Lab 13 Biochem Part 1

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Feb 20, 2024

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BIOCHEMICAL REACTIONS : Part 1 Carbohydrate fermentation Nitrate reduction Gelatin hydrolysis OBJECTIVES: Students should be able to 1. explain the biological basis of each biochemical reaction 2. learn how to perform each biochemical test and interpret the test reaction 3 . understand how each test might be used in the identification of a species INTRODUCTION Bacteria are among the most diverse organisms with respect to the types of enzymes they contain, and the distribution of these activities can be used in distinguishing one organism from another. You will be using some of the more common biochemical tests here and will be introduced to others later in the semester. These tests may prove useful in the identification of your unknown. A variety of media are designed to facilitate determining these biochemical reactions of bacteria. ACTIVITY 1: CARBOHYDRATE FERMENTATION REACTIONS Many bacteria utilize a variety of carbohydrates as a source of energy (ATP) and some can use these carbohydrates through more than one pathway. Strict aerobes oxidize sugars to carbon dioxide and water through the process of aerobic respiration , using an electron transport system and molecular oxygen as the final electron acceptor. Facultative anaerobes and many strict anaerobes perform fermentation reactions. No electron transport system is used in fermentation and oxygen is not involved. Instead, they oxidize sugars to organic intermediates that act as the final electron acceptor and in the process create organic compounds (acids, alcohols, aldehydes) that are the end products of the reaction. Fermentation is not as efficient an energy-yielding process as aerobic respiration. Facultative anaerobes possess the enzymes that allow them to perform either respiration or fermentation depending upon the availability of oxygen. The compounds that an organism can break down through fermentation and the end products they produce are genetically determined. Among the end products commonly generated by fermentation are organic acids and gases such as CO 2 . PHENOL RED CHO BROTH To determine whether an organism can use a specific sugar for fermentation, the test medium contains:
1) a single sugar that may be used for energy production, 2) non-fermentable sources of nitrogen and other nutritional requirements , 3) a pH indicator phenol red ( color < pH 6.8 = yellow; pH 6.8 7.4 = red pH >7.4 = pink/magenta) 4) a Durham tube (an inverted vial) that collects any gas products. Base medium: The specific sugar tested is added to the medium. Pancreatic Digest of Casein 10.0gm Sodium Chloride 5.0gm Phenol Red 18.0mg Final pH 7.4 +/- 0.2 at 25ºC. Growth is determined by turbidity. A positive fermentation reaction is indicated by a change in the color of the phenol red dye from red to yellow, indicating a drop in pH below pH 6.8 due to the production of acid end products. An intense pink color indicates the inability to ferment that carbohydrate and the creation of an alkaline environment from ammonia produced from degradation of proteins in the medium. Gas production, if observed by a bubble within the Durham tube, is also recorded. Un- inoculated controls must be run to accurately evaluate results. MATERIALS Fermentation broths glucose, sucrose, lactose 3 of each for a total of 9 tubes Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus in broth
METHODS 1. Inoculate a loopful of each organism into each type of broth. 2. Incubate for 24 - 48 hours at 37°C. RESULTS glucose/lactose/sucrose Examine the tubes for growth (+), acid (A) and gas production (G) and compare to a control uninoculated tube. Record your results. In describing the reactions of bacteria fermenting a carbohydrate, microbiologists use a shorthand to indicate the result: Yellow = acid production; indicated by “A” Pink = alkaline production; indicated by “K” Red = no reaction; no change in pH Bubble in the Durham vial = gas (CO 2 ) production indicted by a + Compare the fermentation results for these organisms by indicating the color of the tube and whether there is any bubble in the Durham vial by completing the table using the shorthand from above. Organism Glucose Sucrose Lactose E. coli Yellow; A+ Ps. aeruginosa S. aureus DISCUSSION QUESTIONS 1. What does the yellow color indicate? 2. What is the gas that is collected in the Durham vial? 3. Pr. mirabilis can ferment glucose producing gas but is negative for both lactose and sucrose. What would the tubes for Pr. mirabilis look like? 4. Sucrose is a disaccharide composed of glucose and fructose. Explain why some organisms that can ferment glucose cannot ferment sucrose. 5. Would you expect a microbe that ferments lactose to also ferment glucose? Why? 6. What does an intense pink color indicate? How does this occur?
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ACTIVITY 2: GELATIN HYDROLYSIS Many bacteria secrete enzymes that break down macromolecules into smaller subunits that can be transported into the cell and used for growth. For example, amylases will release glucose from starch and lipases will degrade lipids into glycerol and short hydrocarbon chains. This test is performed to determine the ability of bacteria to produce gelatinase , a proteolytic enzyme that degrades gelatin (a protein). This is called gelatin hydrolysis. The medium used is a deep of Nutrient Gelatin, which is made solid by the addition of gelatin instead of agar. Ingredients per liter of deionized water. Gelatin 120.0gm Peptone 5.0gm Beef Extract 3.0gm Final pH 6.8 +/- 0.2 at 25ºC. The result of gelatin hydrolysis is the liquification of the medium. Nutrient gelatin is inoculated by stabbing directly into the center of the tube with an inoculating needle. The tube is incubated at room temperature to keep the gelatin from melting. Positive gelatin hydrolysis is shown by a liquification of the media, usually seen at the surface. It may take as long as a week for this to be visible. MATERIALS E. coli, Bacillus sp. Micrococcus luteus Nutrient gelatin deeps METHODS 1. Inoculate each organism into the Nutrient gelatin using an inoculating needle stabbing straight down into the center of each tube. 2. Incubate at room temperature.
RESULTS Inspect for liquification by tilting the tube. Due to the relative low temperature of the incubation, results may not be valid until a week. DISCUSSION QUESTIONS 1. Why is the incubation temperature less than 37°C? 2. Are the microbes fermenting gelatin? 3. You mistakenly incubate at 37°C. How can you now determine whether the organism is positive or negative for gelatin hydrolysis? 4. What type of molecule is gelatin? What is the action of gelatinase? How does this enzyme help the microbe?
ACTIVITY 3: NITRATE REDUCTION TEST The Nitrate Reduction Test is used to distinguish between bacteria that can use nitrate (N0 3 ) as a final electron acceptor in anaerobic respiration and those that cannot. Organisms that perform nitrate reduction may reduce it to nitrite (N0 2 - ) or to other end products including complete reduction to nitrogen gas (N 2 ). NO 3 - NO 2 - NO N 2 O N 2 The test utilizes Nitrate broth and the tube also contains an inverted Durham vial. Ingredients per liter of deionized water: Pancreatic Digest of Gelatin 5.0gm Beef Extract 3.0gm Potassium Nitrate 1.0gm Final pH 6.9 +/- 0.2 at 25ºC. The reading of the results is dependent on the proper interpretation of the color changes, and these depend on what is added to the tubes. MATERIALS per student pair Nitrate Broth Cultures of E coli , Pseudomonas aeruginosa and Enterococcus faecalis . Sulfanilic acid and dimethyl-naphthylamine Powdered zinc METHODS 1. Inoculate each organism into a tube of nitrate broth. Make sure that there is a Durham vial in the tube. 2. Tubes are incubated at 37 0 C. 3. After incubation, observe for gas in durham vials. Then to the tubes without any gas, add 5 drops each of sulfanilic acid and dimethyl-napthylamine. Record the color change. If there was no color change, add a small pinch of zinc powder. Record the color.
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RESULTS If there is gas in the Durham vial , this indicates that the organism has reduced nitrate to nitrogen gas. (There is no carbohydrate for fermentation so any gas in the vial must be due to the production of N 2. ) This is a positive nitrate reduction test, and no further steps need to be taken. If there is no gas in the Durham vial, the next step is to test for the presence of nitrite (N0 2 - ) . Two reagents ( sulfanilic acid and dimethyl-naphthylamine) are added to the tubes. If there is nitrite in the tube, the medium turns red . This is a positive nitrate reduction test. However, if the medium does not change color , it means that the organism either has not reduced nitrate or that the bacteria have reduced nitrate beyond nitrite such as to NO (nitric oxide) or N 2 0 (nitrous oxide) but not to nitrogen gas. To distinguish between these possibilities, powdered zinc is added to the tube. This will catalyze the reduction of any unreduced nitrate to nitrite, which will then react with the two reagents already in the tube to form a red color. Thus, if the medium turns red after zinc , it is a negative nitrate reduction result (indicating that nitrate was still in the tube). If the medium remains unchanged after adding zinc , then there was no nitrate remaining in the medium, meaning that it was reduced beyond nitrite, and the bacteria are identified as positive for nitrate reduction as there is no nitrate left to be reduced by the zinc. Record your results for each of the organisms in the table below: w/zinc
Gas in Durham vial? Result after sulfanilic acid & dimethyl- napthylamine Result after zinc powder Did nitrate reduction occur? Escherichia coli Pseudomonas aeruginosa Enterococcus faecalis DISCUSSION QUESTIONS 1. Answer the following questions in the table: Gas in durham vial Sulfanilic acid & dimethyl- napthylamine Zinc powder What does a positive reaction look like? Positive reaction indicates the presence of what molecules? What does a negative reaction look like? Negative reaction indicates what possible molecules may be present? 2. How would the tube look at the end of the test if the organism reduces nitrate to NO? If there is no nitrate reduction? 3. Why is zinc powder added to the tube? 4. What does the bubble in the Durham vial indicate? What is the gas in the vial? 5. Why doesn’t the medium contain a pH indicator?