Microbial Growth, Metabolism, Genetics, and Antimicrobials

Physical and chemical growth requirements for microbes

1. What are the physical and chemical growth requirements for microbes?
2. How will microbial growth be affected if each growth requirement increases or decreases?
3. What are the classifications of microbes based on their requirement of: temperature, or pH, or oxygen, or pressure, or salt concentration? Know the differences for these specific requirements between groups.
4. Osmotic pressure vs. hydrostatic pressure
5. What does the term “danger zone” mean in food storage? What will likely happen if food is stored in the danger zone, below or above the danger zone?
6. Effects of hypotonic vs hypertonic vs isotonic solutions on microbial cells
7. Why are nutrients needed?
8. Why are Carbon, Nitrogen, Sulfur, Phosphorus, trace elements, water, hydrogen, oxygen needed? Be specific for each.
9. Know the all classifications of microbes based on carbon and energy sources. Can a phototroph be a chemotroph? Can an autotroph be a heterotroph?
10. What types of microbes cannot survive in any oxygenated environment? In a highly oxygenated environment? In unoxygenated environment? Know how to interpret a microbe’s oxygen requirement given its image of growth in a tube of agar.
11. What are the 4 toxic forms of oxygen? Know how each form harms microbes and how certain microbes overcome their toxicity.
12. What does “aseptic” mean? What is an inoculum? 
13. In clinical testing, what will the samples obtained from patients be used for?
14. List and describe the 3 common plate methods used in isolation of bacteria.  
15. What is agar? How is it used in microbial culturing?
16. Know the three categories of media in microbial culturing
17. Selective vs. differential vs. enriched media. Can a medium be both selective and differential? Give an example. 
18. List and describe all anaerobic culture methods.  
19. Name 4 ways to perverse cultures
20. Exponential growth vs. arithmetic growth. Which one is faster? Which one occurs in microbes?
21. Know how to calculate the total number of microbes if given the number of starting micrones, the doubling time and duration of growth, or the number of generations (times of binary fission division)
22. Name 4 phases of microbial growth. What occurs in each phase? 

1. Define: metabolism, anabolism, catabolism. How are they similar and different?
2. Know the 8 statements that guide the study of metabolic processes
3. List and describe the types of chemical reactions in metabolic processes
4. Catabolic vs. anabolic pathways (energy requirement, energy production, starting materials, products)
5. Exergonic vs. endergonic reactions: energy
6. Closed vs. open system. Which one occurs in a living cell?
7. How many reactions can occur in one catabolic process? 
8. Describe oxidation-reduction reaction, how are electrons transferred in this reaction? What are oxidizer vs. reducer? Are electron carriers the oxidizers or the reducers? Name 3 major electron carriers in the cell?
9. Describe phosphorylation reaction to make ADP and ATP from AMP. Where does the energy used in anabolic pathway come from?
10. What are the roles of enzymes in metabolism?
11. Describe six enzyme categories (names and functions)
12. Components of a holoenzyme. 
13. Are enzymes always proteins? 
14. How do enzymes affect the activation energy requirement in a reaction?
15. What is “enzyme turnover number”? What can affect enzyme turnover number? Be able to interpret an enzyme’s activity on an activity chart and deduce the effects of temperature or pH or substrate concentration or inhibitors. What does “saturation point” mean?
16. Types of enzyme’s inhibitors? How do they inhibit enzyme’s activities?
17. Describe competitive vs. noncompetitive inhibitors of enzymes. What is another name for noncompetitive inhibition?
18. Understand feedback inhibition
19. What does “amphibolic pathway” mean? Give examples. Be able to name the products of anabolism and catabolism for: carbohydrates, amino acids, proteins, nucleotides, fatty acids
20. Describe the pathways of glucose catabolism: glycolysis, Kreb cycle, ETC, fermentation. For each pathway, know the starting materials, products, how many molecules of each materials or products, is energy required? the overall reaction equation, net energy yielded (produced), location of reaction.
21. What is the key difference between aerobic and anaerobic respiration? 
22. What are the two alternative methods to glycolysis? Is there a difference in the amount of energy produced?
23. What is chemiosmosis?
24. Differences in location of glycolysis, Kreb cycle, ETC, and fermentation between prokaryotes and eukaryotes
25. Describe alcohol vs. acid fermentation. What are the indicators if a bacterial species performs alcohol or acid fermentation or both?
26. Describe lipid catabolism.
27. Describe protein catabolism. 
28. What is the common feature in lipid, protein, and carbohydrate catabolism?
29. What are the starting materials in the anabolic pathway for polysaccharides, lipids, amino acids and proteins?

1. Know all definitions/terminologies
2. Know and describe 3 routes in which genetic materials flow in bacteria: within the cell, horizontal transfer, vertical transfer
3. Genome structures of prokaryotes vs. eukaryotes
4. How are chromosomes packaged in eukaryotes vs. prokaryotes?
5. What are the characteristics of plasmids? Types of plasmids? What does “autonomously replicating” mean?
6. How many origins of replication does a plasmid have?
7. What types of bonds hold the DNA double helix together? What does “antiparallel”, “semiconservative”, “bidirectional” mean in DNA replication?
8. How are new nucleotides added into the growing strand of nucleotides? (which enzyme, which direction, which bond, which specific components)
9. Describe ALL steps in DNA replication: enzymes, what occurs, products, energy, what may go wrong at each step? For example, what would likely happen if single-strand binding proteins failed to bind to the unzipped DNA? etc.
10. Know the synthesis of leading strand vs lagging strand
11. How many leading strands and lagging strands can be made at one origin of replication? How are Okazaki fragments sealed (primer removal, DNA nucleotide replacement, sealing)? How many primers are present in a lagging strand with 4 Okazaki fragments and so on?
12. DNA replication in eukaryotes vs. prokaryotes
13. Proof-reading activity of DNA polymerase, RNA polymerase
14. Mutation repair mechanisms: mismatch repair vs nuclease excision repair. What happens in each mechanism, enzymes involved
15. Rolling circle model (link (Links to an external site.)) vs. theta model (or bidirectional model, link (Links to an external site.)) of plasmid replication
16. What are the steps of gene expression?
17. Describe ALL steps of transcription and translations: starting materials, enzymes at each step, energy requirement, location/organelles, additional modification
18. Types of tRNAs
19. What are: promoter, transcription unit, start point?
20. Roles of RNA polymerase. How is RNA polymerase different from DNA polymerase?
21. Know how to convert a DNA sequence into an RNA sequence, and into an amino acid sequence. An in the reverse direction?
22. What are present in a transcription initiation complex? Where is the TATA box located? Rate of transcription? How many mRNA molecules can be made from one gene/gene cluster?
23. Rho-dependent vs. Rho-independent termination of transcription in prokaryotes
24. How is transcription terminated in eukaryotes? (Know differences in transcriptional termination of prokaryotes vs eukaryotes)
25. How are genes arranged in prokaryotes vs. eukaryotes (how many promoters for how many genes? 
26. Describe mRNA processing. Does it occur in prokaryotes or eukaryotes or both? What do the 5’-UTR and 3’-UTR on the mRNA of prokaryotes correspond to on the mRNA of eukaryotes? 
27. What are codons? How many codons code for one amino acid? How many amino acids can be coded for by one codon?
28. What does the statement “The genetic code is redundant” mean?
29. Why must codons be read in the correct reading frame? If provided with the amino acid chart, know how to get the amino acid sequence from mRNA sequence or coding DNA sequence (DNA sequence that is transcribed into exons of mRNA)
30. Know the structural components of tRNAs
31. Prokaryotic vs. eukaryotic ribosomes
32. The 3 sites in ribosomes. What is present at each site during translation?
33. How is translation initiated? Know sequential steps. Energy?
34. What occurs in translational elongation? Steps. Enzymes. Energy.
35. Describe translational termination. What would happen if the release factor cannot hydrolyze the polypeptide? What else could go wrong? 
36. What are polyribosomes? Are they present in prokaryotes or eukaryotes or both? How many proteins/polypeptides can be made from one mRNA molecule? From one coding DNA molecule?
37. How is translational accuracy maintained?
38. What is “wobble”? How are wobbles beneficial?
39. What does it mean to say “bacterial transcription and translation occur simultaneously”? What benefits does simultaneous transcription and translation offer?
40. At which levels can genes be regulated? Describe.
41. What are ways to regulate protein synthesis? To regulate mRNA synthesis? 
42. What is an operon? Describe the structure of an operon.
43. Describe how an inducible operon and a repressible operon is regulated. Know the steps in the examples of Trp operon and Lac operon. 
44. Describe positive regulation vs. negative regulation. Are activators or Repressors involved? Where do activators and repressors bind? What are the outcomes in each type?
45. Are regulatory genes always transcribed and translated into regulator proteins? How do they work in repressible vs. inducible operon regulation? What are co-repressors and inducers; and how do they work?
46. Describe each type of mutations: are they permanent, their effects. Which type of mutations will negatively affect the cells the most?
47. What are mutagens? Describe types of mutagens.

1. Know ALL definitions
2. Know 4 general actions of antimicrobial drugs
3. Know the contributions of Paul Ehrlich, Alexander Fleming, and Gerhard Domagk 
4. What are the 6 mechanisms of action of antimicrobial drugs? For each, name, describe.
5. Name examples cell wall synthesis inhibitors and their specific inhibitory actions
6. What makes a bacterial strain resistant to Penicillin?
7. Why do we use antimicrobial derivatives? What are the derivatives of Penicillin, cephalosporin, monobactam?
8. What are the limitations of cell wall synthesis inhibitors?
9. Name examples protein synthesis inhibitors and their specific inhibitory actions
10 .Name examples cytoplasmic membrane disruptors and their specific inhibitory actions
11. Name examples of metabolic pathways inhibitors and their specific inhibitory actions. What is PABA and how is its activity blocked?
12. Name examples of nucleic acid synthesis inhibitors and their specific inhibitory actions
13. Name examples of pathogen attachment inhibitors and their specific inhibitory actions
14. What are the characteristics of an ideal antimicrobial agent? Must all characteristics be met?
15. Describe the diffusion susceptibility test and result interpretation
16. Describe the routes of drug administration
17. Describe the relative drug concentration in blood when administered by oral vs. intramuscular vs. intravenous routes
18. Name the side effects of antimicrobial drugs
19. How can microbes acquire resistance to antimicrobials? Describe 2 major routes.
20. How do we combat resistance problems in microbes? 
21. What is multiple resistance vs. cross resistance?