Chapter 14 Flashcards
the free energy released from catabolic oxidation reactions is used to driver …
endergonic anabolic rxns
nutrition is the intake and utilization of food to supply … and …
free energy; raw materials
heterotrophic organisms obtain their free energy from compounds synthesized by … or … organisms
chemolithotrophic; photoautotrophic
food contains …, …, …, …, …, and …
proteins; carbohydrates; fats; water; vitamins; minerals
metabolic pathways are sequences of enzyme-catalyzed reactions that occur in
different cellular locations
near-equilibrium reactions are …, whereas reactions that function far from equilibrium serve as … points and render metabolic pathways …
freely reversible; regulatory; irreversible
flux through a metabolic pathway is controlled by regulating the activities of the enzymes that catalyze its
rate-determining steps
the free energy of the “high-energy” compound ATP is made available through cleavage of one or both of its ….
phosphoanhydride bonds
an exergonic rxn such as ATP or PPi hydrolysis can be coupled to an … rxn to make it more favorable
endergonic
substrate-level phosphorylation is the synthesis of ATP from … by … from another compound
ADP; phosphoryl group transfer
the common product of carbohydrate, lipid, and protein catabolism, …, is a “high-energy” …
acetyl-CoA; thioester
the coenzymes … and … are reversibly reduced during the oxidation of metabolites
NAD+; FAD
the Nernst equation relates the electromotive force of a redox rxn to the … and concentrations of the … and …
standard reduction potentials; electron donors; acceptors
electrons flow spontaneously from the reduced member of a redox couple with the … to the oxidized member of a redox couple with the …
lower reduction potential; higher reduction potential
studies of metabolic pathways determine the order of metabolic transformations, their …, their …, and their … to metabolic processes in other tissues
enzymatic mechanisms; regulation; relationships
metabolic pathways are studied using … and … tracers, …, natural and engineered …, …, and … techniques
isotopic; fluorescent; enzyme inhibitors; mutations; DNA microarrays; proteomics
systems biology endeavors to quantitatively describe the properties and dynamics of biological networks as a whole through the integration of …, …, …, and … information
genomic; transcriptomic; proteomic; metabolomic
…: the overall process through which living systems acquire and use free energy to carry out their various functions
metabolism
…, or degradation, in which nutrients and cell constituents are broken down to salvage their components and/or to make energy available
catabolism
…, or biosynthesis, in which biomolecules are synthesized from simpler components
anabolism
in general, catabolic rxns carry out the … of nutrient molecules
exergonic oxidation
…, the intake and utilization of food; affects health, development, and performance
nutrition
some prokaryotes are …, which can synthesize all their cellular constituents from simple molecules such as H2O, CO2, NH3, and H2S
autotrophs
… obtain their energy through the oxidation of inorganic compounds such as NH3, H2S, or even Fe2+
chemolithotrophs
… obtain energy via photosynthesis, a process in which light energy powers the transfer of electrons from inorganic donors to CO2 to produce carbohydrates, which are later oxidized to release free energy
photoautotrophs
… obtain free energy through the oxidation of organic compounds (carbs, lipids, and proteins) and hence ultimately depend on … for those substances
heterotrophs; autotrophs
… must use o2, whereas … employ oxidizing agents such as sulfate or nitrate
obligate aerobes; anaerobes
…, such as E. coli, can grow in either the presence or the absence of O2. …, in contrast, are poisoned by the presence of O2.
facultative anaerobes; obligate anaerobes
animals are obligate …, whose nutrition depends on a balanced intake of the … proteins, carbs, and lipids
aerobic heterotrophs; macronutrients
the metabolic utilization of macronutrients also requires the intake of O2 and water, as well as … composed of … and …
micronutrients; vitamins; minerals
Vitamins can be divided into two groups: … vitamins and … vitamins
water-soluble; fat-soluble
water-soluble vitamins: … … … … … … … … …
biotin (b7_ pantothenic acid (B5_ cobalamin (B12) riboflavin (b2) nicotinamide (niacin; B3) pyridoxine (B6) Folic acid (B9) thiamine (B1) ascorbic acid (C)
fat-soluble vitamins: … … … ...
vit A
vit D
vit E
vit K
the NAD+ component …, or its carboxylic acid analog .. (niaci), relieves the ultimately fatal dietary deficiency disease in humans known as pellagra
nicotinamide; nicotinic acid
most animals, including humans, can synthesize nicotinamide from the amino acid …
tryptophan
… are series of connected enzymatic rxns that produce specific products. their reactants, intermediates, and products are referred to as …
metabolic pathways; metabolites
in degradative pathways, the major nutrients, referred to as …, are exergonically broken down into simpler products. the free energy released in the degradative process is conserved by synthesis of ATP, or by the reduction of a coenzyme such as NADP+
complex metabolites
the pathways for the catabolism of a large number of diverse substances (carbs, lipids, and proteins) converge on a few …, in many cases a two carbon acetyl unit linked to coenzyme A, to form …
common intermediates; acetyl-coenzyme A
when one substances is oxidized (loses e-), another must be … (gain 3-)
reduced
relatively few … serve as starting materials for a host of varied products
metabolites
rxns catalyzed by the six classes of enzymes
… and … (catalyzed by oxidoreductases)
… (catalyzed by transferases and hydrolases)
…
…
…. (catalyzed by isomerases and mutases)
reactions that … or … (catalyzed by hydrolases, lyases, and ligases)
oxidations; reductions group-transfer rxns eliminations isomerizations rearrangements make or break C-C bonds
electron transport and oxidative phosphorylation occur in the …, whereas glycolysis ( a carbohydrate degradation pathway) and fatty acid biosynthesis occur in the …
mitochondria; cytosol
the synthesis of metabolites in specific membrane-bounded compartments in eukaryotic cells requires … to … these substances between compartments. accordingly, … are essential components of many metabolic processes
mechanisms; transport; transport proteins
…: enzymes that catalyze the same rxn but are encoded by different genes and have different kinetic/regulatory properties
isozymes
example of isozyme:
vertebrates possess two homologs of the enzyme …, which catalyzes the interconversion of pyruvate and lactate
lactate dehydrogenase
many metabolic rxns are said to be …, bc their delta g values are close to zero, and they can be relatively easily reversed by changing the ratio of products to reactants
near-equilibrium rxns
enzymes that catalyze near-equilibrium rxns tend to act quickly to restore …, and the net rates of such rxns are effectively controlled by the relative concentrations of … and …
equilibrium concentrations; substrates; products
for enzymes that work on rxns operating far from equilibrium, only changes in the … of the enzyme can significantly alter the rate. the enzyme controls the flow of substrate through the reaction by …, much as a dam controls the flow of a river by varying the opening of its floodgates
activity; varying its activity
…: rate of flow of metabolites through a metabolic pathway
flux
metabolic pathways are … –> a highly exergonic rxn is irreversible. if such a rxn is part of a multistep pathway, it confers … on the pathway; that is, it makes the entire pathway irreversible
irreversible; directionality
every metabolic pathway has a first … –> although most rxns in a metabolic pathway function close to equilibriu, there is generally an irreversible rxn early in the pathway that commits its product to continue down the pathway
committed step
… and … pathways differ
catabolic; anabolic
the existence of independent interconversion routes is an important property of metabolic pathways bc it allows … of the two processes
independent control
the flux of intermediates through a metabolic pathway in a steady state is more or less …; that is the rates of synthesis and breakdown of each pathway intermediate maintain it at a …
constant; constant concentration
the flux of metabolites, J, through each rxn step is the rate of the forward rxn, vf, less that of the reverse rxn, vr:
…
J = vf - vr
At equilibrium, by definition, there is no flux (J = 0), although vf and vr may be quite large. In reactions that are far from equilibrium, vf ≫ vr, the flux is essentially equal to the …
rate of the forward reaction (J ≈ vf).
the rate determining step functions far from … and has a large negative …
equilibrium; free energy change
(mechanisms to control flux through rate-determining steps)
- … control
- … modification (e.g. phosphorylation/dephosphorylation)
- …, where vf and vr may be independently varied
- … control
allosteric
covalent
substrate cycles
genetic
a metabolic pathway is part of a … process
supply-demand
Oxidative metabolism proceeds in a stepwise fashion, so the released free energy can be recovered in a manageable form at each exergonic step of the overall process. These “packets” of energy are conserved by the synthesis of a few types of … whose subsequent exergonic breakdown drives endergonic processes.
“high-energy” intermediates
ATP consists of an … moiety (adenine + ribose) to which … groups are sequentially linked via .. bond followed by two … bonds
adenosine; three phosphoryl; a phosphoester; phosphoanhydride
..: measure of the tendency of phosphorylated compounds to transfer their phosphoryl groups to water
phosphoryl group-transfer potentials
a favorable free energy change for a rxn does not indicate how … the rxn occurs.
quickly
(reasons for high energy character of phosphoanhydride bonds) . The resonance stabilization of a phosphoanhydride bond is less than that of its hydrolysis products. This is because a phosphoanhydride’s two strongly electron-withdrawing groups must compete for the lone pairs of electrons of its bridging oxygen atom, whereas this competition is absent in the hydrolysis products. In other words, the electronic requirements of the phosphoryl groups are less satisfi ed in a …than in its …
phosphoanhydride; hydrolysis products
(reasons for high energy character of phosphoanhydride bonds) Of perhaps greater importance is the destabilizing effect of the ….between the charged groups of a phosphoanhydride compared to those of its hydrolysis products. In the physiological pH range, ATP has three to four negative charges whose mutual electrostatic repulsions are partially relieved by ATP hydrolysis.
electrostatic repulsions
(reasons for high energy character of phosphoanhydride bonds) Another destabilizing influence, which is difficult to assess, is the smaller … of a phosphoanhydride compared to that of its hydrolysis products. Some estimates suggest that this factor provides the dominant thermodynamic driving force for the hydrolysis of phosphoanhydrides
solvation energy
as long as the overall pathway is exergonic, it will …
operate in the forward direction
the initial step in the metabolism of glucose is its conversion to …
glucose-6-phosophate
atp can be regenerated by coupling its synthesis from ADP and Pi to the more exergonic cleavage of …
phosphoenolpyruvate
…, the enzyme that catalyzes the formation of glucose-6-phosphate does not catalyze ATP hydrolysis but instead catalyzes the transfer of a phosphoryl group from ATP directly to glucose
hexokinase
…, transfers a phosphoryl group from phosphoenolpyruvate to ADP to form ATP
pyruvate kinase
in processes of ATP hydrolysis, proteins undergo conformational changes in response to binding ATP. the exergonic hydrolysis of ATP and release of ADP and Pi renders these changes … and thereby drives the processes forward
irreversible
ATP hydrolysis is … favored but … disfavored
thermodynamically; kinetically
although many rxns involve ATP yield ADP and Pi (…), others yield AMP and PPi (…)
orthophosphate cleavage; pyrophosphate cleavage
the pyrophosphate cleavage of ATP ultimately consumes two
high energy phosphoanhydride bonds
atp is continually being … and ..
hydrolyzed; regenerated
atp itself can be regenerated by coupling its formation to a more
highly exergonic metabolic process
other mechanisms generate ATP indirectly, using the energy supplied by transmembrane proton concentration gradients. in oxidative metabolism, this process is called … whereas in photosynthesis, it is termed …
oxidative phosphorylation; photophosphorylation
…: enzymes that transfer phosphoryl groups from ATP to other compounds or from phosphorylated compounds to ADP
kinases
muscle and nerve cells, which have a high ATP turnover, rely on … to regenerate ATP rapidly
phosphoguanidines
the phosphorylation of creatine by creatine kinase is endergonic under standard conditions; however, the intracellular concentrations of its reactants and products are such that it operates
close to equilibrium
… acts as an ATP “buffer” in cells that contain …
phosphocreatine; creatine kinase
…: a phosphoguanidine whose phosphoryl group transfer potential is greater than that of ATP; these compounds can therefore phosphorylate ADP to generate ATP
phosphagen
… are synthesized from ATP and the corresponding … in a rxn catalyzed by the nonspecific enzyme …:
ATP + NDP ADP + NTP
nucleoside triphosphates; nucleoside diphosphate; nucleoside diphosphate kinase
the … bond is involved in substrate-level phosphorylation, an TP generating process that is independent of- and presumably arose before- oxidative phosphorylation
thioester
… consists of a beta-mercaptoethylamine group bonded through an amide linkage to the vitamin … which is attached to a 3’-phosphoadenosine moiety via a pyrophosphate bridge (LOOK AT CELL MOLEC Q)
coenzyme A; pantothenic acid;
CoA functions as a carrier of … and other … groups
acetyl; acyl
a … or … agent is an electron donor
an … or … agent is an electron acceptor
reductant; reducing
oxidant; oxidizing
redox rxns can be divided into two …
half-rxns
a half rxn consists of an e… and its conjugate …
electron donor; electron acceptor
the electron donor and conjugate electron acceptor constitue a … or … analogous to a conjugate acid-base pair
redox couple; conjugate redox pair
the two half-rxns of a redox rxn, each consisting of a conjugate redox pair, can be physically separated to form an ..
.electrochemical cell
….: the tendency for a substance to undergo reduction (gain electrons)
reduction potential
…: electron pressure that the electrochemical cell exerts
electromotive force (emf)
a positive electromotive force indicates a … rxn, one that can do work
spontaneous rxn
the more positive the standard reduction potential, the higher the affinity of the redox couple’s oxidized form for …; that is, the greater the tendency for the redox couple’s oxidized form to … and thus become …
electrons; accept electrons; reduced
the protein components of redox enzymes play active roles in … by modulating the … of their bound redox-active centers
electron-transfer rxns; reduction potentials
NADH functions as an energy rich …
e- transfer coenzyme
the oxidation by o2 of one NADH to NAD+ supplies sufficient free energy to generate almost …
3 ATPs
a metabolic pathway can be understood in terms of the sequence of rxns by which a specific nutrient is … and the … of the conversions
converted to end products; energetics
a metabolic pathway can be understood in terms of the mechanisms by which each intermediate is converted to its …
successor
a metabolic pathway can be understood in terms of the … that regulate the flow of metabolites through the pathway
control mechanisms
the fate of an isotopically labeled atom in a metabolite can be elucidated by following its progress through the
metabolic pathway of interest
one way to perturb a pathway is to add certain substances, called …, that block the pathway at specific points, thereby causing the preceding intermediates to build up
metabolic inhibitors
the basic metabolic pathways in most organisms are essentially
identical
…: chemical agents that induce genetic changes
mutagens
… the entire collection of RNA transcribed by a cell
transcriptome
…: the complete set of proteins synthesized by a cell in response to changing conditions
proteome
…: the cell’s collection of metabolic intermediates
metabolome
… or … are made by depositing numerous diff DNA segments of known gene sequences in a precise array on a solid support such as a coated glass surface. these are often PCR-amplified cDNA clones derived from mRNAs
DNA microarrays; DNA chips
