Bio 132 study list for Midterm I (Feb. 10, 2000)

Below are some questions that will help you prepare for midterm I. Midterm I will cover only the material included in this list, although not all questions on the midterm may be expressly stated below. Some of these points have been covered in class; others will be found in the assigned text material. Important terms which you should understand are underlined below. You will not be required to know the names of specific microorganisms mentioned in class for midterm I, except for those covered below in the study list (for instance, Cyanobacteria).

Lecture 1. History of microbiology (Chapter 1)

Important steps in the development of the field of microbiology were:

disproving spontaneous generation

the visual observation of micro-organisms (the microscope)

aseptic conditions

the development of pure culture techniques for microorganisms

germ theory of disease

the assignment of various org as causative agents of specific diseases

development of vaccines

development of antimicrobial chemotherapy

1. Know Koch's postulates.

Lecture 2. Evolution of microorganisms (Schopf 1978 Sci. Am. article)

Life evolved under anaerobic conditions

Micro-fossil record very early, as long ago as 3.9 billion years (the formation of earth being 4.6 billion years ago)

The evolution of photosynthetic organisms such as Cyanobacteria, (very prevalent in the fossil record about 2 billion years ago) caused the accumulation of atmospheric O2 to present day levels.

Eukaryotes probably evolved from symbiotic relationships between prokaryotes

Whereas eukaryotes are usually obligate aerobes, the capacity for anaerobic growth is common among prokaryotes.

Know this:

1. What is the evidence for the endosymbiont theory for the origin of chloroplasts, and mitochondria ?

2. Why did the production of O2 alter the course of evolution?

3. What evidence suggests a transition from low O2 to high O2 atmosphere about 2 billion years ago?

Lecture 3. Prokaryote cell biology (Chapter 3)

1.In what aspects of their cell structure, do prokaryotes and eukaryotes differ?

2. What is the chemical composition, location and presumed function of:

a. cell wall

b. cytoplasmic membrane

c. outer membrane

d. capsule/glycocalyx/slime

e. fimbriae/pili

f. nucleoid

g. inclusion bodies

h. periplasmic space

3. In what aspects of their cell stucture do gram-positive and gram-negative bacteria differ?

4. What is the cellular/molecular basis of differential gram staining (ie why are gram-positives positive?) Why do some bacteria evolutionarily-related to gram-positive bacteria stain gram-negative?

5. What are endospores? How and when are they formed?

6. Know the basic bacterial cell shapes: cocci, bacilli, vibrios, spirilla, spirochaetes, mycoplasmas

7. What are spheroplasts, protoplasts?

8 What's LPS, where is it and what consequences does it have in disease? (You don't have to be able to draw the struture but do be able to recognize it if you see it. ) You should also know the components of LPS, as well as peptidoglycan.

9. How do flagella of bacteria and flagella of euks differ?

10. Diagram the structure of peptidoglycan (murein) using NAM, NAG and peptide components. What kind of molecules are NAM, NAG? Why is murein so strong? In what ways does murein differ among prokaryotic organisms?

Lecture 4: Microbial Growth and Nutrition (Chapters 5 and 6)

1. Know the four nutritional types of microorganisms, their sources of energy, electrons and carbon. Know one representative microorganism for each type (eg nitrifying bacteria are chemolithotrophic autotrophs)

2. What are the macronutrients?

3 Why is Fe uptake a problem and how do microorganisms solve it?

4. Name and describe the phases of cell growth in a closed system.

5. Vocabulary: osmotolerant, halophile, acidophile, alkalophiles, thermophile, pyschrophile, pyschrotroph, mesophile, barophile, barotolerant, aerobe, obligate aerobe, anaerobe, facultative anaerobe, obligate anaerobe, microaerophile

6. What are the reactive oxygen species , how are they formed and why are they dangerous? What defenses do aerobes have against reactive oxygen species? What types of cells generate reactive oxygen coumpounds for their own purposes?

  1. What are the benefits/problems of high-termperature growth?

Lecture 5: Microbial metabolism: energy conversion (Chapter 9)

1. What are the roles of ATP, NADH and NADPH in cellular metabolism? What aspect of teir chemical structures allows them to function inthese roles?

2. What does standard reduction potential mean? What's a redox couple? How can you tell whether a particular redox couple will act as a donor or acceptor of electrons in reactions with another redox couple? (See Chapter 8 p. 155-157)

3. Vocabulary: anabolism, catabolism, amphibolic pathway

4. What is the starting point, end products and metabolic role of:

a. glycolysis

b. pentose phosphate pathway

c. Entner-Doudoroff pathway

Do they operate in aerobic and anaerobic conditions? Is ATP produced? What important intermediates are generated?

5. What are the substrates and products of the TCA cycle? What are its functions?

6. a. Describe in general terms the electron transport chain and oxidation phosphorylation.

b. Describe the chemiosmotic theory.

c. What's protonmotive force?

d. Why do facultative anaerobes reduce their rate of sugar catabolism when oxygen is available ("the Pasteur effect")?

7. What's the purpose of fermentation? What are some of products generated by fermentation? How are fermentation patterns useful in clinical microbiology?

8. Anaerobic respiration:

a. What electon acceptors can be used besides oxygen?

b. What are the products of these reductions?

c. Does anaerobic respiration generate as much ATP as aerobic respiration?

9. Chemolithotrophic oxidations:

a. What types of electron donor and acceptors are used?

b. How do energy yields compare to oxidation of glucose to CO2?

c. Why do these oxidations (in some cases) not yield NAD(P)H? Why do organisms need NAD(P)H anyway?

10. Photosynthesis:

a. What's the purpose?

b. What's similar about photosynthesis in chloroplasts and cyanobacteria?

c. How are green and purple bacteria different?

d. What's the difference between cyclic and noncyclic photosynthesis?

e. What are differences between photosystems I and II in green plants and cyanobacteria?

12. More vocabulary: nitrifying, denitrifying, oxygenic, anoxygenic, substrate level phosphorylation

Lecture 6: Microbial metabolism: biosynthesis (Chapter 10)

1. Why do biosynthetic pathways use many of the same enzymes as catabolic pathways?

2. Name three ways in which anabolic pathways can be controlled independently of the reverse catabolic pathway. Give an example of each type. Why is this regulation important?

3. Describe the three phases of the Calvin cycle. What are their purposes? Why is ribulose phosphate important?

4. What role do nucleoside diphosphate sugars play in anabolism?

5. Why does the cell make sugars and polysaccharides?

6. In what chemical form do cells assimilate sulfur and phosphorus?

7. What chemical forms of nitrogen can be assimilated? To what types of organic molecules can nitrogen be transferred in assimilatory reactions?

8. What kind of organisms can fix atmospheric N2? What special enzymes and energy sources are required? Why is the process uncommon among aerobic organisms? What special arrangements do aerobic bacteria make to allow nitrogen fixation occur in the presence of O2 ?

9. From which amphibolic pathways are amino acids synthesized? Why is ribose-phosphate important in anabolism? Acetyl CoA?

10. What's a anaplerotic reaction? Give an example.

11. Describe the steps in peptidogycan synthesis. What steps take place in the cytoplasm? Exterior? What's the role of bactoprenol in this process? UDP? What aspects of their structures allow them to function in these roles? What step is sensitive to bacitracin? Penicillin? Cycloserine?

Lecture 7: Environmental microbiology. (Chapter 40).

  1. Vocabulary: primary production, mineralization, elemental cycling, oligotrophic
  2. What kinds of nutritional types (see lecture 4) do we consider primary producers? In what kinds of ecosystems do you find them?
  3. In what ways do microorganisms influence other organisms in their environment?
  4. What is a biofilm? Why do microorganisms form biofilms?
  5. In the carbon cycle, which conversions depend on aerobic vs. anaerobic growth?
  6. What forms of carbon are found in the carbon cycle? Which forms are more oxidized? More reduced?
  7. What forms of nitrogen constitute the nitrogen cycle? What is the consequence of this cycle for green plants? What kinds of metabolic processes cause reduction of nitrogen compounds? Oxidation?
  8. Know the difference between nitrogen fixation, nitrification and denitrification. How does the presence or absence of O2 influence these processes?
  9. What kinds of symbiotic relationships exist between nitrogen-fixing microbes and green plants?
  10. What's the difference between assimilatory and dissimilatory nitrate or sulfate reduction?
  11. What forms of sulfur constitute the sulfur cycle? What kinds of metabolic processes cause sulfate reduction? Sulfate oxidation?
  12. What do we mean by biomagnification? Know an example.
  13. How does the presence or absence of O2 influence the decomposition of lignin?

Lecture 8. Prokaryotic genetics (Chapter 14)

1. What's different about the genomes of prokaryotes and eukaryotes ?

2. Know the potential consequences of DNA after genetic transfer.

3. Be able to describe these processes in some detail:

conjugation, including rolling circle replication

specialized transduction

generalized transduction

transformation

What is the genetic and evolutionary consequences of these processes?

4. Be able to define :

plasmid

lysogen

restriction

pilus

competent

episome

restriction

transposon/transposible element

recombination

homology

replication

transduction

5. How do transposible elements aid in genomic evolution? What are the important components of transposons?

6. What’s horizontal transmission? How can you tell if genes have been horizontally transfered?