not homologous to sequences on the C. trachomatis genome) Metabolism: Cannot synthesize its own ATP, so they cannot be grown on artificial medium and require growing cells to remain viable. Habitat: C. trachomatis-human host cells, C. suis- swine host cells, C. muridarum- mice and hamster host cells. Infectious elementary body form induces endocytosis upon contact with host cell. Once inside, the elementary body germinates to vegetative form, and divides every 2-3 hrs. It then reverts back to the elementary form and is released by the cell through exocytosis. Disease: C. trahomatis causes chlamydia and is the most common STD in the world. C. pneumoniae causes pneumonia and bronchitis

Clostridium botulinum

Broader Categories: Gram-positive, rod-shaped, anaerobic, spore-former Genome: Genome size of 4039 kbp, which is larger than most Gram-positive genomes, indicating the extra genomic requirements needed for sporulation and pathogenic toxin production Metabolism: Lie dormant in very adverse environments. Spores can begin to grow in favorable conditions: non-halophilic salinity and anaerobic conditions. Grows at mesophilic temps. Habitat: Soils and improperly canned food products Disease: A-G subtypes produce different botulin toxin- al except C and D subtypes are human pathogens. The toxin prevents propagation of action potentials to the muscle fibers- causing paralysis by inhibiting muscle contraction. Fatalities usually occur due to asphyxiation

Escherichia coli

Broader Categories: Gram-negative, rod-shaped, aerobic Genome: 1 circular chromosome, (4300 coding sequences) with 1800 known proteins. Some contain circular plasmid. Metabolism: Facultative anaerobe. Uses mixed-acid fermentation in anaerobic conditions. Growth driven by aerobic or anaerobic respiration using a large variety of redox pairs: oxidation of pyruvic acid, formic acid, hydrogen, and amino acids and reduction of oxygen, nitrate, dimethyl sulfoxide, trimethylamine N-oxide. Habitat: Lower intestines of human and mammals, where it aids in digestion processes: vitamin K production, food breakdown and absorption Disease: E. coli O157:H7 (enterohemorrhagic strain) causes food poisoning- leading to bloody diarrhea and kidney failure due to its production of Shiga-like toxin. Also can cause urinary tract infections by ascending infections of the urethra.

Geobacter metallireducens

Broader Categories: Gram-negative, rod-shaped, possesses flagella, and pili Genome: 1 circular chromosome encoding 3621 genes. Plasmid encodes 13 genes, 1 of which is addiction module toxin (gives resistance to bacteria and another encoding plasmid stabilization system protein (allows bacteria to adapt to new environmental conditions) Metabolism: First organism with the ability to oxidize organic compounds and metals (iron, radioactive metals like Uranium, and petroleum compounds) into environmentally benign carbon dioxide while using iron oxide and other available metals an electron acceptors. Habitat: anaerobic conditions in soils and aquatic sediments Disease: Non-pathogenic

Pseudomonas aeruginosa

Broader categories: Gram-negative, rod-shaped, does not produce spores. Habitat: due to its capability to synthesize arginine, P. aeruginosa proliferates in anaerobic conditions. It can be found in environments such as soil, water, humans, animals, plants, sewage, and hospitals. Metabolism: Aerobic respiration. P. aeruginosa can metabolize on hundreds of other things besides arginine, and can respire on nitrate (although it does much better on O2).Genome: a single and supercoiled circular chromosome in the cytoplasm. Disease(s) caused: Causes disease in immuno-compromised patients, such as those with cystic fibrosis, cancer, or AIDS. It further weakens the patient, allowing the patient to become more susceptible to other diseases. Usually this kills the patient. P. aeruginosa forms biofilms in the lung of cystic fibrosis patients; it is the major cause of death in these individuals.

Halobacterium sp.

Lactococcus sp.

Methanococcus sp.

Mycoplasma pneumoniae sp.

Paramecium sp.

Plasmodium falciparum

Prochlorococcus sp.

Pseudomonas aeruginosa

Rhodobacter sp.

Rhodospirillum rubrum

Rickettsia sp.

Saccharomyces cerevesiae

Salmonella enterica

Serratia marcescens

Sinorhizobium meliloti

Staphylococcus epidermidis

Staphylococcus aureus

Streptococcus sp.

Streptomyces sp.

Vibrio cholerae

Vibrio fischeri