Term
| What 2 fundamental tasks must all cells accomplish to grow? |
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Definition
1)they must continually synthesize new components incliding cell walls, membranes, ribsomes, nucleic acids and surfact structures such as flagella
2)they need to harvest energy and convert it to a form that is usable to power biosynthetic reactions, transport nutrients and other molecules & in some cases move |
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Definition
| the sum total of chemical reactions used for biosynthetic and energy-harvesting processes |
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| fuels made from renewable biological source such as plants and organic waste products |
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| Microbial metabolism is important because |
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Definition
| it can be used as identifying markers |
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| metabolism can be viewed as having two components. What are they? |
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Definition
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Definition
*opposite of anabolism. breaks down molecules to store energy.
encompasses processes that harvest energy released during the disassembly or breakdown of compounds such as glucose using that energy to synthesize ATP |
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Definition
| the energy currency of all cells |
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Term
| anabolism or biosynthesis |
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Definition
*using energy to synthesize bigger molecules. also known as biosynthesis. opposite of catabolism
*includes processes that utilize energy stored in ATP to synthesize and assemble subunits of macromolecules that make up the cell including amino acids, nucleotides, and lipids. |
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Term
| _______ generated in catabolism is used in anabolism. |
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Definition
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Definition
| some compounds produced in the steps of the catabolic process can be diverted by the cell and used as precursors of subunits employed in anabolic processes. |
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Definition
stored energy;
can be stored in various forms including chemical bonds, a rock on a hill or water behind a dam |
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Definition
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Definition
| energy in the universe can never be created or destroyed, but it can transfer from one thing to another. |
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Definition
*synthesis of ATP using the energy of a proton motive force created by harvesting radiant energy.
*organisms harvest the energy of sunlight using it to power the synthesis of organic compounds such as glucose (convert the kinetic energy of photons to the potential energy of chemical bonds) |
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Definition
obtain energy by degrading organic compounds such as glucose, releasing the energy of their chemical bonds;
ultimately depend on solar energy harvested by photosynthetic organisms because this is what is used to power the synthesis of glucose |
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Definition
| the energy available to do work; from biological perspective, it is the energy that can be released when a chemical bond is broken |
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Definition
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Definition
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| if the starting compounds have more energy than the final compounds |
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Definition
| if the ending product has more free energy than the starting compounds |
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Definition
| the change in free energy for a given reaction is the same regardless of the number of steps involved |
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Definition
| metabolic processes often occur as a series of sequential chemical reactions which constitute a metabolic pathway using a series of intermediates |
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Definition
| produced as the starting compound |
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Definition
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Definition
*can be linear, branched or cyclical
*its activity can be modulated at certain points (like the flow of a river is controlled by dams)-if a metabolic step is blocked, all products “down stream” will be affected
*a specific enzyme facilitates each step of a metabolic pathway |
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Term
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Definition
the intermediates and end products of metabolic pathways are sometimes organic acids which are weak acids.
depending on the pH, these may exist primarily as either the undissociated form or the dissociated (ionized) form. |
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Definition
inside the cell, the ionized form predominates
outside the cell, the acid may predominate |
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| Critical components of Metabolic Pathways |
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Definition
enzymes
ATP
the chemical energy source
electron carriers
precursor metabolites |
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Term
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Definition
| proteins that function as biological catalysts, accelerating the conversions of one substance, the substrate, into another, the product |
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Definition
| without enzymes, energy-yielding reactions would still occur but at rates so slow they would be imperceptible. |
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Definition
taken to initiate chemical reaction
*by lowering the activation energy barrier, enzymes allow chemicals to undergo rearrangements |
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Term
| adenosine triphosphate (ATP) |
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Definition
*the energy currency of a cell
*serves as the ready and immediate donor of free energy
*cells constantly turn over ATP
*composed of the sugar ribose, the nitrogenous base adenine and three phosphate groups |
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Term
| adenosine diphosphate (ADP) |
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Definition
*viewed as an acceptor of free energy.
*an input of energy is required to add an inorganic phophate group (Pi) to ADP, forming ATP; energy is released when that group is removed from ATP, yielding ADP |
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Term
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Definition
-arranged in tandem
-negative charges repel each other
-bonds that join them are unstable
-they are high energy phosphate bonds (~) - high amount of free energy released when the bonds between the phosphate groups are hydrolyzed |
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Term
| Substrate-level phosphorylation |
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Definition
| uses the chemical energy released in an exergonic reaction to add Pi to ADP |
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Term
| Oxidative phosphorylation |
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Definition
*synthesis of ATP using the proton motive force.
*harvests the energy of proton motive force to add Pi to ADP |
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Term
| 2 processes used by chemoorganotrophs to provide the energy necessary to form the high-energy phosphate bond |
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Definition
| Substrate-level phosphorylation & oxidative phosphorylation |
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Definition
| the form of energy that results from the electrochemical gradient established as protons are expelled from the cell |
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Definition
| utilizing radiant energy of the sun to drive the formation of a proton motive force |
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Definition
| the compound broken down by a cell to release energy |
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Definition
*prokaryotes show remarkable diversity in the variety of energy sources they can use.
*some use organic compounds (glucose), or inorganic compounds (hydrogen sulfide, ammonia) |
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Term
oxidation-reduction reaction
(redox reaction) |
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Definition
| one or more electrons are transferred from one substance to another |
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Definition
| the removal of a hydrogen atom |
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Definition
| the addition of a hydrogen atom |
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Definition
| an oxidation reaction in which an electron and an accompanying proton are removed |
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Definition
| a reduction reaction in which an electron and an accompanying proton are added |
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Definition
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Definition
| a molecule that holds electrons that are removed from the energy source |
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Term
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Definition
| cells have several different types of electron carriers, each serves a different purpose |
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Term
| 3 types of electron carriers that directly participate in reactions that oxidize the energy source |
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Definition
1) NAD+ (nicotinamide adenine dinucleotide)
2)FAD (flavin adenine dinucleotide)
3) NADP+ (NAD phosphate)
(reduced form carriers are NADH, FADH2, NADPH) |
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Term
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Definition
| can each carry a hydride ion, which consists of 2 electrons and one proton |
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Definition
| carries 2 electrons & 2 protons |
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Term
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Definition
| the reducing power of NADH & FADH2 is used to generate the proton motive force, which drives the synthesis of ATP in the process of oxidative phosphorylation |
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Term
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Definition
metabolic intermediates produced at specific steps in catabolic pathways that can be used in anabolic pathways
*in anabolism, they serve as raw material used to make the subunitis of macromolecules
(pyruvate can be converted to the amino acide alanine) |
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Term
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Definition
| can make all of their cell components including proteins, lipids, carbohydrates, and nucleic acids only using a dozen or so precursor metabolited |
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Term
| any essential compounds that a cell cannot synthesize from the appropriate precursor metabolite must be provided from an externl source |
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Definition
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Term
| central metabolic pathways |
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Definition
*used to gradually oxidize glucose, the preferred energy source of many cells, completely to carbon dioxide
-glycolysis
-pentose phosphate pathway
-tricarboxylic acid cycle (TCA cycle) |
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Term
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Definition
*most common pathway
*initiates the breadown of sugars
(glyco means sugar, lysis means dissolution)
*also called embden-meyerhof-parnas pathways |
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Term
| pentose phosphate pathway |
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Definition
*breaks down glucose
*primary role in metabolism is the production of compounds used in biosynthesis |
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Term
| tricarboxylic acid cycle (TCA cycle) |
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Definition
*also called the Krebs Cycle or citric acid cycle
*initiates a series of oxidations that result in the release of two molecules of CO2 |
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Term
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Definition
uses the reducing power accumulated in glycolysis, the transition step and the TCA cycle to generate ATP by oxidative phosphorylation
*Proces that involves transfer of electrons stripped from a chemical energy source to an electron transport chain, generating a proton motive force that is then used to synthesize ATP. |
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Term
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Definition
| electrons are ultimately passed to molecular oxygen, the terminal electron acceptor, producing water |
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Term
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Definition
| similar to aerobic respiration but uses a molecule other than O2 as a terminal electron acceptor |
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Term
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Definition
| metabolic process that stops short of oxidizing the organic molecule completely. using pyruvate or a derivative as a terminal electron acceptor. |
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Definition
| used for the normal growth and function of cell |
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Term
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Definition
| used to take out competing cells, like antibiotics. |
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Term
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Definition
| fermentation always uses an organic molecule as the terminal elctron acceptor |
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Term
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Definition
| In only 1 second, the fastest enxymes can transform more than 10^4 substrate molecules to products |
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Term
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Definition
| More than 1000 different enzymes exist in a cell (usually -ase) |
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Term
| active or catalytic site of an enzyme |
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Definition
| critical site to which a substrate binds by weak forces |
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Term
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Definition
| when the binding of a substrate to the active site causes the shape of the enzyme to change slightly |
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Term
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Definition
| the result of induced fit |
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Term
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Definition
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Term
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Definition
organic cofactors that act as loosely bound carriers of molecules or electrons
*FAD, NAD+, NADP+
*most are derived from vitamins |
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Term
| factors for which enzymes operate optimally |
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Definition
*temperature
*pH
*salt concentration |
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Term
| Optimal enzyme conditions |
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Definition
*low salt concentrations
*pH slightly above 7 |
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Term
| allosteric enzymes/allosteric site |
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Definition
when a regulatory molecule binds, the shape of the enzyme changes
*alters the relative chemical attaraction of the enzyme for its substrate |
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Term
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Definition
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Term
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Definition
| allows the product of the pathway to modulate its own synthesis |
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Term
| non-competitive inhibition |
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Definition
occurs when the inhibitor and the substrate act at different sites to the enzyme
(allosteric inhibitor) |
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Term
| non-competitive, non reversible inhibitors |
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Definition
| damage an enzyme permanently |
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Term
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Definition
the inhibitor binds to the active site of the enzyme, obstructing access of the substrate to that site
(sulfanilamide) |
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Term
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Definition
*2 ATP by substrate-level phosphorylation
*2 NADH + 2H+
*6 different precursor metabolites |
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Term
| Phases of the 10-step pathway of glycolysis |
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Definition
-invetment or preparatory phase
-pay-off phase |
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Term
| Investment/Preparatory phase of glycolysis |
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Definition
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Term
| Pay-off phase of glycolysis |
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Definition
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Term
| for every glucose molecule degraded, the steps of glyocolysis produce |
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Definition
-ATP
-Reducing power
-Precursor metabolites |
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Term
| Energy Expanded (yield of glycolysis) |
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Definition
| 2 ATP molecules (investment phase) |
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Term
| Energy Harvested (yield of glycolysis) |
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Definition
| 4 ATP molecules (pay-off phase) |
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Term
| Net Gain (yield of glycolysis) |
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Definition
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Term
| Reducing Power (yield of glycolysis) |
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Definition
| The payoff phase converts 2 NAD+ to 2 NADH + 2 H+ |
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Term
| Precursor metabolites (yield of glycolysis) |
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Definition
| five intermediates of glycolysis as well as the end product, pyruvate and precursor metabolites used by E. Coli |
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Term
| Pentose Phosphate Pathway |
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Definition
-generates 5- and 7- carbon sugars
-contributes to biosynthesis |
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Term
| Pentose Phosphate Pathway produces what? |
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Definition
-Reducing Power
-Precursor Metabolites |
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Term
| Reducing Power (yield of pentose phosphate pathway) |
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Definition
| a variable amount of reducing power in the form of NADPH is produced |
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Term
| Precursor Metabolites (yield of pentose phosphate pathway) |
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Definition
| two intermediates of the pentose phosphate pathway are precusor metabolites |
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Term
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Definition
links glycolysis to the TCA cycle
-in prokaryotes takes place in cytoplasm
-in eukaryotes takes place in mitocondria |
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Term
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Definition
| carbon dioxide is first removed from the pyruvate |
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Term
| Yield of the transition step |
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Definition
-Reducing Power
-Precursor metabolites |
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Term
| Reducing power (yield of the transition step) |
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Definition
| the transition step, which occurs twice for every molecule of clucose that enters glycolysis, oxidizes pyruvate. This reuces 2 NAD+ to form 2 NADH + 2H+ |
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Term
| Precursor metabolites (yield of the transition step) |
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Definition
| the end product of the transition step, acetyl-CoA is a precursor metabolite |
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Term
| TCA (Tricarboxylic Acid) Cycle |
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Definition
-8 steps
-completes the oxidation of glucose
-generate ATP, reduce power, form 2 more precursor metabolites |
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Term
| TCA (Tricarboxylic Acid) Cycle STEP 1 |
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Definition
| begins when CoA transfers its acetyle group to 4-carbon compound oxaloacetate, thereby forming the 6-carbon compound citrate |
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Term
| TCA (Tricarboxylic Acid) Cycle STEP 2 |
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Definition
| citrate is chemically rearranged to form a structural isomer, isocitrate |
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Term
| TCA (Tricarboxylic Acid) Cycle STEP 3 |
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Definition
| Isocitrate is oxidized and a molecule of CO2 is removed, forming the 5-carbon compound alpha-ketoglutarate. During the oxidation, NAD+ is reduced to form NADH + H+ |
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Term
| TCA (Tricarboxylic Acid) Cycle STEP 4 |
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Definition
| Like the transition step that converts pyruvate to acetyl-CoA, this involves a group of reactions catalyzed by a complex of enzymes. In this step, alpha-ketoglutarate is oxidized, CO2 is removed and CoA is added, producing the 4-carbon compound succinyl-CoA. During the oxidation, NAD+ is reduced to form NADH + H+ |
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Term
| TCA (Tricarboxylic Acid) Cycle STEP 5 |
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Definition
| This removes CoA form succinyl-CoA, harvesting the energy to make ATP. The reaction forms succinate. Note that some types of cells make guanosine triphosphate (GTP) rather than ATP at this step. This compound, however can be converted to ATP |
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Term
| TCA (Tricarboxylic Acid) Cycle STEP 6 |
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Definition
| succinate is oxidized to form fumarate. During the oxidation, FAD is reduced to form FADH2 |
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Term
| TCA (Tricarboxylic Acid) Cycle STEP 7 |
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Definition
| a molecule of water is added to fumarate, forming malate |
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Term
| TCA (Tricarboxylic Acid) Cycle STEP 8 |
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Definition
| Malate is oxidized to form oxaloacetate; note that oxaloacetate is the starting compound to which acetyl-CoA is added to initiate the cycle. Furing the oxidation, NAD+ is reduced to form NADH + H+ |
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Term
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Definition
-the TCA cycle turns once for each acetyl-CoA that enters, which means it turns twice because 2 molecules of acetyl-CoA are generated for each glucose molecule that enters glycolysis
They generate
-ATP
-Reducing Power
-Precursor Metabolites |
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Term
| ATP Yield of the TCA cycle |
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Definition
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Term
| Reducing Power - Yield of the TCA cycle |
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Definition
| redox reactions at steps 3, 4, 6 and 8 produce a total of 6 NADG + 6H+ and 2 FADH2 |
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Term
| Precursor metabolites - Yield of the TCA cycle |
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Definition
| two precursor metabolites used by E.coli are formed as a result of steps 3 & 8 |
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Term
| oxidative phosphorylation |
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Definition
| occurs through the combined action of electron transport chain and ATP synthase |
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Term
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Definition
generates proton motive force
-group of membrane-embedded electron carriers that pass electrons sequentially from one to another
-Found in the cytoplasmic membrane (prokaryotes) and the inner membrane of the mitochondria (eukaryotes) |
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Term
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Definition
| harvests the energy of the proton motive force to drive the synthesis of ATP |
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Term
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Definition
-Peter Mitchell, 1961
-mechanism by which ATP synthesis is linked to electron transport |
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Term
| 4 types of electron carriers participate in the electron transport chain |
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Definition
1. flavorproteins
2. iron-sulfur proteins
3. quinones
4. cytochromes |
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Term
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Definition
proteins to which an organic molecule called a flavin is attached
ex: FAD |
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Term
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Definition
| proteins that contain iron and sulfur molecules arranged in a cluster |
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Term
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Definition
| lipid-soluble molecules that move freely in the membrane and can therefore transfer electrons between different enzyme structures in the membrane. EX: ubiquinone |
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Term
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Definition
| proteins that contain heme, a chemical structure that holds an iron atom in the center EX: cytochrome c |
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Term
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Definition
-some electron carriers on accept hydrogen atoms, while some only accept electrons
-protons are pumped from one side of the membrane to the other, establishing a concentration gradient across the membrane |
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Term
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Definition
-have 4 different protin complexes, 3 of which function as proton pumps (complexes I, III, IV)
-2 electron carriers (coenzyme Q and cytochrome c) shuttle electrons between the complexes |
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Term
| Components of Electron Transport Chain of Mitochondria |
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Definition
Complex I
Complex II
Coenzyme Q
Complex III
Cytochrome c
Complex IV |
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Term
| Complex I (electron transport chain of mitochondria) |
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Definition
-also called NADH dehydrogenase complex
-accepts electrons from NADH, ultimately transferring them to coenzyme Q; in the process, 4 protons are pumped across the membrane |
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Term
| Complex II (electron transport chain of mitochondria) |
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Definition
-also called succinate dehydrogenase complex
-acceots electrons from TCA cycle, when FADH2 is formed during the oxidation of succinate. Electrons are then transferred to coenzyme Q |
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Term
| Coenzyme Q (electron transport chain of mitochondria) |
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Definition
-also called ubiquinone
-lipid soluble carrier accepts electrons from either complex I or complex II and then shuttles them to complex III. Note that the electrons carried by FADH2 have entered the electron transport chain "downstream" of those carried by NADH. Because of this, a pair of electrons carried by NADH result in more protons being expelled than does a pari carried by FADH2 |
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Term
| Complex III (electron transport chain of mitochondria) |
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Definition
-also called cytochrom bc1 complex
-this accepts electrons from coenzyme Q, ultimately transferring them to cytochrome c; in the process, 4 protons are pumped across the membrane |
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Term
| cytochrome c (electron transport chain of mitochondria) |
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Definition
| this accepts electrons from complex III and then shuttles them to complex IV |
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Term
| Complex IV (electron transport chain of mitochondria) |
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Definition
-also called cytochrome c oxidase complex
-accepts electrons from cytochrome c, ultimately transferring them to oxygen (O2) forming H2O. In the process, 2 protons are pumped across the membrane.
-is a terminal oxidoreductase, meaning that it transfers the electrons to the terminal electron acceptor, which, in this case is O2 |
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Term
| Electron Transport Chains of Prokaryotes |
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Definition
| -a single species may have several alternative carriers so that the system as a whole can function optimally under changeable growth conditions |
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Term
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Definition
-rapid biochemical test
-important in the identification of certain organisms |
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Term
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Definition
-uses 2 different NADH dehydrogenases
1.proton pump
2.?
-one form functions optimally only in high O2 conditions and results in the expulsion of 4 protons. The other results in the ejection of only 2 protons, but can more effectively scavenge O2 and thus is particularly useful when the supply of O2 is limited. |
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Term
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Definition
less efficient form of energy transformation than aerobic respiration.
-source of vitamin K, which helps coagulate the blood |
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Term
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Definition
-group of obligate anaerobes
-use sulfate as a terminal electron acceptor, producing hydrogen sulfide as an end product. |
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Term
| ATP Synthase-harvesting the proton motive force to synthesize ATP |
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Definition
-permits protons to flow bck into the bacterial cell in a controlled manner, harvesting the energy released to fuel the addition of a phosphate group in ADP
-one molecule of ATP is formed from the entry of approximately 3 protons |
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