Chapter 5. Intermediary Metabolism
1. Define metabolism, anabolism, and catabolism. What is the difference between anabolism and
    catabolism?
2. You must be familiar with microbes nutritional requirements: carbon source, energy source
3. Identify and define the components of an enzyme. What is the complete enzyme/incomplete
     enzyme?
4. What are the factors that affect enzyme function?
5. What is an enzyme cofactor?
6. You need to know the concepts of competitive, allosteric and feedback inhibition
7.  What are the chemical definitions of “oxidation” and “reduction”. What is meant by a "coupled"
    oxidation-reduction reaction.
8. Briefly describe the two different processes in which cells are able make ATP.
    What are the names that are used to describe these processes. Be able to explain why one of
    these  processes can generate most of the ATP.
9. Aerobic respiration involves the breakdown of sugars (other molecules too) by using 3 metabolic
     pathways: glycolysis, Kreb's cycle and electron transport chain.
10. Describe in conceptual terms the outline of reactions involved in glycolysis.  What are the end
    products of glycolysis in the absence of oxygen? Why is it necessary to generate these end
    products even though they are highly toxic to the cell’s metabolism?
11. What happens in Krebs cycle? What comes in/out? Where does it take place?
12. What happens in the electron transport chain? What is chemiosmosis? How it relates to
     production of energy? What comes in/out? Where does it take place?
13. What happens in fermentation?
14. For each of these metabolic pathways you need to know: 1) Where are they taking place in both
     pro- and eukaryotes, 2) What comes in, and 3) What comes out.
15. Finally, you need to know how aerobic, anaerobic and fermentation relate in terms of 1) net
     energy production and 2) final electron acceptors.

Chapter 6. Growth and culturing of bacteria
1. Understand the reason that we describe the growth of bacteria as “exponential growth”. Be able to     calculate how many cells exist in a population from the initial number and the number of cell
    divisions attained or from the initial number, the incubation time, and the generation time.
2. What are the two ways in which we can “plate” bacteria in order to determine the population size
    of live organisms? How does a microbiologist define whether a microorganism is alive or not?
3. How do we calculate the population size of a bacterial culture by a colony forming unit (CFU)
    assay? In this context, understand the concept of a “dilution factor and serial dilution’. What is the
    dilution factor when we make a 1:9 dilution?
4. Be able to demonstrate how one would calculate the colony forming units per ml using the assay
    from  questions 3.
5. What are the other ways by which we can determine directly or indirectly the population size of a
    microbial culture? In particular, understand what “absorbance” or “turbidity” measurements are.
    How  the  “Petroff Hausser” chamber is used? Advantage and a disadvantage?
6. Understand how physical factors (temperature, pH, osmotic pressure, etc) can affect bacterial
    growth.
7. How can organisms that live in extreme temperature environments survive and have functional
    metabolism? (membranes and internal regulation!)
8. Understand that the optimum temperature for growth of any organism is simply a reflection of the
    optimum temperature for enzymatic activity for the majority of the enzymes in the cells of the
    organism. Why does the enzymatic activity fall off rather sharply when we exceed the optimum
    temperature? What is happening to the enzymes? What do we mean by the terms psychrophiles,
    mesophiles, and thermophiles? What determines the temperature extremes beyond which cells can
    no longer function no matter how much time we allow those cells to adapt to the temperature
    extremes by evolution.
9. Define the process of osmosis. Why is osmosis important to microorganisms and how do we use
    the effects of osmosis to preserve foods.
10. What is the difference between bacteria that are obligate aerobes, obligate anaerobes, and
    facultative anaerobes? What enzymes are critical in the survival of these organisms?
11. What effect do variations in the pH of the environment have on the ability of enzymes within a cell
    to function?
12. Be able to list the most important macronutrients and trace elements. Where macronutrients will
    be utilized? Where trace elements will be utilized?

Bacteriological media and techniques.
1. How does one do an “isolation streak plate” in bacteriology and why would we want to carry out
    this process. What are disavantages of pour plate and streak plate isolation techniques?
2. What do we mean by complex media, defined medium?
3. When can we use liquid or solid culture medium?
4. What are the special properties of agar used to produce solid microbiological media? Why do
    common hardeners such as gelatin not work for this purpose?
5. What do we mean by a selective medium and when would we use such a medium?
6. What do we mean by a differential medium? What type of information do we get by plating an
    unknown bacterial culture on a differential medium? Be able to give at least two examples.
7. What are some of the reasons that we frequently plate clinical bacterial unknowns on blood agar?
8. In addition to MSA and Mac media, you need to knwo whether Brilliant green agar (BGA) is
    selective or differential. What makes it selesctive or differential?

Chapter 7. Microbial genetics
1. You need to define the following terms: genotype, gene, allele, phenotype, chromosome, genome,
    haploid and diploid.
2. Be able to describe the structure of DNA (phosphodiester backbone, double stranded, hydrogen
    bonded base pairs). What do we associate with 3' or 5' ends?
3. What are the concepts that are collectively known as the "central dogma"?
4. What are the differences between DNA and RNA?

Replication, Transcription, RNA Processing and the Genetic Code
1. Define replication. Name and be able to identify the components of this process. Learn the location
    of all these components in the replication bubble. Why replication is said to be semiconservative?
2. Define transcription.  What is the role of sigma? What is the role of RNA polymerase? .
3. What is your interpretation of mono and plycistronic mRNAs?
4. What we mean when we say the genetic code is "degenerate"? What are sense, nonsense codons?
5. Describe the functions of DNA sequences known as "exons" and "introns" in eucaryotic genes.
6. Briefly describe the post-transcriptional modifications of mRNA in eucaryotic cells. What is the
    function of the CAP structure and the poly A tail on eukaryotic mRNA?
7. What do we mean when we say that transcription and translation are coupled in bacteria but can
    not be coupled in eukaryotic cells?
8. What is the function of the “Shine-Dalgarno” sequence in mRNA transcripts in bacterial cells?
9. Describe what is meant by operons in bacterial cells. What is the advantage to bacteria to have
    operons? Why can eukaryotic cells not have operons?
10. In translation, you need to knwo the energy requirement (ATP) per amino acid. Where are the
      codons, anti-codons found? What is the start, stop codon(s)?
11. Why

Control of Gene Expression in Bacteria
1. Why is it of critical importance for bacteria to finely control gene expression?
2. Be able to explain why the control of expression of gene products (enzymes) used in metabolism.
    Why are some enzymes inducible while others are constitutive?
3. Understand the role of promoter and operator in operons.
3.  Explain the rationale as to why a bacterium having a source of glucose will not use a source of
    lactose sugar that becomes available (you need not know the mechanism by which this is done).
4. What does the term "constitutive synthesis" of a gene product mean and why is the synthesis of
    glucose constitutive?
5. Learn gene regulation by using the lactose operon as an example.
   You need (as it applies to the Lac operon) the mechanisms involved in the control of gene
    expression by catabolite repression.  How this system works when:
    a) You only have lactose
    b) You only have glucose
    c) You have lots of lactose and lots of glucose
    d) You have lots of lactose and no glucose
6. What is the role of cAMP? How camp and glucose interact with each other?

Mutations and Mutagenesis
1. Define what is meant by a "point mutation".  Be able to describe mutations which are and which
    are not point mutations. What do we mean by a "silent" mutation and why are most point mutations
    silent.
2. Know what is meant by point mutations and framshift mutations.  Why would you
    expect that most point mutations that cause a change in the activity of a gene product would
    decrease the activity rather than increasing it?
3. What is meant by a nonsense mutation? Why do large deletions or insertions in a gene in the DNA
    as well as nonsense mutations usually cause the complete loss of activity of the gene product?
4. What is a mutagen?  What is the advantage of using mutagens? What are the most classical
    mutagens?
5. How can you select mutants? Provide examples of positive selection. Be familiar with
    auxotrophs and replica plating.
6. The Ames test measures the mutagenic potential of a chemical in people by measuring the
    mutagenic effect on bacteria.  What is the basic assumption?  What part of the Ames test makes the
    results relevant to humans?

Chapter 8. Gene Transfer in Bacteria
 1. What was the classical experiment by Griffith that established the presence of a “transforming
    factor”?
2. What is transformation? Why it occurs in nature? When can bacteria uptake DNA?
3. What is transduction? How this genetic exchange is mediated?
4. What is called a virus that infect bacteria? What is the name for a virus that can be either lytic or
    lysogenic?
5. Establish the difference between specialized and generalized transduction.
6. What is conjugation? How is this mechanism mediated?
7. Be able to understand the genotype (outcome) of the recipient during the three conjugation
    processes.
8. What are the phenotypes of bacteria involved in conjugation?
9. Define plasmids? Why are plasmids important?
10. What are transposons? Why are they important? Can these elements move only within the
       bacterial chromosome?
11. You should be able to use the U-tube experiment to demonstrate the 3 forms of gene transfer.