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Chapter 6
Metabolic Pathways
128
Microbiology
Undergraduate 1
10/25/2010

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Term
Metabolism
Definition
The sum of all biochemical processes taking place in a living cell
Term
Anabolism
Definition
An energy-requiring process involving the synthesis of larger organic compounds from smaller ones
Term
Catabolism
Definition
an energy-liberating process in which larger organic compounds are broken down into smaller ones
Term
Endergonic Reaction
Definition
A chemical process that requires energy
Term
Exergonic Reaction
Definition
A chemical process releasing energy
Term
Metabolic Processes
Definition
occur in the cell cytosol, on the cell (plasma) membrane, in the periplasmic space (gram-negative bacteria), in eukaryotic organelles, and outside the cell
∙ cells need a large variety of enzymes
Term
Enzyme
Definition
A reusable protein molecule that brings about a chemical change while itself remaining unchanged
 increase the probability of chemical reactions while remaining unchanged
 accomplish in fractions of a second what otherwise might take hours, days, or longer to happen spontaneously under normal biological conditions
Term
1. Enzymes are reusable
 once a chemical reaction has occurred, the enzyme is released to participate in another identical reaction

1. Enzymes
Definition
1. are reusable
 once a chemical reaction has occurred, they are released to participate in another identical reaction
Term
2. Enzyme
Definition
they are highly specific
 it functions in one type of chemical reaction usually will not participate in another type of reaction
Term
3. Enzymes
Definition
3. They have an active site
 each has a special pocket or cleft called an active site which has a specific 3D shape complementary to a reactant called a substrate. The active site positions the substrate such that it is highly likely a chemical reaction will occur to form one or more products
Term
Active Site
Definition
the region of an enzyme where the substrate binds
Term
Substrate
Definition
The structure or substances upon which an enzyme acts
Term
Products
Definition
A substance or substances resulting from a chemical reaction
Term
4. Enzymes
Definition
They are required in minute amounts
 because it can be use thousands of times to catalyze the same reaction, only minute amounts of a particular ones are needed to ensure that a fast and efficient metabolic effect occurs
Term
Enzyme-Substrate Complex
Definition
The association of an enzyme with its substrate at the active site
 chemical bonds in the substrate are stretched or weakened by the enzyme, causing the bond to break. Are forced to overlap in the spot where the chemical bond will form
 in this complex, the electrons shells
Term
Activation Energy
Definition
the energy that is required for a chemical reaction to occur
 the enzymes create an alternate pathway of less resistance and a lower activation energy barrier; they destabilize the chemical bonds and form new ones by separating or joining atoms in a carefully orchestrated fashion
Term
Lysozome
Definition
An enzyme found in tears and saliva that digests the peptidoglycan of gram-positive bacteria cell walls
Term
Cofactor
Definition
An inorganic substance that acts with and is essential to the activity of an enzyme (e.g. include metal ions [ Mg2+, Fe2+, Zn2+] and some vitamins)
 participate in catalytic reactions,
Term
Coenzyme
Definition
A small, organic molecule that forms the nonprotein part of an enzyme molecule
 e.g. nicotinamide adenine dinucleotide (NAD+) and Flavin Adenine Dinucleotide (FAD) [ play significant role as electron carriers in metabolism]
Term
Metabolic Pathway
Definition
a sequence of linked enzyme-catalyzed reactions in a cell
 each reaction catalyzed by a different enzyme, in which the product (output) of one reaction serves as a substrate (input) for the next reaction
 starts with the initial substrate and finished with the final end product; products of “in-between” stages are called “intermediates”
 can be anabolic, where larger molecules are synthesized from smaller monomer
 other pathways are catabolic because they break larger molecules into smaller ones
 can be linear, branched, or cyclic
Term
Enzyme Inhibition by Environmental Factors
Definition
 enzymes are sensitive to temperature changes (high temperature = denaturation of protein enzyme)
 increase or decrease in protons (H+) will interfere with reaction rate, extreme changes can lead to denaturation or enzyme and metabolic inhibition
 chemicals applied to the environment like alcohols and phenol inactivate enzymes and precipitate proteins, making them natural disinfectants; or other natural chemicals interfere w/enzyme action (penicillin) or w/a cell’s ability to carry out a critical enzyme reaction (sulfa drugs) making them effective antibiotics
Term
Enzyme Inhibition by Metabolic Pathways
Definition
- one of the most common ways of modulating enzyme activity is for the final end product of a metabolic pathway to inhibit an enzyme in that pathway
-if the first enzyme in the pathway is inhibited, then no product is available as input for the rest of the pathway
Term
Feedback Inhibition
Definition
The slowing down or prevention of a metabolic pathway when excess end product binds noncompetitively to an enzyme in the pathway
Term
Noncompetitive Inhibition
Definition
The prevention of a chemical reaction by a chemical that binds elsewhere than to active site of an enzyme
 when the final end product or any molecule binds to a non-active site on the enzyme, the shape of the active site changes and can no longer bind substrate
Term
Noncompetitive Inhibition
Definition
The prevention of a chemical reaction by a chemical that binds elsewhere than to active site of an enzyme
 when the final end product or any molecule binds to a non-active site on the enzyme, the shape of the active site changes and can no longer bind substrate
Term
Competitive Inhibition
Definition
the prevention of a chemical reaction by a chemical that competes with the normal substrate for an enzyme’s active site
 blocking its active site so the normal substrate cannot bind
Term
Adenosine Triphosphate (ATP)
Definition
A molecule in cells that provides most of the energy for metabolism
 bacterial and archaeal cells it is formed on the cell membrane, while eukaryotes reactions primarily in the mitochondria
 provides energy for binary fission, flagellar motion, active transport, and spore formation
 chemical level, it fuels protein synthesis and carbohydrate breakdown
 cells need to have a continual supply of ATP and it cannot be stored
 relatively unstable because of the 3 phosphate groups packed tightly together
Term
Adenosine Diphosphate (ADP)
Definition
A molecule in cells that is the product of ATP hydrolysis
 more stable
Term
Phosphorylation
Definition
the addition of a phosphate group to a molecule
Term
ATP/ADP Cycle
Definition
the cellular processes of synthesis and hydrolysis of ATP
 continuous cycle
Term
Mole
Definition
the molecular weight of substance expressed in grams
Term
Calories
Definition
unites of energy defined in the amount of heat required to raise one gram of water 1OC
Term
Cellular Respiration
Definition
the process of converting chemical energy into cellular energy in the form of ATP
Term
Aerobic Respiration
Definition
the process for transforming energy to ATP in which the final electron acceptor in the electron transport chain is the oxygen gas (O2)
Term
Anaerobic Respiration
Definition
the production of ATP where the final electron acceptor is an inorganic molecule other than oxygen gas (O2) (e.g. nitrate and sulfate)
Term
Fermentation
Definition
A metabolic pathway in which carbohydrates serve as electron donors, the final electron acceptor is not oxygen gas (O2) and NADH is reoxidized to NAD+ for reuse in glyocolysis for generation of ATP
-the catabolism of glucose starts with a little energy being converted to ATP, which builds to a point where large amounts of energy are converted to ATP, and the original glucose molecule has been depleted of its useful energy
-3 stages of energy extraction 1.) glyocolysis 2.) citric acid cycle 3.) oxidative phosphorylation
Term
Glycolysis
Definition
A metabolic pathway in which glucose is broken down into two molecules of pyruvate with a net gain of two ATP molecules
 occurs in cytosol of all microorganisms and involves metabolic pathway that converts an initial 6-carbon substrate into two 3-carbon molecules.
 first part is endergonic ATP is hydrolyzed (consumed) in reaction 1 (produces glucose-6-phosphate and 3 produces fructose-1, 6-bisphosphate) the phosphate group from ATP attaches to the product
 exergonic: during reactions 7 and 10 ATP is generated, enough energy is release to synthesize an ATP molecule from ADP and phosphate, resulting in a total of 4 ATP molecules
 1 and 3 the net gain from glycolysis is 2 molecules of ATP
 rxn 6 releases 2 high energy electrons and two protons (H+) which are picked up by the coenzyme NAD+ reducing it to NADH
Term
Glucose
Definition
A six carbon sugar used as a major energy source for metabolism
Term
Pyruvate
Definition
the end product of the glycolysis metabolic pathway
Term
Substrate Level Phosphorylation
Definition
the formation of ATP resulting from the transfer of phosphate from a substrate to ADP
Term
Reducing (Reduction)
Definition
referring to the process of a substance gaining electron pairs
Term
Citric Acid/Kreb's Cycle
Definition
A metabolic pathway in which acetyl groups are completely oxidized to carbon dioxide gas and some ATP molecules are formed
 end product formed is used as one substrate to initiate the pathway
 all of the reactions are catalyzed by enzymes, and all take place along the cell membrane of bacterial and archaeal cells, including protozoa, algae, and fungi occur in mitochondria
 like a wheel constantly turning
Term
Coenzyme A (CoA)
Definition
A small, organic molecule of cellular respiration that functions in release of carbon dioxide gas (CO2) and the transfer of electrons and protons to another coenzyme
Term
Acetyl CoA
Definition
one of the starting compounds for the Krebs cycle
Term
Oxidation
Definition
the process of removing electron pairs from a substance
Term
Oxidative Phosphorylation
Definition
A series of sequential steps in which energy is released from electrons as they pass from coenzymes to cytochromes and ultimately to oxygen gas (O2) the energy is used to combine phosphate ions with ADP molecules to from ATP molecules
 responsible for producing 34 molecules of ATP per glucose; involves the NAD+ and FAD coenzymes that underwent reduction to NADH and FADH2 during glycosis and citric acid
Term
Cytochromes
Definition
A compound containing protein and iron that plays a role as an electron carrier in cellular respiration and photosynthesis
Term
Electron Transport Chain
Definition
A series of proteins that transfer electrons in cellular respiration to generate ATP
Term
Chemiosmosis
Definition
the use of a proton gradient across a membrane to generate cellular energy in the form of ATP
Term
ATP Synthase
Definition
the enzyme involved in forming ATP by using the energy in a proton gradient
Term
Deanimation
Definition
a biochemical process in which amino groups are enzymatically removed from amino acids or other organic compounds
Term
Beta Oxidation
Definition
The breakdown of fatty acids during cellular metabolism through the successive removal from one end of two carbon units
Term
Anaerobic Respiration
Definition
relies on terminal, usually inorganic electron acceptors other than oxygen for ATP production
Term
anoxic
Definition
without oxygen gas (O2)
Term
Fermentation
Definition
enzymatic process for producing ATP using endogenous organic compounds as both electron donors and acceptors-exogenous electron acceptors (O2, NO3-, SO42-, CO3) are absent
 makes few ATP molecules in the absence of cellular respiration, but the citric acid cycle, and oxidative phosphorylation are shut down, so the products of glycolysis (pyruvate) are shuttled through a pathway that produces other final end products
 ensure a constant supply of NAD+ for glycolysis and the production of two ATP molecules per glucose
Term
Lactic Acid Fermentation
Definition
A catabolic process that produces lactic acid during the reoxidation of NADH to NAD+ for reuse in glycolysis to generate ATP
 by S. lactis, the acid will curdle milk products
Term
Alcohol Fermentation
Definition
A catabolic process that forms ethyl alcohol during the reoxidation of NADH to NAD+ for reuse in glycolysis to generate ATP
 C. albicans, controls carbohydrate to alcohol product
Term
Photosynthesis
Definition
A biochemical process in which light energy is converted to chemical energy, which is then used for carbohydrate synthesis
 in eukaryotes, takes place in chloroplasts of organisms like diatoms, dinoflagelates, and green algae/ chlorophyll in bacteria
Term
Oxygenic Photosynthesis
Definition
A form of photosynthesis in which molecular oxygen (O2) is produced
Term
Energy Fixing Reaction
Definition
A reaction in the first part of photosynthesis where light energy is converted into chemical energy in the form of ATP
Term
Chlorophyll α
Definition
a magnesium-containing lipid soluble compound, a light energy is absorbed by the green pigment
Term
Photosystems
Definition
A group of pigments that act as a light trapping system for photosynthesis
Term
Photophosphorylation
Definition
the generation of ATP through the trapping of light
Term
Carbon Fixing Reactions
Definition
A chemical reaction in the second part of photosynthesis in which carbohydrates are formed
 carbon dioxide is trapped into carbohydrates and other organic compounds
Term
Bacteriochlorophylls
Definition
A pigment located in the membrane system of purple sulfur bacteria that upon excitement by light, loses electron and initiates photosynthetic reactions
Term
Anoxygenic Photosynthesis
Definition
A form of photosynthesis in which molecular oxygen (O2) is not produced
Term
Autotrophs
Definition
An organism that uses carbon dioxide (CO2) as a carbon source
Term
Photoautotrophs
Definition
An organism that uses light energy to synthesize nutrients from carbon dioxide gas (CO2)
Term
Chemoautotroph
Definition
An organism that derives energy from inorganic chemical and uses the energy to synthesize nutrients from carbon dioxide gas (CO2)
Term
Nitrogen Cycle
Definition
A biogeochemical cycle that cycle nitrogen gas into nitrogenous compounds and back again
Term
Heterotrophs
Definition
An organism that requires preformed organic matter for its energy and carbon needs
Term
Photoheterotrophs
Definition
An organism that uses light energy to synthesize nutrients from organic carbon compounds
 like fatty acids and alcohols, include certain green nonsulfur and purple nonsulfur
Term
Chemohetertrophs
Definition
An organism that derives energy from organic chemicals and uses the energy to synthesize nutrients from carbon compounds other than carbon dioxide gas (CO2)
 glucose
Term
Saprobes
Definition
A type of heterotrophic organism that feeds on dead organic matter, like rotting wood or compost
Term
Pathogens
Definition
A microorganism or virus that causes disease
Term
Parasites
Definition
A type of heterotrophic organism that feeds on live organic matter like another organism
Term
Enzymes
Definition
catalyze all cellular reactions, they are not changed by the reactions and can be reused, their activity is highly specific, and act on specific substrates, and are used in small quantities
Term
Enzyme-Substrate Complex
Definition
Through this complex, enzymes increase the probability of a chemical reaction, and bind to the substrate at the active site, which is specific to the substrate
Term
Activation Energy
Definition
Enzymes lower this so a reaction is more likely to occur, by weakening chemical bonds in the substrate
Term
Enzymes
Definition
can be made entirely of proteins or contain a metal ion (cofactor) or an organic molecule (coenzyme)
Term
Metabolic Pathway
Definition
a sequence of chemical reactions, each reaction is catalyzed by a different enzyme and the product of one reaction serves as the substrate for the next
Term
Metabolism
Definition
regulated and be inhibited by enzymes
Term
Feedback inhibition
Definition
hinders metabolic pathways by excess products inhibiting an enzyme in the pathway so no product is available to feed the next reaction
Term
Noncompetitive Inhibition
Definition
changing the shape of the active site
Term
Competitive Inhibition
Definition
blocking an active site
Term
ATP (adenosine triphosphate)
Definition
Energy in this form is required for metabolism, because it is the cellular "energy currency" providing energy for movement, cell division, and protein synthesis
Term
Adensonsine diphosphate (ADP) and a free phosphate group
Definition
What results when energy is released from ATP when the bond holding the last phosphate group on the molecule is broken?
Term
Phosphorylation
Definition
adding a phosphate gorup to a molecule
Term
ATP cannot be stored because it is relatively unstable
Energy must be stored in more stable forms like glycogen and lipids
Definition
What form of energy can be stored? what form of energy cannot be stored?
Term
Adenine, Ribose, 3 phosphate groups
Definition
What is ATP composed of?
Term
Glucose
Definition
contains stored energy that can be extracted, and released slowly by converting to ATP thorugh metabolic pathways
Term
Cellular Respiration
Definition
a series of catabolic pathways for the production of ATP, which cells make ATP by harvesting energy through this process.
Term
Aerobic Respiration
Definition
If oxygen is consumed while making ATP
Term
Anaerobic Respiration
Definition
if oxygen is not consumed while making ATP
Term
oxygen
Definition
required to create ATP during Aerobic Respiration
Term
Glycolysis
Definition
is the splitting of 1-6Carbon glucose molecule into 2-3Carbon molecules, which requires 2 ATP molecules to start, but releases 4 ATP with a net gain of 2 ATP and 2 NADH molecules
Term
Citric Acid Cycle/Kreb's Cycle
Definition
extracts more energy from pyruvate, constantly turning wheel that picks up pyruvate molecules from glycolysis and spitting out carbon dioxide, ATP, NADH, and FADH2
Term
Transition from gylcolysis to Kreb's
Definition
enzymes remove a carbon from each pyruvate molecule, combines the carbon with coenzyme A (CoA) to form acetyl CoA releasing 2 NADH and 2 CO2
Term
2 ATP, 2 FADH2, 4 CO2, 6 NADH
Definition
For each two pyruvate molecules that enter the Kreb's cycle, what molecules are formed?
Term
Oxidative Phosphorylation
Definition
it makes the most ATP molecules, pairs of electrona re passed from one chemical to another, releasing energy, which is used to combine phosphate with ADP to form ATP, it is composed of electron carriers called cytochromes, and coenzyme carriers NADH, and FADH2 provide the electrons for this process
Term
Cytochromes
Definition
electron carriers
Term
Chemiosmosis
Definition
Electrons moves down the electron transport chain and pump protons out of the cell, the protons outside the membrane build up a concentration gradient
Term
ATP synthase
Definition
A channel opens and the protons flow in through, which harnesses the energy from the flowing protons to phosphorylate ADP to ATP
Term
Oxygen
Definition
Accepts the electron pair at the end of this process, acquires 2 protons, and becomes water
Term
Fats
Definition
Chemical bonds that make up this molecule store large amounts of enegy making it good energy sources
Term
Saccharides
Definition
What are other potential energy sources for prokaryotes?
Term
proteins
Definition
When fats and carbohydrates are lacking cells use this?
Term
Deamination
Definition
the replacement of the amino group in a protein with a carbonyl group in protein breakdown
Term
Beta Oxidation
Definition
Fatty acids are broken down through this process
Term
Anaerobic Respiration
Definition
produces ATP using other final electron acceptors (inorganic), anaerobes use moelcules rather than oxygen as the final electron receptor in the ETC, it produces less ATP than its alternative
Term
Fermentation
Definition
produces ATP using an organic final electron receptor, it is used when oxygen and other alternative electron acceptors are unavailable
Term
Pyruvate
Definition
can be converted to lactic acid to reform NAD+ coenzymes so glycolysis can produce ATP from glucose
Term
Eukaryotic Fermentation
Definition
yeast used in alcoholic fermentation to create alcoholic beverages
Term
Photosynthesis
Definition
a process to acquire chemical energy, light energy is converted to cehmical energy, which is stored as an organic compound
Term
Chloroplasts
Definition
In eukaryotes, photosynthesis is carried out in these organelles
Term
Prokaryotic Photosynthesis
Definition
photosynthesis is carried out in the cell membrane
Term
Chlorphyll α
Definition
the green pigment that absorbs light energy
Term
bacteriochlorophylls
Definition
Some bacteria use this as other pigments
Term
Bacteriorhodopsin
Definition
Some archaea use this as a pigment
Term
1.) Energy Fixing Reaction
2.) Carbon Fixing Reaction
Definition
Photosynthesis is divided into two different sets of reactions
Term
Autotroph
Definition
synthesize their own food from simple carbon sources like carbon dioxide
Term
Photoautotroph
Definition
use light as their energy source
Term
Chemoautotroph
Definition
use inorganic compounds as their energy source
Term
Heterotroph
Definition
gain energy and carbon from outside sources
Term
Photoheterotrophs
Definition
use light as their energy source and organic compounds as their source of carbon
Term
Chemoheterotrophs
Definition
use organic compounds both for energy and carbon sources
Term
Saprobes
Definition
feed exclusively on dead organic matter
Term
Parasite
Definition
feed on living organic matter
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