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Micro Exam3: Microbial metabolism and biochemical assays
Terms in this set (83)
Metabolism: What is it? (List 4)
1) Sum total of all chemical reactions in living organisms
2) Two general types
3) Coupled reactions
Metabolism: What are two general types? (List 2)
Metabolism: What is anabolism?
building bonds,capturing energy
Metabolism: What is catabolism?
breaking bonds, releasing energy
Characteristics of enzymes: What are they? (List 6)
1) Almost all enzymes are proteins
2) Enzymes can only speed up reactions that would occur anyway
3) Enzymes are able to work at biological temperatures
4) Enzymes are sensitive to certain conditions
5) basis of their 3-D shape
Enzymes can be regulated
6) Enzymes can be regulated
Characteristics of enzymes: What is an exception to almost all enzymes being protein?
Characteristics of enzymes: What to remember when enzymes are sensitive to certain conditions?
Remember: functional proteins work on the basis of their 3-D shape
Enzyme components: What are they? (List 3)
1) Some enzymes require non-protein cofactors or coenzymes
Enzyme components: What are the cofactors? (List 3)
1) Usually metal ions
2) Ca++, Mg++, etc.
3) Help form bridge between enzyme and substrate
Enzyme components: What are coenzymes?
NAD, FAD, CoA, etc.
Factors influencing activity: What are they? (List 6)
3) Amount of substrate
4) Amount of enzyme
5) Competitive inhibition
6) Feedback inhibition
Energy production: What are they? (List 2)
1) Biochemical pathway
2) Oxi-redux reactions
Energy production: What is biochemical pathway?
Sequence of enzyme catalyzed chemical reactions in cell
Energy production: What are oxi-redux reactions? (List 3)
1) Electrons pulled off and passed along in series of reactions
2) Oxidation = removal of one or more electrons from substance (often along with a H+)
3) Reduction = substance gains one or more electrons
Oxidation-Reduction Rxns: What are they? (List 2)
1) In biological systems, the electrons are often associated with hydrogen atoms.
2) Biological oxidations are often dehydrogenations.
Carbohydrate catabolism: What is it? (List 3)
1) Oxidation of carbohydrates = one of primary energy sources in cell
2) Most common = glucose
3) Two most frequently used methods
Carbohydrate catabolism: What are two most frequently used methods? (List 2)
1) Cellular respiration
Carbohydrate catabolism: What is Cellular respiration? (List 2)
1) Complete breakdown of glucose into H2O, CO2 and energy
2) Four steps: glycolysis, intermediate step, Krebs cycle, ETS
Carbohydrate catabolism: What is Fermentation?
Partial breakdown into lactic acid or ethanol and CO2
Why does bacteria have so many pathways?
Bacteria have many different pathways for carbohydrate metabolism
based on the enzymes they are able to produce.
Glycolysis = Embden-Meyerhof pathway: What is the overview? (List 2)
1) Begin with 1 mole of glucose = C6H12O6
2) Series of enzyme mediated reactions result in formation of 2 moles of pyruvic acid (3C) and energy transfer molecules
4ATP (2 net)
Entner-Doudoroff Pathway: What happens? (List 4)
1) Each step in glycolysis is enzyme mediated
3) If organisms lack this enzyme, they can't progress down Embden-Meyerhof pathway
4)Entner-Doudoroff pathway provides alternative way to go from glucose-6-phosphate to pyruvic acid
Entner-Doudoroff Pathway: What is Phosphofructokinase?
Phosphofructokinase is an enzyme which phosphorylates fructose-6-phosphate, producing fructose 1,6 bisphosphate
1) Independent of glycolysis
2) Produces NADPH & ATP
3) Two key enzymes
4) Absent in gram-positive bacteria
5) Found in some gram negative bacteria, such as Pseudomonas, Rhizobium,Agrobacterium, Zymomonas, etc.
Entner-Doudoroff Pathway: What are two key enzymes? (List 2)
1) 6-phosphogluconate dehydrogenase
2) 2-keto-3-deoxyglucosephosphate aldolase
Pentose phosphate pathway: What is it? (List 2)
1) Major uses
2) Key intermediate = ribulose-5-phosphate
Pentose phosphate pathway: What are 5 major uses?
1) generate pentoses from hexoses
2) generate hexoses from pentoses (gluconeogenesis)
3) break down pentoses as a source of cellular energy
Produces acetate and pyruvate
4) generate NADPH
Important coenzyme used by cells for reductive biosynthesis
5) generates sugar diversity
Produces a variety of sugar derivatives in ancillary reactions
Pentose phosphate pathway: What is Key intermediate = ribulose-5-phosphate?
Source of ribose and deoxyribose for nucleic acid production
Aerobic respiration: What is it? ( List 4)
1) More ATP produced by oxidative phosphorylation
2) Final electron acceptor is inorganic = O2
3) Results in complete catabolism of glucose
4) Three steps
Aerobic respiration: What are the three steps?
1) Intermediate step
2) Krebs cycle
3) Electron Transport System (ETS)
Electron transport system: What is it? (List 3)
1) Electrons from NADH and FADH2 passed along series of carrier molecules embedded in cristae (eukaryotes) or plasma membrane (prokaryotes)
2) 3 types of carrier molecules
3) Energy released drives generation of ATP via chemiosmosis
Electron transport system: What are the 3 types of carrier molecules?
Without oxygen: fermentation: What is it? (List 3)
1) Final electron acceptor is organic = pyruvic acid
2) Anaerobic respiration: less ATP produced
Without oxygen: fermentation: What are the results? (List 2)
1) Lactic acid
2) Ethanol + CO2
Without oxygen: fermentation: What is Lactic Acid Fermentation?
causes food spoilage, production of yogurt, pickles, sauerkraut
(Examples: Lactobacillus, Streptococcus)
Without oxygen: fermentation: What is Alcohol fermentation?
Many bacteria and yeasts
Summary for fermentation: What is it? (List 5)
1) No new electron transfer molecules (either NADH,FADH2, or ATP) produced in intermediate step
2) The electrons from the 2NADH made during glycolysis are removed and transferred to pyruvic acid, the final electron acceptor. Therefore, they are unavailable for making more ATP in the ETS.
3) If lactic acid is end product, no CO2 is produced during fermentation
4) If ethanol is the end product, 2 CO2 are produced during fermentation
5) The total ATP produced net in fermentation = 2
Homolactic vs. heterolactic fermentation: What are the two types of lactic acid fermentation?
1) Homolactic fermentation
2) Heterolactic fermentation
Homolactic vs. heterolactic fermentation: What it is homolactic fermentation? (List 3)
1) Produces only lactic acid using pyruvic acid
2) Usually begins with Embden-Meyerhof pathway
3) Characteristic of Streptococci and some Lactobacilli
Homolactic vs. heterolactic fermentation: What is heterolactic fermentation? (List 3)
1) produces lactic acid, ethanol and CO2 using pyruvic acid and acetate
2) Begins with the pentose phosphate pathway
3) Characteristic of some Lactobacilli and Leuconos
Fermentation in enteric bacteria: What is it? (List 2)
1) Type and proportion of products of anaerobic fermentation used to separate enteric bacteria into various genera
2) Two major patterns
Fermentation in enteric bacteria: What are two major patterns?
1) Mixed-Acid Fermentation
2) 2,3 butanediol fermentation
Fermentation in enteric bacteria: What is Mixed-Acid Fermentation? (List 3)
1) Produces acetic, lactic, and succinic acid
2) Also produces ethanol and CO2 and H2
3) CO2 and H2 are produced in equal amounts
Fermentation in enteric bacteria: What is 2,3 butanediol fermentation? (List 3)
1) Major products are butanediol, ethanol, CO2, and H2
2) Much more CO2 is produced than H2
3) Also produces small amounts of succinic, lactic, and acetic acids
Mixed-Acid Fermentation: What is it? (List 3)
1) CO2 is produced only from formic acid via formate hydrogen lyase
2) HCOOH H2 + CO2
3) Therefore, equal amounts of H2 & CO2
2,3 butanediol fermentation: What is it?
Produce CO2 from formic acid and from formation of butanediol
Anaerobic Respiration: What is it? (List 2)
1) The final electron acceptor in the electron transport chain is not O2.
2) Yields less energy than aerobic respiration because only part of the Krebs cycles operations under anaerobic conditions.
Photosynthesis: What is it? (List 2)
Photosynthesis: What is photo?
Conversion of light energy into chemical energy (ATP)
Photosynthesis: What is conversion of light energy into chemical energy (ATP)?
Light-dependent (light) reactions
Photosynthesis: What is synthesis?
Fixing carbon into organic molecules
Photosynthesis: What is fixing carbon into organic molecules?
Light-independent (dark) reaction, Calvin-Benson cycle
Photosynthesis: What are two types?
Photosynthesis: What is Oxygenic?
6 CO2 + 12 H2O + Light energy -> C6H12O6 + 6 H2O + 6 O2
Photosynthesis: What is Anoxygenic?
CO2 + 2 H2S + Light energy -> [CH2O] + H2O + 2 S0
Halobacterium: What does it use?
Halobacterium uses bacteriorhodopsin, not chlorophyll, to generate electrons for a chemiosmotic proton pump.
Nutritional classification: What is Photoautotrophs?
Source of energy = light
Carbon source = CO2
Nutritional classification: What is Photoheterotrophs?
Source of energy = light
Carbon source = organic
Nutritional classification: What is Chemoautotrophs?
Source of energy = reduced inorganic compounds
Carbon source = CO2
Nutritional classification: What is Chemoheterotrophs?
Source of energy and carbon = glucose
saprophytes (decaying matter), parasites (living matter)
Carbohydrate fermentation: What is it? (List 4)
1) Investigates ability of particular bacterium to metabolize specific sugars and determines method they use
2) Phenol red used as pH indicator
3) Durham tube captures gas
Carbohydrate fermentation: What are the results?
A, AG, AGR, negative
MR-VP Medium: What are they? (List 3)
1) Medium = glucose broth + peptone & dipotassium phosphate
2) Used to differentiate gram neg enteric bacteria
3) Two tests in one
MR-VP Medium: What are two tests in one? (List 2)
1) Mixed acid fermentation
2) 2,3 butanediol fermentation
MR-VP Medium: What is Mixed acid fermentation? (List 2)
1) Results = methyl red added to determine pH change
2) Durham tube used to visualize gas production
MR-VP Medium: What is 2,3 butanediol fermentation? (List 4)
1) Voges-Proskauer test
2) Gram negative enterics which do not use mixed-acid fermentation sometimes produce 2,3 butanediol
3) Add Barritt's reagent to convert butanediol to acetoin
4) Pink to red color change after 30 minute incubation is positive
Citrate Test: What is it? (List 2)
1) Citrate in media is only source of oxidizable carbohydrate
2) pH indicator called Brom thymol blue
Citrate Test: What is Citrate in media is only source of oxidizable carbohydrate? (List 3)
1) Citrate split to produce oxaloacetate + pyruvate
2) Products fermented
3) Also contains ammonium salts as nitrogen source
Citrate Test: What is pH indicator called Brom thymol blue? (List 2)
1) Color change when citrate is used due to production of ammonia, which makes pH alkaline
2) As pH increases, color changes from green to blue
Nitrate reduction tests: What are they? (List 4)
1) Used to detect gram negative rods
2) Nitrate is final electron acceptor in anaerobic respiration, reducing nitrate to nitrite
3) Durham tube for gas, reagents used to determine presence of nitrite
4) Negative tests are double-checked with Zinc dust
Catalase tests: What are they? (List 4)
1) H2O2 produced as by-product of aerobic respiration using oxygen
2) Protect themselves against oxidation by producing catalase
3) Produced by aerobes + facultative anaerobes, but not by obligate anaerobes
4) Test by adding H2O2 to cells on a glass slide and watching for bubbles
Glucose O/F Medium: How many ingredients are there?
Glucose O/F Medium: What are the 3 ingredients?
3) Brom-thymol blue
Glucose O/F Medium: What is glucose?
energy either via fermentation and/or respiration
Glucose O/F Medium: What is peptone?
amino acid source
Glucose O/F Medium: What is brom-thymol blue?
Glucose O/F Medium: What is pH indicator?
1) Yellow = acid
2) Blue = alkaline
Glucose O/F Medium: What may be added to the top to stimulate anaerobic conditions?
Indole production: What is it? (List 3)
1) Some bacteria can cleave amino acid tryptophan to prod indole + pyruvic acid
2) Presence of indole detected by Kovac's reagent
3) Forms pinkish red layer on surface
Urea hydrolysis: What is it? (List 5)
1) Produced when protein and nucleic acids broken down
2) Organisms able to make urease convert urea to ammonia and CO2
3) Ammonia becomes ammonium hydroxide in water
4) pH increases
5) Phenol red indicator used to detect change
Phenylalanine deamination: What is it? (List 3)
1) Differentiates some gram negative organisms
2) Oxidative deamination of phenylalanine catalyzed by phenylalanine deaminase
3) Detects presence of enzyme by adding 10% ferric chloride
Kligler's Iron Agar: What is it? (List 3)
1) Differentiates gram negative enterics
2) Multiple test medium
3) Phenol red
Kligler's Iron Agar: What is the multiple test medium? (List 2)
1) Fermentation of glucose and lactose
2) Production of H2S from cysteine catabolism
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