Carbon (C), Nitrogen (N), Oxygen (O), Hydrogen (H)
-creates CARBOHYDRATES, LIPIDS, PROTEINS, and NUCLEIC ACIDS
-most organisms (like humans) break down carbohydrates in order to create ATP for energy
-carbohydrates are also used for structures (ex. cellulose, peptidoglycan)
-lipids are used for cell membranes, energy storage
-proteins are used for enzymes, which build up complex carbohydrate structures or break them down for energy; proteins require a specific temperature and pH to work properly (in humans it's 98.6 degrees Fahrenheit); they are also used for structural purposes
-nucleic acids are necessary to store information that leads to protein synthesis (messenger RNA), create RNA, which is necessary to duplicate DNA, and also stores ATP
Fungi: Single celled eukaryotic organisms that cluster to create the things that are seen (fungus, mushrooms, etc.)
Protista: Single celled eukaryotic cells that cause things like malaria; this kingdom is relevant to humans because a lot of infections contracted are via protista
Monera: Prokaryotic cells (no plasma membrane, nucleus, mitochondria, etc.)
-this group houses categories like ARCHEOBACTERIA (almost all extremophiles), GRAM POSITIVE and GRAM NEGATIVE bacteria (take up certain stains), MYCOPLASMA (no peptidoglycan layer), CYANOBACTERIA (undergo photosynthesis), SPIROCHETES (posses flagella), and RICKETTSIAS and CHLAMYDIAS (intracellular parasites that infect eukaryotic cells)
First step in breaking down glucose for ATP
-takes place under ANAEROBIC conditions (does not require oxygen)
1. A phosphate group from ATP is transferred to glucose, forming GLUCOSE 6-PHOSPHATE
2. The glucose molecule is rearranged to form FRUCTOSE, and a second phosphate group is transferred to this structure (from another molecule of ATP) in order to create FRUCTOSE 1,6-DIPHOSPHATE
3. The six carbon sugar fructose is split into two different three carbon sugars; FROM THIS POINT ON THE SAME THING OCCURS TO BOTH THREE CARBON SUGARS
4. Another phosphate group is added, and two hydrogen atoms, with their electrons, are transferred to a molecule of NAD, creating NADH
5. A phosphate group is transferred to a molecule of ADP, forming ATP
6. The remaining phosphate group is moved from the end to the middle carbon atom, and a molecule of water is ejected
7. The phosphate group is transferred to another molecule of ADP, producing another molecule of ATP and leaving PYRUVIC ACID (also known as PYRUVATE); a three carbon compound
Glycolysis ultimately nets 2 ATP (creates 4, but uses 2), and creates 2 molecules of pyruvic acid
-this is a very inefficient breakdown of glucose, and the resulting NADH from this process must be transformed back into NAD for the next round of glycolysis
Textbook: Figure 5.11
When observing bacteria within a medium, the growth can be carefully observed and put into a graph
The bacteria first undergoes a LAG PHASE; this phase is very metabolically active, yet the cell number does not increase very much
Once the cells start growing, they will begin to grow exponentially; this is called the LOG PHASE
-here, a generation time can be established (how long does it take for the cell population to double, etc.)
After a while, the cell population will plateau; this is called the STATIONARY PHASE
-at this point, the cells are still dividing, but cells are also dying at an equal rate
-this is because cells are excreting waste into the medium, making it unsuitable to grow
Cells will then begin to die off in the DEATH PHASE
-much like the log phase, calculations can be made on the population; death rate, etc.
Textbook: Figure 6.3
When attempting to grow cultures within the lab, factors such as temperature, pH, and oxygen requirements are necessary to successfully maintain a cell population
-Most pathogenic bacteria are neutrophils; they thrive in a neutral pH
-HELICOBACTOR PYLORATE is one of the few acidophils that are pathogenic to humans
-VIBRIOCHOLERA is one of the few alkaliphiles that are pathogenic to humans
Temperature (Figure 6.14)
-Most pathogenic bacteria MESOPHILES; work in warm temperatures
-PSYCHROPHILES work in cold temperatures; and example of a psychrophile that can affect humans is LISTERIA, which is found in dairy products
-Thermophiles work at higher temperatures
-Extreme thermophiles work at very hot temperatures
-we use these extremophiles for a lot of everyday life; ex. enzymes in detergents that can digest fats found in the soil of laundry
Oxygen (Figure 6.15)
-OBLIGATE AEROBES absolutely need oxygen to grow; if placed in a stationary tube, the organisms will only grow on the surface-OBLIGATE ANAEROBES cannot grow in the presence of oxygen; grow at the bottom of the test tube
-obligate anaerobes are killed by SUPEROXIDE (O2-), a highly toxic anion found in the air; most organisms have enzymes SUPEROXIDE DIMUTASE, which converts O2- into H2O2 or regular oxygen, and CATALASE, which converts H2O2 into water and oxygen; obligate anaerobes do not possess these enzymes
-MICROAEROPHILES sit just underneath the surface; need oxygen, but very little
-FACULTATIVE ANAEROBES can grow with or without oxygen; in the presence of oxygen, they will grow quickly; without oxygen, they will undergo glycolysis and fermentation; a majority of pathogenic bacteria are facultative anaerobes
To culture obligate anaerobes, all molecular oxygen must be removed and kept out of the medium; this is done via SEALED ANAEROBIC JARS, which contain chemical substances that remove oxygen and generate carbon dioxide or water (Figure 6.22)
Only clostridia and bacillus both create endospores and are harmful to humans
In the event that these organisms notice that an environment is becoming uninhabitable, they begin to create an endospore
1. The cell will begin to wall off a copy of DNA, RNA, ribosomes, enzymes, calcium, dipicolinic acid-anything necessary to create a healthy cell; this is called the CORE
2. The core becomes surrounded by a double membrane; within the double membrane is a peptidoglycan layer; this is called the CORTEX and allows the endospore to survive osmotic pressure changes
3. Wrapped around the cortex is a protein layer called a SPORE COAT; this prevents the endospore from being assaulted by things like chemicals, radiation
4. The spore is then released from the vegetative cell, which has now died
The endospore can live for thousands of years; eventually, when conditions are favorable, the cell will GERMINATE
-the spore coat disintegrates, the peptidoglycan layer breaks down to an extent, allowing nutrients to rush into the core; the cell can now regrow into a vegetative state
Textbook: Figure 6.18a, 16b
Natural Media: The environment in which the organisms grow in nature; pieces of the environment, such as water samples, soil, etc. can be extracted and used as media in a lab setting
Synthetic Medium: The ingredients to this medium is very exact and precisely measured; the composition will always be consistent
Complex Medium: Contains reasonably familiar material, but varies slightly in chemical composition from batch to batch; contains the nutrients necessary for most organisms to grow, but the composition itself is non defined
Selective Medium: Encourages the growth of some organisms, and suppresses the growth of others; used when trying to pinpoint a disease to a certain, suspected organism
Differential Medium: Contains a constitute that causes an observable change (color, change in pH, etc.) in the medium when a particular biochemical reaction occurs; this allows observers to distinguish a certain types of colonies growing on the same plate
Enriching Medium: Similar to selective medium; encourages growth for a specific organism via a growth factor; does not actively kill other bacteria, but stimulates the growth of one particular organism
1. Bacterial cells that are in or on our body outnumber human cells 10:1. It is estimated that there are 10^30 bacteria on earth.
2. Bacterial size is recorded in micrometers. Most bacteria fall into the size range of between 2-4 micrometers whereas most viruses fall into a size range of 30-300 nanometers.
3. Depending on the type of electron microscope, it can magnify from 50,000X to 500,000X. Electron microscopes differ from light microscopes since they use a beam of electrons instead of a beam of light. They also focus the electron beam with electromagnets whereas light beams are focused with glass lenses.
4. The cell wall is outside the cell membrane of bacterial cells. It gives the cell shape and helps to prevent it from bursting if fluids flow into the cell.
5. The peptidoglycan layer is a major component of the cell wall and is composed of N-acetylglucosamine, N-acetylmuramic acid and a tetrapeptide. Gram positive organisms have a very thick peptidoglycan layer whereas gram negative organisms have a much thinner layer. Peptide bond cross-links hold the layers together.
6. Gram negative bacteria also have an outer membrane component of their cell wall which is directly outside of the peptidoglycan layer. This membrane contains Lipopolysaccharide (LPS) and the Lipid A portion of LPS is called endotoxin. When it is released into the human body during a bacterial infection, it causes blood vessels to dilate with a subsequent dangerous drop in blood pressure.
7. Active cell metabolism takes place within and between the peptidoglycan layer and cell (plasma) membrane of bacteria which is called periplasm. In gram negative organisms, a gap is observed between the peptidoglycan layer and cell membrane called the periplasmic space.
8. The bacterial plasma membrane regulates movement of material into and out of a cell. It also is the location for the electron transport chain carrier compounds and ATP synthase.
9. Enzymes work at an optimal pH and temperature.
10. Glycolysis takes place whether oxygen is present or not. It yields 2 ATP molecules and two NADH molecules from one molecule of glucose.
11. Organisms ferment to recycle NAD. The NADH produced during glycolysis passes off electrons and hydrogen to other molecules so that NAD can be regenerated to be used again during glycolysis.
12. 38 ATP molecules are generated in bacteria when a molecule of glucose is metabolized to carbon dioxide and water by all of the following processes working together: Glycolysis, Krebs Cycle, the Electron Transport Chain and Oxidative Phosphorylation.
13. The electron and hydrogen from NADH are passed to the electron transport chain at a higher entry point (energy level) and 3 ATP molecules are produced from 1 NADH molecule. In comparison, FADH2 passes its hydrogens to the electron transport chain at a lower point (energy level) so only 2 ATP molecules are produced.
14. The electron transport carrier molecules are embedded in the cytoplasmic membrane of the bacterial cell whereas in eukaryotic cells these carrier molecules are located in the mitochondria.
15. The electron transport chain pushes H+ (protons) out of the cell at certain points. The electrons from those Hydrogen atoms continue to be passed down the carriers in the chain with oxygen being the final electron acceptor to form water (with the addition of protons). This overall process creates a proton concentration gradient across the membrane with the proton concentration greatest outside of the cell. This also creates an electrochemical gradient across the membrane with the more positive side of the membrane on the outside. Both gradients are favorable for moving protons from the outside through the channel of the ATP synthase complex. This is referred to as the proton motive force. Energy is released as protons move through the channel and it is captured into the high energy phosphate bond (ADP + Pi to yield ATP) with the help of the ATP synthase enzyme. This process is called chemiosmosis.
16. Intermediate carbon compounds within the Glycolytic pathway and Krebs cycle can be used as building blocks in biosynthetic pathways. That is why these pathways are called amphibolic. A healthy cell must maintain a balance of carbon compounds being used for energy production as well as being used as building blocks for cell structures/components.
17. Review Figure 5.24 to see how these other carbon compounds can be metabolized so they can enter either the Glycolysis pathway or the Krebs cycle. The metabolic pathway called beta oxidation is often used by the cell to do this.
18. The 6 carbons of glucose are lost as 6 molecules of CO2 either during the Krebs cycle or before the start of this cycle when pyruvic acid is converted to Acetyl-CoA.
19. Oxidative enzymes in organisms can cause an unwanted by-product called superoxide (O2-) to form in a cell which is a very toxic form of oxygen. Organisms that can make superoxide dismutase can convert the superoxide to O2 and H2O2. If the organism also makes the enzyme catalase , it will break down the H2O2 (which is also toxic to cells) to water and oxygen. The pattern of oxygen use in a bacterial cell will depend on what enzymes the cell can make to deal with superoxide. Know the terms that are used to describe the oxygen requirements of microorganisms.
20. Bacterial cells can communicate with each other by a process called quorum sensing. The bacterial cells release an inducer and when cells reach a certain concentration (quorum) the inducer will activate genes in these cells. This allows the cells to produce proteins, such as enzymes, in unison, which can help these cells to grow in that particular environment. A community of bacterial cells composed of different species or only one are often referred to as a biofilm.
21. The plural of the word medium is media.
1. What benefits do we receive from microorganisms?
2. What contributions did the following scientists make to Microbiology: Hooke, Pasteur, van Leeuwenhoek, Lister, Metchnikoff, Jenner, Erlich, Beijerinck, Waksman and Fleming.
3. What are Koch's Postulates?
4. Define chemical reactions.
5. Define ionic and covalent bonds.
6. What characteristic of water makes it a good solvent?
7. What functions do carbohydrates, nucleotides, proteins, and lipids have in bacterial cells?
8. Why is ATP important?
9. Define Taxonomy. In the five-kingdom system of classification, the Kingdom Monera is also called Kingdom Prokaryotae. What are the other 4 kingdoms in this classification system?
10. Linnaeus originated binomial nomenclature. Define what that means. Is it possible to look at a name of an organism and tell something about it?
11. Define the resolving power of a light microscope? What 2 things can be adjusted on a light microscope for maximum resolving power. Why do you add oil to the slide when using the 100x objective?
12. Define acidic and basic dyes. Why do bacterial cells need to be stained for best viewing even when they are magnified under a light microscope?
13. What are the six bacterial shapes?
14. An acid-fast stain is used to stain bacteria in the genus Mycobacterium due to what component that surrounds its peptidoglycan layer?
15. Do bacteria in the genus Mycoplasma have cell walls?
16. The flagellum is composed of a hook, filament and basal body (rod surrounded by 2 or 4 rings). How do these parts generate movement?
17. Why does the body of a spirochete rotate like a corkscrew?
18. Describe the 2 types of pili.
19. Bacterial capsules protect the bacteria from what?
20. What is one of the many things that a slime layer can do for bacteria?
21. Name one difference between eukaryotic DNA, ribosomes, plasma membrane and flagella compared to those structures in a bacterial cell.
22. Name one similarity between the 4 cellular components in point 9 when comparing the eukaryotic cell versus the bacterial cell.
23. What would happen to a bacterial cell placed in a hypotonic solution?
24. Describe simple diffusion, facilitated diffusion, active transport and osmosis.
25. Why does the cell need to use ATP to move material across the cell membrane during active transport?
26. What advantage does an endospore provide to a bacterial cell that can produce one?
27. Photoheterotrophs obtain chemical energy from light. How do chemoheterotrophs obtain chemical energy? What can an autotroph use as a carbon source that a heterotroph can't?
28. Enzymes are proteins which act as a catalyst in a metabolic reaction. What does a catalyst actually do? What is the difference between an apoenzyme and holoenzyme?
29. NAD and FAD are coenzymes that are associated with enzymes involved with the breakdown of glucose. What do those two molecules do during the breakdown of glucose?
30. Enzymes can be inhibited by a competitive inhibitor or a non-competitive inhibitor. What is the difference between the two?
31. Define fermentation which takes place in the absence of oxygen.
32. Fermentation products from bacteria are very useful to human life. Name any two fermentation products and what they can be used for.
33. Can the fermentation products help in the identification of a microorganism? Explain.
34. The energy from ATP is released when the high energy phosphate bond is broken. What are some specific things that a bacterial cell does that would require energy (ATP)?
35. What is the difference between anaerobic and aerobic respiration?
36. Bacterial cells divide by binary fission. If a bacterial cell does not separate after dividing, what type of cellular arrangement might one see when looking at cells using a microscope?
37. Describe the 4 phases of bacterial growth.
38. What does a pure culture of bacteria mean?
39. To determine cell concentration in a turbid broth, one would need to perform a serial dilution. Why? What are some other methods that can be used to measure bacterial growth?
40. When one wants to grow a microorganism in a lab, what physical factors do you need to take into consideration to get optimal growth of that organism?
41. When making up a medium that an organism can grow in, name some nutritional factors that you may need to include to get the organism to grow.
42. Why would an organism want to make an exoenzyme?
43. What advantage does a bacterial endospore give to a cell that can make one? Name 2 genera of bacteria that can make endospores and can also cause human disease.
44. What is the difference between the vegetative cycle of a cell and its sporulation cycle?
45. What is the difference between a defined synthetic medium and a complex medium?
46. What is a fastidious organism?
47. If a bacterial cell did not have enough carbohydrates for energy production, what carbon compounds could they use?
48. All catabolic reactions involve electron transfer which allows energy to be captured and used to make the high-energy phosphate bonds in ATP. Define oxidation and reduction.