Study Guide for Exam 1

Intro, Structure and Function of Prokaryotes

1. Famous microbiologists.  know what country they were from.  know what particular advance they are associated with.  For Pasteur and Koch, this is several. For the others: Semmelweis and Lister: various forms of aseptic technique in medicine. Leeuwenhoek, first viewing of microbes; Jenner, using cowpox in vaccinations;  Ehrlich, the idea of antibiotics. Know who lived during the "golden age" of microbiology (circa 1850-1920) and who lived earlier (Jenner, Leeuwenhoek).

2. What are the 3 domains of living things? Which are prokaryotic and which are eukaryotic? What are the 4 Kingdoms of eukaryotes? Which have microbes in them, or better, which have organisms that Microbiologists sometimes study?  Know the binomial naming system for bacteria, the Genus species method where the genus is capitalized, the species epithet is not, and the whole name is underlined or italicized. Why do most scientists NOT consider viruses to be alive?

3. How did people in early history have a basic understanding of some of the principles of microbiology? When did people first discover that microbes exist? How long has microbiology been a science? How did microbiology contribute to the science we now call molecular biology? What are some of the pressing issues in contemporary microbiology? What are various subdivisions of microbiology called, like the study of viruses, the study of fungi, etc? Know the basic concepts of science. What is a control?

4. Be sure to know all your basic chemistry. Know the definitions including suspension and solution, molecule, compound, different types of bonds (hydrogen, covalent, etc.), hydrophilic and hydrophobic. Be able to explain the pH scale and why neutral is 7 instead of some more reasonable number; know the chemical and numerical basis for how pH 5 differs from pH 6.  Know the four classes of biological molecules, which molecules are low molecular weight versus polymers, the definition of polymer. Know the functional groups and the basic structures of biological molecules. understand the importance of water in living systems.

5. Begin to know the relative sizes of all the things we talk about in class. Know the prefixes of the metric system. Know the fundamental principles of light microscopy: wavelength, contrast, magnification, resolution.  Know the different types of light microscopy.  Know how electron microscopy differs; be able to compare to light microscopy. Which type of electron microscopy magnifies the most, TEM or SEM? Which produces 3D images rather than 2D cross sections? Be able to write a short paragraph outlining how fluorescence and laser confocal microscopy work.

6. What did Schleiden and Schwann say about living things? What features are common, if slightly different, to both eukaryotic cells and prokaryotic cells? What things are particular to one or the other? How big are bacteria, typically?  What shapes do they come in? In what arrangements are they sometimes stuck together?

7. Carefully study how bacteria are put together. What molecules are the different parts of a cell made of? What is the difference between Gram negative and Gram positive cells? What do they have in common?  What molecules can be found in one but not the other? Briefly, how are Archaebacteria different from Eubacteria?

8. What is the structure of a cell membrane? What are the two major components? What is a cell wall made of?  What is the structure and function of: peptidoglycan, the outer membrane, a capsule or slime layer, S layer,  flagella, fimbriae and pili? Know all about tonicity and osmosis. Be sure you understand the lab experiment you did and see how it was intended to demonstrate osmosis and how the peptidoglycan works. Know the various types of molecules found in a bacterial cell wall and know whether they are associated with Gram negative, Gram positive, or both. (e.g., teichoic acid? mycolic acid? LPS?)  Why do bacteria have slime layers and capsules?  What are fimbriae and pili used for? What is the periplasmic space? What makes up the periplasm? Be able to draw a diagram of a bacterial cell or recognize and label parts on a diagram.

9. What is the structure and function of the things inside a bacterial cell? What two "structures" are made of DNA?  Why are there inclusions and granules?  What are magnetosomes for?

10. How is the purpose of a simple stain different from that of a differential stain like a Gram stain?  What are the steps in the Gram stain?  Know what result you will get if you mess up a particular step in the procedure.

11. What is aseptic technique;  what is it for?  What are some things not allowed in the lab?  Where do you dispose of used slides? Be able to correctly write and spell the names of some of the bacteria we have worked with in lab. Where is the fire extinguisher in the lab?

12. Know the principles of spectrophotometry.  What is a control, what is it's purpose?  Define a colony.  Define a pure culture.

Metabolism

1. Definitions: What is metabolism? What are anabolism, and catabolism? Be able to recognize examples of each.  What are autotrophs and heterotrophs? Chemolithotrophs, chemoorganotrophs, photoautotrophs?

2. What is oxidation?  Reduction? Be able to identify which molecules in a reaction are getting oxidized and which are getting reduced. Why is it that a dehydrogenation is an oxidation?  Be able to look at the structure of a molecule and determine whether a bacterium is likely to get much energy out of the molecule or not (how reduced is it?) Know that the oxidation number of H is +1 and of O is -2; be able to do a redox calculation.

3. Why is it important to cells to make ATP? If every oxidation is coupled to a reduction and many reactions are reversible, why do oxidations release energy?

4. What is a biochemical pathway? What are enzymes made of? What is a catalyst? How many enzyme molecules are needed to turn 100 molecules of PEP into 100 molecules of pyruvic acid?  How many different ways of slowing or stopping the function of an enzyme are there? What are: an apoenzyme? holoenzyme? cofactor ("coenzyme")?

Self Quiz on Metabolism -1  Do these on the computer. Decide on your answer, then highlight the invisible text after the "*" by selecting it with your cursor.

5. C₆H₁₂O₆  +  6 O₂  goes to 6 CO₂  + 6 H₂O
This equation describes the complete oxidation of glucose. Estimate how many NADHs will be made in this process, remembering that NADH carries 2 electrons per molecule. First calculate the oxidation number for glucose, then for CO₂, remember that glucose has 6 carbons.

6. What are the main pathways of central metabolism, and what are the main things that happen in each: What are the results of glycolysis? Krebs Cycle? What makes the Krebs cycle a cycle? What happens during electron transport? How does chemiosmosis work?

7. Oxidative metabolism is a term used to describe the process cells use to get energy out of a molecule like glucose and into the form of ATP, using molecular oxygen as terminal electron acceptor. The energy in glucose appears in different forms throughout this process. What forms are these?

8. What is a "phosphorylation"? What different types of phosphorylations can occur in metabolism?

9. Besides "glycolysis", how else can some cells break down glucose? What special things should you remember about these other 2 pathways?

10. Respiration is defined as an energy releasing process that produces carbon dioxide as a waste product, and this is coupled to an electron transport system for getting rid of the electrons after the carbon atoms have been oxidized. What is the difference between oxidative respiration and anaerobic respiration? How is fermentation different from anaerobic respiration?

11. What is the role of fermentation in food production? In bacterial identification? In fermentation, energy rich molecules are thrown away.  Are the enzymes of the Krebs cycle needed by anaerobes? Why or why not?

12. Central metabolism describes primarily glycolysis and Krebs Cycle and refers to the fact that many other carbon sources besides glucose can be used as nutrients. When these substances are broken down, they are "funneled" into glycolysis and Krebs cycle and are further broken down by these pathways. In addition to providing energy, what other important role does Central Metabolism play?