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151 Cards in this Set
- Front
- Back
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What is microbial metabolism? |
Summed collection of controlled biochemical reactions that take place within a microbe |
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What is catabolism? |
When complex molecules are broken down to produce energy & smaller molecules |
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What is anabolism? |
When smaller molecules & energy are used to build complex molecules |
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How is ATP produced? |
Phosphorylation |
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What is phosphorylation? |
When phosphate is added to a substrate |
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What are the 3 ways cell phosphorylate ADP into ATP? |
--Substrate Level Phosphorylation --Oxidative Phosphorylation --Photophosphorylation |
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What is substrate level phosphorylation? |
Phosphate is transferred from another organic compound to ADP |
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What is oxidative phosphorylation? |
Energy from redox reaction(s) of respiration is used to attach inorganic phosphate to ADP |
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What is photophosphorylation? |
Light energy is used to phosphorylate ADP with inorganic phosphate |
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What is the function of ADP in microbe metabolism? |
ATP is the energy currency of microbes. After ADP is phosphorylated into ATP, breaking a phosphate bond releases energy (returning ATP to ADP) that's used to drive cellular processes. ADP molecules can be "recharged" to ATP again & again like a rechargeable battery. |
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What does the suffix "-ase" generally signify? |
Denotes name of an enzyme |
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What is a hydrolase? |
An enzyme that catabolizes a molecule via hydrolysis |
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What is a nuclease? |
A hydrolase enzyme which breaks the phosphate bond of nucleic acids via hydrolysis |
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What is an isomerase? |
Enzymes which rearrange atoms within a molecule, but do not add or remove anything from the molecule [NOTE: "iso-" meaning equal or same] |
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What is a ligase? |
(AKA - polymerase) Enzyme which joins two molecules together (anabolic), usually using energy supplied by ATP |
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What is a polymerase? |
(AKA - lipase)
Enzyme which joins two molecules together (anabolic), usually using energy supplied by ATP |
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What is a lyase? |
Enzyme which splits lg. molecules (catabolic) without using water |
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What is an oxidoreductase? |
Enzyme which removes electrons from (oxidizes) or adds electrons to (reduces) various substrates |
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What is a transferase? |
Enzyme which transfers functional groups (e.g., amino acids, phosphate groups, etc.) between molecules |
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What are the 6 basic categories of enzymes (based on mode of action)? |
--Hydrolase --Isomerase --Ligase --Lyase --Oxidoreductase --Transferase |
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What is an enzyme? |
An organic protein catalyst |
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How to enzymes catalyze reactions? |
By reducing the amt. of activation energy required for a reaction to occur |
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What is a substrate? |
The molecule which an enzyme acts on |
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What is an active site? |
The site at which an enzyme binds to a substrate |
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What is specificity as it relates to enzymes? |
Enzymes are very specific & generally only react with certain substrates |
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What is a cofactor as it relates to enzymes? |
A substance whose presence is required (other than substrate) in order for an enzyme to work |
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What is a coenzyme? |
Vitamin-derived substance that acts as a cofactor (e.g., NAD+) |
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What is a vitamin? |
Organic molecules required for metabolism & cannot be synthesized by certain organisms |
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What is an apoenzyme? |
Protein portion of an enzyme that is inactive if not bound to a cofactor |
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What is a holoenzyme? |
Active enzyme that forms when an apoenzyme binds with its cofactor(s) |
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What is activation energy? |
Amt. of energy required to trigger a chemical reaction |
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Why are enzymes needed for metabolism? |
While enough heat would provide the activation energy required to trigger a reaction, the amt. of heat required is often too high to allow cells to live. Enzymes reduce the amt. of activation energy required for a reaction, allowing cells to live & metabolic reactions to occur. |
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How does temperature affect enzyme action? |
Because enzymes are proteins, they can become denatured if temperatures are too high/low. When enzyme becomes denatured, its shape changes and then it can no longer fit with its substrate. |
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What does it mean for a protein to become denatured? |
When noncovalent bonds break, protein loses its specific 3D structure, so they're no longer functional |
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How does pH affect enzyme action? |
Ions released from acids & bases interfere with hydrogen bonding & cause enzyme to become denatured. When enzyme becomes denatured, its shape changes and then it can no longer fit with its substrate. |
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How does enzyme concentration affect enzyme action? |
Increasing enzyme concentration to substrate concentration increases enzyme activity as more enzymes bond with active sites until all active sites have been filled (saturation point). Decreasing enzyme concentration to substrate concentration decreases enzyme efficiency as there are more substrate active sites than can be filled by enzymes. |
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How does substrate concentration affect enzyme action? |
Increasing substrate concentration to enzyme concentration increases enzyme activity as more active sites become available for enzymes to bond with until all enzymes are bound to active sites (saturation point). Decreasing substrate concentration to enzyme concentration decreases enzyme activity as less active sites are available for enzymes to bind with. |
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What are competitive inhibitors? |
Inhibitory substance shaped such that they fit into an enzyme's active site & prevent normal substrate from binding |
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What are noncompetitive inhibitors? |
Inhibitory substance that binds to an allosteric site elsewhere on the substrate, but changes the shape of the active site so that the enzyme cannot bind |
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What are the 2 types of phosphorylation that generate ATP in aerobic respiration? |
Substrate-level phosphorylation: In the presence of a specific holoenzyme, PEP directly transfers a phosphate to ADP to create ATP. Oxidative phosphorylation: Proton motive force propels protons down electrochemical gradient and through ATP synthases that phosphorylate ADP to ATP. |
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What is carbohydrate metabolism? |
Various biochemical processes responsible for the building, breakdown, and conversion of sugars in organisms |
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What are the 3 main stages of aerobic respiration? |
1. Acetyl-CoA synthesis: Pyruvic acid generated by glycolysis yields 2 Acetyl-CoA, 2 CO2, & 2 NADH molecules per glucose. 2. Krebs cycle: Acetyl-CoA is broken down to yield 2 ATP, 6 NADH, 2 FADH2, & 4 CO2 molecules per glucose. 3. Electron transport chain (ETC): 34 molecules of ATP are oxidatively phosphorylated to ATP via chemiosmosis from NADH & FADH2. |
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What are the major stages of glycolysis? |
1. Energy-investment stage: 2 molecules of ATP invested to phosphorylate glucose into fructose 1,6-biphosphate 2. Lysis stage: Fructose 1,6-biphosphate is cleaved into 2 3-carbon atoms. 3. Energy-conserving stage: G3P is oxidized into a total of 4 ATP (net 2 ATP) & 2 pyruvic acid. |
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What are the products of glycolysis? |
4 ATP total (2 net ATP) 2 pyruvic acid |
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What are the products of the Krebs cycle? |
(per glucose molecule) 2 ATP 4 CO2 6 NADH 2 FADH2 |
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What is the significance of the Krebs cycle in aerobic respiration? |
While little ATP is produced directly, much energy is transferred via electrons to NADH & FADH2 which carry a large amount of energy that can phosphorylate ADP to ATP in the electron transport chain. |
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What is the significance of the electron transport chain (ETC)? |
Most significant production of ATP via step-wise series of redox reactions |
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What are the products of the electron transport chain (ETC)? |
(per glucose molecule) 34 ATP 6 CO2 6 (metabolic) water |
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How is oxidative phosphorylation involved in the electron transport chain (ETC)? |
Proton motive force propels protons down electrochemical gradient and through ATP synthases that phosphorylate ADP to ATP |
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What are the 4 types of electron carriers in the electron transport chain (ETC)? |
Flavoproteins: coenzyme integral membrane proteins derived from vitamin B2 (riboflavin) Ubiquinones: lipid-soluble non-protein carriers derived from vitamin K Metal-containing proteins: integral proteins containing a range of metal atoms Cytochromes: integral proteins associated with heme |
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What is the significance of electron carriers in the electron transport chain (ETC)? |
Can alternate between reduced and oxidative states to pass electrons down the ETC |
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What is chemiosmosis? |
Process by which ATP is synthesized by using energy released by ions flowing down their electrochemical gradient across a membrane |
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How is a proton gradient created & used to create ATP? |
Chemicals diffuse down their electrochemical gradients while the membrane maintains the gradient (proton gradient) by blocking diffusion of chemicals, creating potential energy (proton motive force). Protons are propelled down the proton gradient by proton motive force through protein channels (ATP synthases) that phosphorylate ADP molecules into ATP. |
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What net ATP is produced by glycolysis/fermentation vs. aerobic respiration? |
Glycolysis/fermentation: 2 ATP Aerobic respiration: 36-38 ATP |
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Describe the process of fermentation. |
1. Sugar is partially oxidized to produce 2 net ATP, 2 NADH, 2 pyruvic acid during glycolysis. 2. Pyruvic acid breakdown yields acids, alcohols, and CO2 while NADH are oxidized into NAD+ |
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How are fats metabolized into substrates to be used in glycolysis & the Krebs cycle? |
1. Lipase catabolizes lipids into glycerol & 3 fatty acids 2. Glycerol is converted into DHAP to be catabolized via glycolysis & the Krebs cycle 3. Fatty acids are catabolized via beta-oxidation to produce Acetyl-CoA, NADH, & FADH2 4. Acetyl-CoA enters the Krebs cycle while NADH & FADH2 can undergo redox reactions in the ETC to yield ATP |
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How are proteins metabolized into substrates to be used in glycolysis & the Krebs cycle? |
1. Prokaryotes secrete proteases which catabolize proteins into their various amino acids 3. Deaminated amino acids enter the Krebs cycle & amino groups are recycled into other amino acids or converted into nitrogenous wastes |
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What is photosynthesis? |
Process by which light energy utilized to synthesize carbohydrates from CO2 & water |
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What are light-dependent reactions in photosynthesis? |
Reactions that require light energy to store energy in ATP & NADPH molecules |
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What are light-independent reactions in photosynthesis?
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Reactions that synthesize glucose from CO2 & water without requiring light energy |
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What are the products of photosynthesis? |
Glucose (&/or starch) Oxygen |
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What is an amphibolic reaction? |
A biochemical pathway that involves both anabolism & catabolism (e.g., Krebs cycle) |
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What are major elements? |
Elements needed in large amounts for cellular metabolism (N, O, C, H, S, P = No One Can Hate Salt & Pepper) |
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What are trace elements? |
Elements needed in small amounts for cellular metabolism (Co, Zn, Fe, Se) |
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What are growth factors? |
Organic molecules that cannot be synthesized by microbes |
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Why is oxygen (O) toxic to cells? |
Oxygen is an excellent oxidizing agent (oxidant), so it steal electrons from nearby compounds who then steal electrons from other compounds, creating a damaging chain of oxidations |
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What are the 4 basic groups of organisms based on their carbon (C) & energy sources? |
1. Photoautotrophs 2. Photoheterotrophs 3. Chemoautotrophs 4. Chemoheterotrophs |
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What is the carbon (C) & energy source of a photoautotroph? |
Carbon source: CO2 Energy source: Light |
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What is the carbon (C) & energy source of a photoheterotroph? |
Carbon source: Organic compounds Energy source: Light |
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What is the carbon (C) & energy source of a chemoautotroph? |
Carbon source: CO2 Energy source: Chemical compounds |
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What is the carbon (C) & energy source of a chemoheterotroph? |
Carbon source: Organic compounds Energy source: Chemical compounds |
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What is a carteinoid? |
Pigment that remove excess energy from singlet oxygen (O2) |
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What are superoxide disumtases? |
Enzymes that contain metal ions & convert superoxide radicals (O2-) into hydrogen peroxide (H2O2) |
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What is catalase? |
Enzyme that converts hydrogen peroxide (H2O2) into water & molecular oxygen (O2) |
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What are antioxidants? |
Substances that reduce toxic forms of oxygen |
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What are obligate anaerobes? |
Organisms that are poisoned by oxygen |
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What are facultative anaerobes? |
Organisms who can maintain life through fermentation or anaerobic respiration, but whose metabolic efficiency is reduced in absence of oxygen |
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What are obligate aerobes? |
Organism that requires oxygen to maintain life |
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What is a psychrophile? |
Organism that grow best at temps below 15°C and die much above 20°C |
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In what types of environments can psychrophiles be found? |
--Snowfields --Ice --Cold water |
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What is a mesophile? |
Organisms that grow best between 20°C & 40°C, but can survive at higher/lower temperatures |
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What is a thermophile? |
Organisms that grow at temperatures above 40°C |
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In what types of environments can thermophiles be found? |
--Compost piles --Hot springs |
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What are hyperthermophiles? |
Organisms that grow best in temperatures greater than 80°C |
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What diseases are caused by thermophiles? |
None because they "freeze" at body temperature |
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What is an acidophile? |
Organisms that grow best in acidic habitats |
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In what environment can acidophiles be found? |
Mines & water running thru waste rock, habitats with a pH as low as 0.0 |
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What are neutrophiles? |
Grow best in pH between 6.5 & 7.5 [NOTE: most bacteria & protozoa] |
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What are alkalinophiles? |
Organisms that live in alkaline soils & water |
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What is crenation? |
Shriveling of cytoplasm due to loss of water thru osmosis [NOTE: cells in hypertonic solution] |
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How is a high concentration of salt or sugar an effective preservative? |
Solutes (salt & sugar) draw water out of cell (crenation) to prevent growth & reproduction of microbes |
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What is an obligate halophile? |
Organism that has adapted to grow under high osmotic pressures |
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What are facultative halophiles? |
Organisms that can tolerate high salt concentrations, but don't require them |
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What is quorum sensing? |
How microorganisms respond to the density of nearby microorganisms |
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How is quorum sensing utilized in the formation of biofilms? |
Microbes secrete quorum-sensing molecules that act to communicate # & type of of cells within biofilm, increasing the number of quorum-sensing molecules as the biofilm increases |
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What is a colony? |
Culture that is visible on the surface of solid media |
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What is a streak plate? |
Method of obtaining a pure culture in which a sterile inoculating loop is used to spread an inoculum across the surface of a solid medium in a way that gradually dilutes the sample to a point that colony forming units (CFUs) are isolated from each other |
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What is a pour plate? |
Method of obtaining a pure culture in which colony forming units (CFUs) are isolated from one another using a series of repeated dilutions |
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What is an defined (synthetic) medium? |
Medium for growing cultures in which the exact chemical composition is known |
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What is a complex medium? |
Medium for growing cultures in which the exact chemical composition isn't known because the partial digestion of medium components release many different chemicals in a variety of compositions |
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What is selective media? |
Medium for growing cultures which contain substances that either favor or inhibit the growth of certain microorganisms |
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What is a differential media? |
Medium for growing cultures formulated such that either the presence of visible changes in the medium or colony growth differentiate among various bacteria growing on medium |
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What is an enrichment culture? |
Culture using a selective medium designed to increase very small numbers of a chosen microbe to observable levels |
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What is cold enrichment? |
Technique to enrich a culture with cold-tolerant species where incubation occurs in a refrigerator instead of at 37°C |
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What is anaerobic media? |
Medium for growing cultures which contains compounds that chemically combine with free oxygen & remove it from the medium |
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What is generation time? |
Time required for a population of cells to double in # |
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What is a growth curve? |
Graph that plots the #s of organisms in a growing population over time |
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What are the phases of a growth curve? |
1. Lag phase: cells adjust to new environment & most don't reproduce immediately. 2. Log phase: after cells have synthesized necessary chemicals for metabolism in their new environment, they enter a phase of rapid growth & logarithmic reproduction. 3. Stationary phase: growth & reproduction level out as nutrients are depleted & wastes accumulate. 4. Death phase: if nutrients aren't added or wastes removed, population reaches point in which cells are dying faster than they are reproducing. |
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What is a plate count? |
Method of estimating microbe population where a step-wise dilution (serial dilution) of a liquid culture in which each dilution is cultured on agar until the colonies can be counted and multiplied by the reciprocal of of the dilution |
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What is a membrane filtration? |
Method of estimating microbe population where a large sample is poured or drawn through a membrane filter with pores just small enough to trap the cells & colonies are counted after the membrane is transferred to solid medium |
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When is a membrane filtration preferred? |
When the population density of a microbe is very small |
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What is a direct microscope count? |
Method of estimating microbe population where a mL of sample is positioned on a glass slide composed of an etched grid (cell counter slide) and the number of bacteria per mL is calculated by multiplying the mean population per grid square by 1.25 x 10^6 |
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What is the direct microscope count method suitable for? |
Stained prokaryotes & relatively large eukaryotes |
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What is turbidity? |
Cloudiness, generally produced by bacterial reproduction in a broth culture |
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How is turbidity used to indirectly calculate microbe population size? |
Changes in turbidity within a culture are measured by a spectrophotometer to measure the amt. of light transmitted thru a culture |
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What is a gene? |
Basic unit of heredity from 1 generation to next |
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What is a plasmid? |
Small, circular molecules of DNA that replicate independently of the chromosome |
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What is a chromosome? |
DNA forming complex with associated proteins in cell |
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What is a genome? |
Complete set of genetic material in a cell |
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Describe the structure of DNA? |
Nucleotide base pairs bound together by hydrogen bonds along a sugar-phosphate backbone to form a helical, double strand |
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What is the function of DNA? |
Contain the genetic instructions for development & function of living things |
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What are the structural components of a nucleotide? |
--Pentose sugar (i.e., ribose or dioxyribose) --Nitrogenous base (G, C, A, or T/U) |
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Describe the process of DNA replication. |
1. DNA helicase unzips the double helix. 2. Primase makes short RNA primer for new strand to attach to. 3. DNA polymerase synthesizes complementary strand. 4. DNA ligase ligates (attaches) DNA pieces to form a continuous strand. |
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What is the difference between a leading strand & a lagging strand during DNA replication? |
Leading strand: Faster DNA replication because polymerase can follow DNA helicase in same direction Lagging strand: Slower because goes opposite direction of DNA helicase and Okasaki fragments must be stitched together |
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Describe the process by which mRNA is made. |
1. RNA polymerase bind to nucleotide sequences that initiate transcription (promoters). 2. RNA polymerase unzips helix in a bubble as it moves along strand. 3. Transcription ends when RNA polymerase transcribes a terminator sequence and the mRNA strand is released. |
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What is the function of mRNA? |
Carries genetic information obtained from DNA in form of codons that code for specific amino acids |
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How does the genetic code code for proteins? |
mRNA interacts with ribosomes that translate codons into amino acids that are connected accordingly & packaged into proteins |
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What is a codon? |
Triplets of mRNA nucleotides that code for specific amino acids |
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What is an anticodon? |
Triplets of nucleotide bases that correspond to complementary codon on mRNA |
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What is a start codon? |
Triplet of mRNA nucleotide bases that identifies where translation of a gene begins |
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What is a stop codon? |
Triplet of mRNA nucleotide bases that identifies where translation of a gene ends |
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What is the function of a ribosome? |
Attaches to mRNA at binding site & adds sequential amino acids to the polypeptide chain the mRNA codes for until it reaches a stop codon |
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What is the A site (in translation)? |
Site in ribosome complex which holds the new amino acid to be added to the polypeptide chain |
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What is the P site (in translation)? |
Site in ribosome complex which binds the amino acids in a growing polypeptide chain |
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What is the E site (in translation)? |
Site in ribosome complex where tRNA releases boded amino acid in translated polypeptide chain |
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What is a genotype? |
Genetic composition of an organism |
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What is a phenotype? |
Physical characteristics displayed by an organism as a result of genetic composition |
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What is a mutation? |
A change in a DNA sequence |
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What is a substitution mutation? |
A change in a DNA sequence in which 1 base is substituted for another base |
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What is a frameshift mutation? |
A change in DNA sequence in which an extra letter is inserted into codon strand resulting in shift in codon reading |
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What is a silent mutation? |
A substitution mutation that codes for the same amino acid resulting in no change of sequence in polypeptide |
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What is a missense mutation? |
A substitution mutation that codes for a different amino acid which may or may not be noticeable |
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What is a nonsense mutation? |
A substitution mutation that codes for a stop codon, prematurely stopping polypeptide chain production |
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What is a mutagen? |
A physical or chemical agent that causes a change in DNA sequence |
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What is transformation (of DNA)? |
Recipient cell takes up DNA from its environment |
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What is transduction (of DNA)? |
Horizontal gene transfer by which DNA from 1 cell is introduced to another via replicating virus |
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What is conjugation? |
Bacterial gene transfer mediated by pili |
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What is the significance F plasmids during conjugation? |
Cells that contain F plasmids (F+) serve as donors during conjugation to cells not containing F plasmids (F-) |
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What are R plasmids? |
Plasmids that make a code for antibiotic resistance |
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What is the medical significance of R plasmids? |
Antibiotic resistance can be spread between diverse bacteria |
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How do bacterial viruses participate in transduction? |
A phage injects its DNA into a host until the host's DNA disintegrates & phage DNA is replicated instead, but sometimes some of the host's DNA is incorporated into the phage's DNA & is injected into a new host where the new DNA is incorporated into the new host's |
