1 chapter 9 introduction to metabolism chapter glossary activation energy active site allosteric...
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Chapter 9Introduction to Metabolism
CHAPTER GLOSSARYActivation energyActive siteAllosteric 異位 enzymeAnabolism 合成代謝Apoenzyme 脢本體Catabolism 分解代謝CatalystCoenzymeDenaturationElectron transport chain (ETC)Endergonic 吸收能量的 reactionEntropy 熵 ; 亂度
EnzymeEquilibriumExergonic 釋出能量的 reactionFeedback inhibitonFree energy changeHoloenzyme 全酵素MetabolismMichaelis constant (Km)Phosphorelay systemProsthetic group 輔基Reducing powerReversible covalent modificationStandard reduction potential
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metabolism is the total of all chemical reactions in the cell and is divided into two parts catabolism ( 分解代謝 ) anabolism ( 合成代謝 )
Figure 9.1 Overview of Metabolism
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Catabolism ( 分解代謝 ) fueling 供給燃料 reactions energy-conserving 保存 reactions provide ready source or reducing power (electrons) generate precursors for biosynthesis
Anabolism ( 合成代謝 )
the synthesis of complex organic molecules from simpler ones requires energy from fueling reactions
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Microbial Metabolism have representatives in all five major nutritional types contribute to cycling of elements in ecosystems
some cycling reactions performed only by microbes
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Microbial Cells Must Do Work
chemical work synthesis of complex molecules
transport work take up of nutrients, elimination of wastes, and maintenance of
ion balances mechanical work
cell motility and movement of structures within cells
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The Laws of Thermodynamics thermodynamics
a science that analyzes energy changes in a collection of matter called a system (e.g., a cell)
all other matter in the universe 宇宙 is called the surroundings 環境
First Law of Thermodynamics energy can be neither created nor destroyed total energy in universe remains constant
However, energy may be redistributed either within a system or between the system and its surroundings
Second Law of Thermodynamics physical and chemical processes proceed in such a way that
the disorder of the universe increases to the maximum possible entropy 熵
amount of disorder in a system Heat is released by one chemical reaction and absorbed by
another
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Energy Units
calorie (cal) amount of heat energy needed to raise 1 gram of water from
14.5 to 15.5°C joules (J)
units of work capable of being done by a unit of energy 1 cal of heat is equivalent to 4.1840 J of work
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Free Energy and Reactions
G = H - TS expresses the change in energy that can occur in chemical
reactions and other processes used to indicate if a reaction will proceed spontaneously
if G is negative, reaction is spontaneous if G is positive, reaction is not spontaneous
G free energy change amount of energy available to do work
H change in enthalpy (heat content; 焓 , 熱含
量 ) T
temperature in Kelvin S
change in entropy 熵
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Chemical equilibrium equilibrium
A + B C + D reaction is at equilibrium when rate of forward reaction = rate of
reverse reaction equilibrium constant (Keq)
expresses the equilibrium concentrations of products and reactants to one another
Standard free energy change (Go)
free energy change defined at standard conditions of concentration, pressure, temperature, and pH
Go´ standard free energy change at pH 7 directly related to Keq
Go´ = -2.303RT•logKeq
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Go and Equilibrium
Exergonic reactions
Go´ is negative
(reaction proceeds spontaneously)
Endergonic reactions
Go´ is positive
(reaction will not proceed spontaneously)
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Energy Currency of the CellAdenosine 5’-triphosphate (ATP)
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Role of ATP in Metabolism
The cell’s energy cycle
high energy molecule exergonic breakdown of ATP is coupled with
endergonic reactions to make them more favorable
ATP +H2O ADP + Pi + H+
Go´ = - 7.3 kcal/mol
guanosine 5ˈ- triphosphate, cytosine 5ˈ- triphosphate and uridine 5ˈ- triphosphate also supply some energy
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Oxidation-Reduction Reactions and Electron Carriers
many metabolic processes involve oxidation-reduction reactions (electron transfers)
electron carriers are often used to transfer electrons from an electron donor to an electron acceptor
Oxidation-Reduction (Redox) Reactions transfer of electrons from a donor to an acceptor
can result in energy release, which can be conserved and used to form ATP
the more electrons a molecule has, the more energy rich it is
Redox: Two Half Reactions one is electron donating (oxidizing reaction) one is electron accepting reaction (reducing reaction) acceptor and donor are conjugate redox pair
acceptor + ne- donorreduction
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Standard Reduction Potential (E0)
equilibrium constant for an oxidation-reduction reaction
a measure of the tendency of the reducing agent to lose electrons
more negative E0 better electron donor
more positive E0 better electron acceptor
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The greater the difference between the E0 of the donor and the E0 of the acceptorthe more negative the Go´
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Electron Transport Chain (ETC) electron carriers organized into ETC with the first electron
carrier having the most negative E’o as a result the potential energy stored in first redox couple is
released and used to form ATP first carrier is reduced and electrons moved to the next
carrier and so on
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Electron carriers
NAD nicotinamide adenine dinucleotide
NADP nicotinamide adenine dinucleotide
phosphate
located in plasma membranes of chemoorganotrophs in bacteria and archaeal cells
located in internal mitochondrial membranes in eukaryotic cells examples of electron carriers include NAD, NADP, and others
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Electron carriers FAD
flavin adenine dinucleotide FMN
flavin mononucleotide riboflavin phosphate
coenzyme Q (CoQ) a quinone also called ubiquinone
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Electron carriers cytochromes
use iron to transfer electrons iron is part of a heme
group
nonheme iron proteins e.g., ferrodoxin use iron to transport electrons
iron is not part of a heme group
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Enzymes
carry out reactions at physiological conditions so they proceed in a timely manner
enzymes speed up the rate at which a reaction proceeds toward its final equilibrium
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Structure and Classification of Enzymes
some enzymes are composed solely of one or more polypeptides some enzymes are composed of one or more polypeptides and
nonprotein components
protein catalysts have great specificity for the reaction catalyzed and the
molecules acted on catalyst 催化劑
substance that increases the rate of a reaction without being permanently altered
substrates reacting molecules
products substances formed by reaction
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Enzyme structure apoenzyme
protein component of an enzyme cofactor
nonprotein component of an enzyme prosthetic group – firmly attached coenzyme – loosely attached
holoenzyme = apoenzyme + cofactor
Coenzymes often act as carriers, transporting
substances around the cell
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The Mechanism of Enzyme Reactionsa typical exergonic reaction
A + B AB‡ C + D
transition-state complex – resembles both the substrates and the products
activation energy – energy required to form transition-state complex
enzyme speeds up reaction by lowering Ea
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How enzymes lower Ea
by increasing concentrations of substrates at active site of enzyme
by orienting substrates properly with respect to each other in order to form the transition-state complex
two models for enzyme-substrate interaction lock and key and induced fit
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Lock and Key Model of Enzyme Function
The induced Fit Model of Enzyme Function
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The Effect of Environment on Enzyme Activity enzyme activity is significantly impacted by substrate concentration,
pH, and temperature
Effect of [substrate]
rate increases as [substrate] increases
no further increase occurs after all enzyme molecules are saturated with substrate
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Effect of pH and temperature each enzyme has specific pH and temperature optima denaturation
loss of enzyme’s structure and activity when temperature and pH rise too much above optima
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Enzyme Inhibition
Competitive Inhibition of Enzyme Activity
competitive inhibitor directly competes with binding of substrate to active site
noncompetitive inhibitor binds enzyme at site other than active site changes enzyme’s shape so that it becomes less active
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Ribozymes Thomas Cech and Sidney Altman discovered that some RNA
molecules also can catalyze reactions examples
catalyze peptide bond formation self-splicing involved in self-replication
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Regulation of Metabolism important for conservation of energy and materials maintenance of metabolic balance despite changes in
environment
three major mechanisms metabolic channeling regulation of the synthesis of a particular enzyme
(transcriptional and translational) direct stimulation or inhibition of the activity of a critical enzyme
post-translational
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Metabolic Channeling
differential localization of enzymes and metabolites compartmentation
differential distribution of enzymes and metabolites among separate cell structures or organelles
can generate marked variations in metabolite concentrations
Post-Translational Regulation of Enzyme Activity two important reversible control measures
allosteric regulation covalent modification
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Allosteric Regulation most regulatory enzymes activity altered by small molecule
allosteric effector binds non-covalently at regulatory site changes shape of enzyme and alters activity of catalytic site positive effector increases enzyme activity negative effector inhibits the enzyme
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Covalent Modification of Enzymes reversible on and off switch addition or removal of a chemical group (phosphate, methyl,
adenyl) advantages of this method
respond to more stimuli in varied and sophisticated ways regulation on enzymes that catalyze covalent modification adds
second level
Regulation of glutamine synthetase activity by covalent modification
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Feedback Inhibition also called end product inhibition inhibition of one or more critical enzymes in a pathway regulates
entire pathway pacemaker enzyme
catalyzes the slowest or rate-limiting reaction in the pathway
•each end product regulates its own branch of the pathway •each end product regulates the initial pacemaker enzyme•isoenzymes – different enzymes that catalyze same reaction