Final Exam Flashcards
What is metabolism?
Metabolism is the overall process through which living systems acquire and use free energy to carry out their various functions, is traditionally divided into two parts:
Catabolism, how energy is gained from the break-down
Anabolism, how energy is used for biosynthesis
Metabolism are the reactions by which biomolecules are built and broken down
difference between catabolism and anabolism
Anabolism is the building of complex molecules from numerous simple ones. Think of protein synthesis.
Catabolism is the breakdown of complex molecules into numerous simple ones.
is catabolism exergonic or endergonic
In general, catabolic reactions carry out the exergonic oxidation of nutrient molecules. The free energy thereby released is used to drive such endergonic processes as anabolic reactions, the performance of mechanical work, and the active transport of molecules against concentration gradients.Exergonic and endergonic processes are often coupled through the intermediate synthesis of a “high-energy” compound such as ATP.
In an exergonic reaction, energy is released to the surroundings. The bonds being formed are stronger than the bonds being broken. In an endergonic reaction, energy is absorbed from the surroundings. The bonds being formed are weaker than the bonds being broken.
Many of the specific reactions of metabolism are common to all organisms, with variations due primarily to the sources of the free energy that supports them. What are the different metabolic sources of energy?
Autotrophs are organisms that can produce their own food from the substances available in their surroundings using light (photosynthesis) or chemical energy (chemosynthesis).
(a) plants, (b) algae, and (c) certain bacteria.
Heterotrophs cannot synthesize their own food and rely on other organisms — both plants and animals — for nutrition.
An autotroph is an organism that can synthesize their organic molecules from simple inorganic substances. They are producers. A heterotroph is a consumer and it obtains organic molecules from other organisms.
Organisms can be further classified by the identity of?
the oxidizing agent for nutrient breakdown/by their requirement for oxygen
the oxidizing agent for nutrient breakdown/by their requirement for oxygen
Obligate aerobes (which include animals) must use O2, whereas anaerobes employ oxidizing agents such as sulfate or nitrate. Facultative anaerobes, such as E. coli, can grow in either the presence or the absence of O2 . Obligate anaerobes, in contrast, are poisoned by the presence of O2
isozymes
An intriguing manifestation of specialization of tissues and subcellular compartments is the existence of _____, enzymes that catalyze the same reaction but are encoded by different genes and have different kinetic or regulatory properties.
A
isozymes
Different tissues often express different isozymes to match tissue function.
using different forms of the same enzyme to catalyze a given biochemical reaction. These different forms of the same enzyme are known as isozymes or isoenzymes. Isozymes arise from different genes, have different sequences of amino acids and a different structure yet catalyze the same reaction, have different properties and exhibit different enzymes kinetics and are usually controlled by different allosteric effectors.
Energy from oxidation of metabolic fuel is released stepwise. In what form is it stored and made available to drive endergonic processes?
ATP - the primary energy “currency” of the cell.
Why are phosphoanhydride bonds “high-energy”?
- Resonance stabilization of products larger than that of substrates.
- Mutual repulsion of negatively charged groups larger in substrates than in products.
- Smaller solvation energy of phosphoanhydride as compared to hydrolysis products.
Why is ATP so stable, despite the large amount of free energy released by its hydrolysis?
How can you drive an endergonic reaction?
Couple it with an exergonic reaction. Purpose of Coupled Reactions?
A
The hydrolysis of a “high-energy” compound, while releasing considerable free energy, is not in itself a useful reaction. However, the exergonic reactions of “high-energy” compounds can be coupled to endergonic processes to drive them to completion
Inorganic pyrophosphatase function
supply additional “driving force”.
Catalyzes Additional Phosphoanhydride Bond Cleavage by suppling additional “driving force”.
is an enzyme that catalyzes the conversion of one ion of pyrophosphate to two phosphate ions.[1] This is a highly exergonic reaction, and therefore can be coupled to unfavorable biochemical transformations in order to drive these transformations to completion.[2]
Explain how cellular ATP is replenished by phosphagens.
A
utilizes phosphocreatine and ADP to regenerate ATP in the cell when at rest (relies on concentration of substrate and products to determine if reaction should go forward or reverse)
What are thioesters?
“primitive” high-energy compounds
involved in substrate-level phosphorylation
acetyl-coenzyme A (acetyl-CoA)
Phosphocreatine function?
Phosphocreatine provides a “high-energy” reservoir for ATP formation (in muscles, nerves). How is phosphocreatine regenerated?
ATP + creatine –>ADP + phosphocreatine
most common source of energy in organisms? most common electron carriers?
OXIDATION-REDUCTION REACTIONS
“REDOX REACTIONS”
- NAD+ transfers 2 electrons
- FAD transfers one electron
- Fe2+/3+
They accept high energy electrons and carry them ultimately to the electron transport chain where they are used to synthesize ATP molecules
NAD + and FAD are not direct sources of energy, so what do they do?
A
When these electron carrier molecules accept the electrons, they are reduced into and form energy molecules NADH and FADH2
How do redox reactions occur? Loss of electrons is what? Gain of electrons is?
electrons are transferred from electron donor
(reducing agent) to electron acceptor (oxidizing agent)
loss of electrons = oxidation; gain of electrons = reduction
Slides 25-39 Glycolysis reactions
What is homolactic fermentation?
The process in which Under anaerobic conditions in muscle, pyruvate is reduced to lactate to regenerate NAD +
slide 41
What catalyzes the oxidation of NADH by pyruvate to yield NAD+ and lactate.
lactate dehydrogenase (LDH)
This reaction is often classified as Reaction 11 of glycolysis. The lactate dehydrogenase reaction is freely reversible, so pyruvate and lactate concentrations are readily equilibrated.
What is Alcoholic Fermentation?
Alcoholic Fermentation Converts Pyruvate to Ethanol and CO2
In yeast and certain other microorganisms, pyruvate is decarboxylated to yield CO 2 and acetaldehyde, which is then reduced by NADH to yield NAD +and ethanol.
the conversion of pyruvate to ethanol and CO2. to regenerate NAD+ FOR glycolysis
Yeast produces ethanol and CO 2 via what two consecutive reactions?
The decarboxylation of pyruvate to form acetaldehyde and CO 2 as catalyzed by pyruvate decarboxylase (an enzyme not present in animals).
The reduction of acetaldehyde to ethanol by NADH as catalyzed by alcohol dehydrogenase (Section 11-1C), thereby regenerating NAD + for use in the GAPDH reaction of glycolysis.
which needs a cofactor, Alcoholic Fermentation or Homolactic Fermentation?
Alcoholic Fermentation,
TPP Is an Essential Cofactor of Pyruvate Decarboxylase. Pyruvate decarboxylase contains the coenzyme thiamine
pyrophosphate
pyruvate is decarboxylated by a thiamine pyrophosphate (TPP)–dependent mechanism, and the resulting acetaldehyde is reduced to ethanol.
Compare the ATP yields and rates of ATP production for anaerobic and aerobic degradation of glucose.
he rate of ATP production by anaerobic glycolysis can be up to 100 times faster than that of oxidative phosphorylation
But Aerobic yields more ATP 32 per glucose and Fermentation is 2 ATP per glucose
Consequently, when tissues such as muscle are rapidly consuming ATP, they regenerate it almost entirely by anaerobic glycolysis.
What makes Enzymes candidates for flux-control points? Name three
Enzymes that function with large negative free energy changes.
hexokinase-not required when glycogen is source for glycolysis (as often in muscle)
, phosphofructokinase- major control point for glycolysis in muscle
and pyruvate kinase-last reaction of glycolysis
are metabolically irreversible.
Inhibitors and activators of the flux control points
Hexokinase- G6P inhibitor
Phosphofructokinase- ATP inhibitor, Activators- AMP, F2,6P
Pyruvate Kinase- ATP Inhibit, Activator AMP,PEP,FBP
What is the primary flux control point for glycolysis and why?
Phosphofructokinase.
Because when the G6P source for glycolysis is glycogen, rather than glucose, as is often the case in skeletal muscle, the hexokinase reaction is not required.
Pyruvate kinase catalyzes the last reaction of glycolysis and is therefore unlikely to be the primary point for regulating flux through the entire pathway.
Evidently, PFK, an elaborately regulated enzyme functioning far from equilibrium, is the major control point for glycolysis in muscle under most conditions.
What is the pentose phosphate pathway?
What two things do it generate?
alternative pathway to glycolysis
provides NADPH for fatty acids and cholesterol and ribose-5-phosphate for nucleotide biosynthesis (R5P)
difference between glucose and glycogen
Glucose is a single sugar unit or monosaccharide. Glycogen is a multi-sugar unit or polysaccharide
function of glycogen and starch?
Store glucose for metabolic use
Glycogen broken down so it can enter glycolysis
In animals, a constant supply of glucose is essential for tissues such as?
the brain and red blood cells which depend almost entirely on glucose as an energy source
The mobilization of glucose from glycogen stores, primarily in where?, provides a constant supply of how much glucose to all tissues.
liVER
When glucose is plentiful, such as immediately after a meal, glycogen synthesis accelerates. Yet the liver’s capacity to store glycogen is sufficient to supply the brain with glucose for only about half a day. Under fasting conditions, most of the body’s glucose needs are met by what?
gluconeogenesis (literally, new glucose synthesis) from noncarbohydrate precursors such as amino acids.
structure of glycogen and starch? its branched at how many residues
α(1→4)-linked D-glucose with α(1→6)-linked branches every 8–14 (10) residues, highly branched
amylose has no branches
amylopectin has branches every 24-30 residues
in glycogen how are the glucose units removed
glucose units are removed from the nonreducing ends which
allows rapid mobilization of large amounts of glucose
difference between non reducing and reducing end?
reducing end - aldehyde/acetal can be relatively easily oxidized
nonreducing end- not an aldehyde
what is glycogenolysis?
the breakdown of glycogen
List the three enzymes involved in glycogen degradation and describe the type of reactions they catalyze. slide 11-24
1.Glycogen phosphorylase (or simply phosphorylase) catalyzes glycogen phosphorolysis (bond cleavage by the substitution of a phosphate group) to yield glucose-1-phosphate (G1P)
Leaves a limit branch
2. Glycogen debranching enzyme removes glycogen’s branches, thereby making additional glucose residues accessible to glycogen phosphorylase.
Phosphoglucomutase converts G1P to G6P, which has several metabolic fates (
Glucose mobilization in the liver involves a series of conversions from glycogen to glucose-1-phosphate to glucose-6-phosphate and finally to glucose.
difference between glycogen phosphorylase a and b difference between glycogen synthase a and glycogen synthase b
glycogen synthase a dephosphorylated
is more active
glycogen synthase b phosphorylated
is less active
glycogen phosphorylase a at Ser14 is more active
glycogen phosphorylase b is less active it is dephosphrylated
glycogen phosphorylase is activated by phosphorylation (b → a), whereas glycogen synthase is inactivated by phosphorylation (a → b). Conversely, dephosphorylation inactivates glycogen phosphorylase and activates glycogen synthase.
List the three enzymes involved in glycogen synthesis
UDP–glucose pyrophosphorylase, glycogen synthase, and glycogen branching enzyme.
How is glycogen synthesis initiated?
Glycogen synthase only extends existing chains.
Glycogenin
Glycogenin is glycosylated on a Tyr residue by tyrosine glycosyltransferase. Glycogenin can extend chain by up to seven residues, using UDPG.
Glycogen granules consist of 1 molecule glycogen (with up to 120,000 glucose units), 1 molecule of glycogenin, 1 molecule of glycogen synthase, plus other enzymes and regulatory proteins.
Why is glucose stored in form of glycogen?
To avoid “osmotic stress” (high osmotic pressure).
Osmotic pressure is a colligative property, i.e. it is dependent on the number of dissolved particles, not on their properties (such as size).
Concentration of glycogen in liver cell ≈ 10 nM
Concentration of glucose contained in glycogen ≈ 0.4 M
What two enzymes in glycogen synthesis and degradation are under allosteric control and covalent modification?
A
Glycogen Phosphorylase and Glycogen Synthase
Glycogen metabolism is ultimately under the control of hormones such as ?
A
insulin, glucagon, and epinephrine.
What is Gluconeogenesis and where does It occur?
A
necessary when glucose and glycogen supplies are depleted
occurs in liver (and kidney)
When dietary sources of glucose are not available and when the liver has exhausted its supply of glycogen, glucose is synthesized from noncarbohydrate precursors (lactate, pyruvate, and amino acids.) by gluconeogenesis.
pyruvate is converted to glucose.
The 4 noncarbohydrate precursors that can be converted to glucose include?
the glycolysis products lactate and pyruvate, citric acid cycle intermediates, and the carbon skeletons of most amino acids.
What must all the noncarbohydrate precursors convert to very first thing in the reaction? (a citric cycle intermediate)
A
First, however, all these substances must be converted to the four-carbon compound oxaloacetate (at left), which itself is a citric acid cycle intermediate
How is gluconeogenesis related to glycolysis
Gluconeogenesis is mostly the reverse of glycolysis with the pyruvate kinase reaction bypassed by the pyruvate carboxylase and phosphoenolpyruvate carboxykinase reactions, and the phosphofructokinase and hexokinase reactions bypassed by phosphatase reactions.
What is the problem that occurs when trying to synthesize oxaloacetate?
Glycolysis and gluconeogenesis occur in cytosol, oxaloacetate is produced in mitochondrion.
No transporter for oxaloacetate across the inner mitochondrial membrane exists.
Gluconeogenesis Requires Metabolite Transport between Mitochondria and Cytosol.
Route 2 results in transport of reducing equivalents; NADH is used in mitochondrion and produced in cytosol.
Cytosolic NADH is required for gluconeogenesis.
Cytosolic NADH is also generated by lactate dehydrogenase reaction.
Glucogenesis produces how many ATP/mol vs glycolysis
…uses 6 mol ATP/mol glucose…
Glycolysis produces 2 mol ATP/mol glucose.
Other Carbohydrate Biosynthetic Pathways
O-linked oligosaccharides- synthesis in Golgi apparatus.
-attached to Ser, Thr of polypeptide, determined by secondary or tertiary structure
O-Linked oligosaccharides are synthesized by the sequential addition of sugars to a protein.
N-linked oligosaccharides
attached to Asn
N-Linked oligosaccharides are assembled on a dolichol carrier and then transferred to a protein.
Formation of glycosidic bond requires?
nucleotide sugars/energy:
CAC?
-A multistep catalytic process that oxidizes the acetyl group of acetyl-CoA derived from carbohydrates, fatty acids, and amino acids to 2 molecules of CO2 with the concomitant reduction of NAD + and FAD to NADH and FADH2 and the production of GTP. Reduced compounds NADH and FAD conserve the liberated free energy.
-Recovers energy from metabolic fuels/release stored energy
-Pyruvate derived from glucose can be split into CO 2and a two carbon fragment that enters the cycle for oxidation as acetyl-CoA
-Citric acid cycle supplies the reactants for a variety of biosynthetic pathways.
-8 reactions
it accounts for the major portion of carbohydrate, fatty acid, and amino acid oxidation, the citric acid cycle is often considered the “hub” of cellular metabolism.
-Reoxidation of NADH and FADH 2 by O2 during electron transport and oxidative phosphorylation yields H2O and ATP.
One complete round of the citric acid cycle yields?
two molecules of CO2, three NADH, one FADH2 , and one “high-energy” compound (GTP or ATP)
The oxidation of an acetyl group to 2 CO 2requires the transfer of how many electrons?
Where is the free energy of oxidation of the acetyl group conserved in?
Where is energy recovered?
How much ATP are formed when the pairs of electrons eventually transfer to O2?
A
-4 electrons. The reduction of 3 NAD +to 3 NADH accounts for three pairs of electrons; the reduction of FAD to FADH 2 accounts for the fourth pair.
-the reduced enzymes NADH and FADH2
-Energy is also recovered as GTP (or ATP)
-10 ATP
Are the carbon atoms of the two molecules of CO 2produced in one round of the cycle the two carbons of the acetyl group that began the round?
No, These acetyl carbon atoms are lost in subsequent rounds of the cycle. However, the net effect of each round of the cycle is the oxidation of one acetyl group to 2 CO2 .
How Is acetyl-CoA formed?
A
Acetyl-CoA is formed from pyruvate through oxidative decarboxylation by a multienzyme complex named pyruvate dehydrogenase that catalyzes a five-part reaction in which pyruvate releases CO 2 and the remaining acetyl group becomes linked to coenzyme A.
This reaction sequence requires 5 cofactors.
pyruvate dehydrogenase contains multiple copies of what three enzymes/subunits?
A
pyruvate dehydrogenase (E1)
dihydrolipoyl transacetylase (E2)
dihydrolipoyl dehydrogenase (E3)
Pyruvate dehydrogenase (E1), a TPP-requiring enzyme, decarboxylates pyruvate, yielding a hydroxyethyl-TPP carbanion
the hydroxyethyl group is transferred to a lipoamide of E2 (dihydrolipoyl transacetylase)
Hydroxyethyl is oxidized to acetyl and lipoid disulfide is reduced
(transfer of acetyl group to lipoamide)
generating an active E1
This results in the formation of acetyllipoamide
E2 then catalyzes the transfer of an acetyl group from lipoamide to CoA, yielding acetyl-CoA
Acetyl-CoA has now been formed, but the lipoamide group of E2 must be regenerated.
Dihydrolipoyl dehydrogenase (E3) reoxidizes dihydrolipoamide to lipoamide to complete the catalytic cycle of E2. E3 is reduced as a result.
re-oxidation of reduced E3
The sulfhydryl groups are reoxidized by a mechanism in which FAD funnels electrons to NAD+, yielding NADH
E1 is pyruvate dehydrogenase which uses thiamine pyrophosphate (TPP) as a cofactor to decarboxylate pyruvate and transfer the remaining hydroxyethyl fragment to the lipoamide cofactor attached to E2. This results in the formation of acetyllipoamide, equivalent to reduction of lipoamide (and oxidation of the hydroxyethyl fragment), as becomes clear upon subsequent transfer of the acetyl residue to coenzyme A, catalyzed by E2, a acetyltransferase and E3, which regenerates lipoamide from dihydrolipoamide, is dihydrolipoyl dehydrogenase
FAD is reduced by lipoamide
NAD+ is reduced by FADH2
Where are the coenzymes located on the enzymes?
A
-TPP is bound to E1.
-Lipoic acid is covalently linked to a -Lys on E2 (lipoamide)
-CoA is a substrate for E2
-FAD is bound to E3
-NAD+ is a substrate for E3
What Is The Glyoxylate Cycle?
Shares Some Steps with the Citric Acid Cycle
allows plants to generate oxaloacetate from acetyl-CoA, thus allowing to make glucose from acetyl-CoA
shared between glyoxysomes and mitochondria
absent in animals
does not produce CO2
operates only in plants, bacteria, and fungi, requires the glyoxysomal enzymes isocitrate lyase and malate synthase. This variation of the citric acid cycle permits net synthesis of glucose from acetyl-CoA.
Pathways Using Citric Acid Cycle Intermediates
gluconeogenesis (including shuttle)
fatty acid synthesis uses acetyl-CoA; has to be transported from mitochondrion to cytosol in form of citrate
synthesis of some amino acids uses a-ketoglutarate or oxaloacetate
hemoglobin, cytochromes
What is Electron Transport and Oxidative Phosphorylations function?
The citric acid cycle thus produces the reduced coenzymes NADH and FADH2, which then pass their electrons to O 2 to produce H2 O in the processes of electron transport and oxidative phosphorylation.
The process of electron transport results in a transmembrane proton concentration gradient that drives ATP synthesis
the electrons from reduced fuel molecules are transferred to molecular oxygen in eukaryotes. We also examine how the energy of fuel oxidation is conserved and used to synthesize ATP.
The 12 electron pairs released during glucose oxidation are not transferred directly to O2 . Rather, they are transferred to the coenzymes NAD +and FAD to form 10 NADH and 2 FADH 2
the site of eukaryotic oxidative metabolism.
the mitochondrion
mitochondrion inner and out membrane
outer membrane
contains porins
relatively permeable (for molecules ≤ 10,000 Da)
inner membrane
permeable for O2, CO2, H2O
contains transport proteins that control passage of metabolites (ATP, ADP, pyruvate, Ca2+, Pi, …)
important for compartimentalization between mitochondria and cytosol
What is produced in the cytosol by glycolysis that must gain access to the mitochondrial electron-transport chain for aerobic oxidation? The inner mitochondrial membrane lacks a transport protein specifically for it. How are “reduction equivalents” transported into mitochondria?
NADH
However, the inner mitochondrial membrane lacks an NADH transport protein.
the malate–aspartate shuttle (Fig. 16-20), in which, when run in reverse, cytosolic oxaloacetate is reduced to malate for transport into the mitochondrion. When malate is reoxidized in the matrix, it gives up the reducing equivalents that originated in the cytosol.
The glycerophosphate shuttle is expressed at variable levels in different animal tissues and is especially active in insect flight muscle (the tissue with the largest known sustained power output).
What is produced in the cytosol by glycolysis that must gain access to the mitochondrial electron-transport chain for aerobic oxidation? The inner mitochondrial membrane lacks a transport protein specifically for it. How are “reduction equivalents” transported into mitochondria?
NADH
However, the inner mitochondrial membrane lacks an NADH transport protein.
the malate–aspartate shuttle (Fig. 16-20), in which, when run in reverse, cytosolic oxaloacetate is reduced to malate for transport into the mitochondrion. When malate is reoxidized in the matrix, it gives up the reducing equivalents that originated in the cytosol.
The glycerophosphate shuttle is expressed at variable levels in different animal tissues and is especially active in insect flight muscle (the tissue with the largest known sustained power output).
What is the ADP–ATP translocator?
Most of the ATP generated in the mitochondrial matrix through oxidative phosphorylation is used in the cytosol.
The inner mitochondrial membrane contains an ADP–ATP translocator (also called the adenine nucleotide translocase) that transports ATP out of the matrix in exchange for ADP produced in the cytosol by ATP-consuming reactions.
ATP out, ADP in
antiport electrogenic
ATP is synthesized from ADP + Pi in the mitochondrion but is utilized in the cytosol. How is Phosphate imported into the mitochondrion? What drives this process?
The Pi is returned to the mitochondrion by the phosphate carrier,Pi Transporter, an electroneutral Pi-H+ symport that is driven by ΔpH.
cotransporter for Pi and H+
phosphate import into mitochondrion driven by transmembrane proton gradient
proton gradient not only driving force for ATP synthesis, also for transport of substrates ADP, Pi
Whatt drives the transport of ATP, ADP, and Pi.
the free energy of the proton gradient drives the transport of ATP, ADP, and Pi.
protons flow down their concentration gradient and bind to ATP synthase which turns and makes ATP from ADP
electron carriers
carry electrons from NADH and FADH2 to O2
are located in the inner mitochondrial membrane
some are mobile, some are relatively immobile as parts of large enzyme complexes
during electron transfer what happens to protons?
protons are translocated out of the mitochondrion to form an electrochemical gradient/proton gradient across the inner mitochondrial membrane whose free energy drives ATP synthesis from ADP and P ithrough oxidative phosphorylation.
electrons from the reduces coenzymes NADH and FADH2 go through what before reducing O2 to H2O
they pass through a series of redox centers in the electron transport chain
describe the thermodynamic efficiency of electron transport
A
an exergonic process
by inspecting the standard reduction potentials of the redox centers
efficiency, under standard conditions: 35 %
efficiency, under cellular conditions: ~ 70 %
Oxidation of NADH and FADH 2 is carried out by?
the electron-transport chain, a series of four protein complexes containing redox centers with progressively greater affinities for electrons (increasing standard reduction potentials). Electrons travel through the chain from lower to higher standard reduction potentials
What complexes/carriers are involved in the electron transport chain?
slides 107-116
Electrons are carried from Complexes I and II to Complex III by the lipid coenzyme Q (CoQ or ubiquinone; so named because of its ubiquity in respiring organisms), and from Complex III to Complex IV by the small soluble protein cytochrome c.
ATP is not synthesized by complexes I, III, or IV.
What is Oxidative Phosphorylation?
electron transport causes proton transfer across the inner mitochondrial membrane from the matrix, a region of low [H+ ], to the intermembrane space (which is in contact with the cytosol), a region of high [H+ ] to form an electrochemical gradient across the inner mitochondrial membrane. whose energy is used to endergonically synthesize ATP from ADP+Pi
via ATP synthase
The free energy released by electron transport through complexes I, III, and IV has to be conserved in some form usable by ATP synthase, to allow the synthesis of ATP from ADP and Pi (“energy coupling”).
What is ATP Synthase function?
The endergonic synthesis of ATP from ADP and P i in mitochondria is catalyzed by an ATP synthase (also known as Complex V) that is driven by the electrontransport process.
Where does ATP Synthase get its energy from?/ What links ATP synthase to electrons transport?
The free energy released by electron transport through Complexes I–IV must be conserved in a form that the ATP synthase can use. Such energy conservation is referred to as energy coupling.
ATP synthesis is coupled to electron transport through the production of a transmembrane proton gradient during electron transport by Complexes I, III, and IV.
What is the Chemiosmotic Theory?
what’s a prerequisite
Electron transport and ATP synthesis are coupled via a transmembrane proton gradient
The Chemiosmotic Theory Links Electron Transport to ATP Synthesis/Electron transport and ATP synthesis are coupled via a transmembrane proton gradient
Explanation: Mitchell’s theory states that the free energy of electron transport is conserved by pumping H+ from the mitochondrial matrix to the intermembrane space to create an electrochemical H + gradient across the inner mitochondrial membrane. The electrochemical potential of this gradient is harnessed to synthesize ATP
Prerequ:
The inner mitochondrial membrane (or the plasmamembrane of bacteria) has to be impermeable for H+, OH-, and other ions.
Compounds that make the inner membrane permeable for protons dissipate the gradient; no ATP synthesis occurs. Electron transport is “uncoupled” from ATP synthesis./allow electron transport (from NADH and succinate oxidation) to continue but inhibit ATP synthesis
What generates a proton gradient? What complexes?
What is the point of the free energy sequestered by the resulting electrochemical gradient?
A
Electron transport, as we have seen, causes Complexes I, III, and IV to transport protons across the inner mitochondrial membrane from the matrix, a region of low [H+ ], to the intermembrane space (which is in contact with the cytosol), a region of high [H+ ].
A
It powers ATP synthesis.
The free energy change of transporting a proton from one side of the membrane to the other has what 2 components?
a chemical (based on concentration difference) as well as an electrical (based on charge) component, since H + is an ion
what is electrochemical gradient also known as?
A
“electrochemical gradient”, also called “protonmotive force”, “pmf”
Describe the Binding change mechanism.
The sites, rotation, how affinity is determined, where does atp synthesis occur
What mechanism is crucial?
This mechanism elucidates the conformational change in the structure of ATP synthase that results in ATP production.
Steps followed for binding change mechanism
The steps in the binding change mechanism are as follows:
-F(0)F(1) ATP synthase acts as a rotary motor, with protons assisting in the spin movement of the subunits that make up the α and β subunits.
-The release of ATP is caused by the rotation of the γ subunit.
-The complex comprises three conformations: open (“O”), loose (“L”), and tight (“T”).
-ADP + Pi first bind to the L site.
-ADP converts to ATP at the T site after the conformational change but does not dissociate.
-The T site undergoes conformational changes and converts to an open site. ATP is released from this open site.
3 sites with different affinities (high, medium, low)
affinity determined by position of central stalk
rotation → sites switch their affinities
catalysis (ATP synthesis/hydrolysis) occurs in high-affinity (tight) site
ATP synthesis from ADP and Pi in the high-affinity site occurs spontaneous. It is the release of ATP from this site that requires (most of the) energy.
What is the brownian ratchet?
represents proton flow through F0
What are uncouples?
Uncouplers - make the membrane permeable for protons, thereby dissipating the gradient.
Agents that discharge the proton gradient can uncouple oxidative phosphorylation from electron transport.
Coupling of electron transport and oxidative phosphorylation requires proton gradient.
Existence of proton gradient depends on impermeability of membrane.
Uncouplers uncouple electron transport from oxidative phosphorylation. Instead, what is generated? Give an example
What are uncouplers blocked by?
Heat. (thermogenesis)
Thermogenesis in Brown Adipose Tissue
Brown adipose tissue occurs in newborn and in coldadapted animals. (brown – rich in mitochondria)
BAT mitochondria contain uncoupling protein, which contains a proton channel and allows flux of protons back into the mitochondrial matrix.
Uncoupling protein is blocked by ATP, ADP, GTP, GDP.
PHYSIOLOGICAL IMPLICATIONS OF AEROBIC METABOLISM
advantages and disadvantages
Advantages:
much higher energy yield from given amount of fuel
oxidative detoxification possible (cytochrome P450)
Disadvantages:
absolute O2 dependence in most organisms (→ heart attack, stroke)
reactive oxygen species as byproducts
What are the reactive oxygen species radicals?
A
reactive species is
* partially reduced oxygen
* highly reactive
* harmful to cell/organism lipids, DNA, and enzymes
-mostly harms mitochondria
involved in Parkinson’s, Alzheimer’s, Huntington’s diseases; also in “normal” aging process
what are Antioxidant Mechanisms
Antioxidant Mechanisms
antioxidants destroy oxidative free radicals
superoxide dismutase
very fast reaction rates
List of lipids
Fatty acids
Triacylglycerols (triglycerides)
Glycerophospholipids (“phosphoglycerides”, “phospholipids”)
Sphingolipids (e.g. sphingmyelin, cerebrosides, gangliosides)
Steroids (e.g. cholesterol, steroid hormones)
fatty acid oxidation (b oxidation)
Acyl group of fatty acids are activated by their attachment to coenzyme A
Fatty acid oxidation begins with the activation of the acyl group by formation of a thioester with CoA. The acyl group is transferred to carni-tine for transport into the mitochondria, where it is re-esterified to CoA.
-β oxidation occurs in four reactions: (1) formation of an α, β double bond,(2) hydration of the double bond, (3) dehydrogenation to form a β -ketoacyl-CoA, and (4) thiolysis by CoA to produce acetyl-CoA and an acyl-CoA shortened by two carbons. This process is repeated until fatty acids with even numbers of carbon atoms are converted to acetyl-CoA and the fatty acids with odd numbers of carbon atoms are converted to acetyl-CoA and one molecule of propionyl-CoA. The acetyl-CoA is oxidized by the citric acid cycle and oxidative phosphorylation to generate ATP. Propionyl-CoA is converted to the citric acid cycle intermediate succinyl-CoA, in part, by the coenzyme B12 -containing enzyme methylmalonyl-CoA mutase.
-The oxidation of unsaturated fatty acids requires an isomerase to convert Δ 3 double bonds to Δ 2 double bonds and a reductase to re-move Δ 4 double bonds. The oxidation of odd-chain fatty acids yields propionyl-CoA, which is converted to succinyl-CoA through a cobala-min (B12 )-dependent pathway. Very long chain fatty acids are partially oxidized by a three-enzyme system in peroxisomes
after the formation of fatty acyl-CoA?
The acyl group is transferred by a carnitine shuttle (leaves CoA in cytosol). The resulting acyl-carnitine is transported into the mitochondria for oxidation and where it is re-esterified to CoA
Carnitine is returned to cytosol.
What reaction occurs after the acyl group is transferred into the mitochondria?A
The degradation of fatty acyl-CoA to acetyl-CoA via β oxidation which occurs in 4 reactions.
Formation of a trans-α, β double bond through dehydrogenation by the flavoenzyme acyl-CoA dehydrogenase (AD).
FADH2 is reoxidized by electron transport chain via ETF
Hydration of the double bond by enoyl-CoA hydratase (EH) to form a 3-L-hydroxyacyl-CoA.
NAD+ -dependent dehydrogenation of the β -hydroxyacyl-CoA by 3-Lhydroxyacyl-CoA dehydrogenase (HAD) to form the corresponding β -ketoacyl-CoA.
/dehydration to form a β-ketoacyl-CoA
NADH reoxidized by e.t chain
Cα —C β cleavage in a thiolysis reaction with CoA as catalyzed by 𝛃 -ketoacylCoA thiolase (KT; also called just thiolase) to form acetyl-CoA and a new acyl-CoA containing two fewer C atoms than the original one.
/thiolysis by CoA to produce acetyl-CoA and an acyl-CoA shortened by 2 carbons.
Oxidation of Odd-Chain Fatty Acids occurs where
in plants and marine organisms
Most fatty acids, for reasons explained in Section 20-4, have even numbers of carbon atoms and are therefore completely converted to acetyl-CoA. Some plants and marine organisms, however, synthesize fatty acids with an odd number of carbon atoms.
Oxidation of Odd-Chain Fatty Acids Yields Propionyl-CoA
The final round of β oxidation of these fatty acids yields propionyl-CoA, which is converted to succinyl-CoA for entry into the citric acid cycle.
Succinyl-CoA Is Not Directly Consumed by the Citric Acid Cycle. How then?
A
In order for succinyl-CoA to undergo net oxidation by the citric acid cycle, it must first be converted to pyruvate and then to acetyl-CoA
by MethylmalonylCoA mutase that catalyzes the conversion of a metabolite to a citric acid cycle intermediate other than acetyl-CoA.
function of ketone bodies?
A
Acetyl-CoA may be reversibly converted to ketone bodies in the liver to be used as fuel by other tissues.
It serves as
- fuel for heart, skeletal muscle, other tissues
- fuel for brain (during starvation)
ketogenesis
function of ketone bodies?
A
Acetyl-CoA may be reversibly converted to ketone bodies in the liver to be used as fuel by other tissues.
It serves as
- fuel for heart, skeletal muscle, other tissues
- fuel for brain (during starvation)
ketogenesis
What is ketosis?
A
Indeed, in individuals with ketosis, a pathological condition in which acetoacetate is produced faster than it is metabolized (a symptom of diabetes; Section 22-4B), the breath has the characteristic sweet smell of acetone.
difference between fatty acid biosynthesis and degradation
Biosynthesis similar to reversal od degradation
Biosynthesis occurs in the cytoplasm. Degradation occurs in the mitochondria.
Biosynthesis acyl-ACP (only Carry proteins)anchors to ACP, Degradation acyl-CoA anchors to CoA
in C2 steps, biosynthesis (Molonyl,-CoA), Degradation (acetyl-CoA)
Biosynthesis, only NADPH both redox rxns, Degradation FAD and NAD+
Biosynthesis D-b-hydroxyacyl-ACP instead of L-b-hydroxyacyl-CoA
Biosynthesis- all activities on one complex
slide:
reversal of b-oxidation steps, except…
NADPH instead of NADH, FADH2
all activities on one enzyme complex
ACP instead of CoA
malonyl-ACP instead of acetyl-CoA
D-b-hydroxyacyl-ACP instead of L-b-hydroxyacyl-CoA
FA biosynthesis
The tricarboxylate transport system transfers acetyl-CoA into the cytosol for fatty acid synthesis.
Fatty acid synthesis begins with the carboxylation of acetyl-CoA to generate malonyl-CoA.
Fatty acid synthase carries out seven reactions and lengthens a fatty acid two carbons at a time.
Elongases and desaturases may modify fatty acids.
Triacylglycerols are synthesized from glycerol and fatty acids.
Fatty acid oxidation and synthesis are regulated by?
A
hormones and cellular factors.
The opposing pathways of fatty acid degradation and synthesis are hormonally regulated. Glucagon and epinephrine activate hormone-sensitive lipase in adipose tissue, thereby increasing the supply of fatty acids for oxidation in other tissues, and inactivate acetyl-CoA carboxylase. Insulin has the opposite effect. Insulin also regulates the levels of acetyl-CoA carboxylase and fatty acid synthase by controlling their rates of synthesis.
Cholesterol metabolism slides 171-end
The degradation of an amino acid almost always begins with?
Deamination, the removal of its amino group in a PLP-Facilitated transamination reaction.
This is one of the major degradation pathways which convert essential amino acids to non-essential amino acids (amino acids that can be synthesized de novo by the organism).
Transamination interconverts an amino acid and an α-keto acid.
amino groups from most amino acids are funneled into glutamate or aspartate
coenzyme of aminotransferases is pyridoxal-5’-phosphate
Transamination does not result in net deamination; products are glutamate or (to a lesser extent) aspartate. What happens to glutamate? What does it release and accept?
A
Glutamate, however, can be oxidatively deaminated by glutamate dehydrogenase (GDH), yielding ammonia and regenerating α-ketoglutarate for use in additional transamination reactions.
Releases ammonia for disposal
Glutamate dehydrogenase, a mitochondrial enzyme, is the only known enzyme that can accept either NAD +or NADP +as its redox coenzyme.
net deamination of glutamate by glutamate dehydrogenase
glutamate dehydrogenase accepts NAD +and NADP
What eventually happens to the ammonia liberated in the GDH reaction?
It is excreted in the form of urea. Thus, the glutamate dehydrogenase reaction functions to eliminate amino groups from amino acids that undergo transamination reactions with α-ketoglutarate.
Living organisms excrete the excess nitrogen arising from the metabolic breakdown of amino acids in one of three ways:
Many aquatic animals simply excrete ammonia. Where water is less plentiful, however, processes have evolved that convert ammonia to less toxic waste products that require less water for excretion. One such product is urea, which is produced by most terrestrial vertebrates; another is uric acid, which is excreted by birds and terrestrial reptiles.
We focus our attention on urea formation.
What occurs in the urea cycle? How many reactions take place?
Urea is synthesized in the liver by the enzymes of the urea cycle. It is then secreted into the bloodstream and sequestered by the kidneys for excretion in the urine.
ive enzymatic reactions are involved in the urea cycle, two of which are mitochondrial and three cytosolic
A nitrogen atom from ammonia (a product of the oxidative deamination of glutamate) and bicarbonate are incorporated into carbamoyl phosphate for entry into the urea cycle.
A second nitrogen atom introduced from aspartate enters the cycle to produce urea for excretion.
urea cycle reactions.
ketogenic and glycogenic amino acids
Other Products of Amino Acid Metabolism
heme
physiologically active amines (hormones, neurotransmitters)
nitric oxide, NO
nitric oxide
- “messenger”, causes relaxation of smooth muscle, vasodilation - radical, gas
Assimilation of fixed nitrogen into biological molecules:
glutamine synthetase and glutamate synthase
nitrogen fixation
most plants do not have symbiotic nitrogen-fixating bacteria
have to take up nitrate or ammonia, generated by - lightning discharge - decaying organic matter - fertilizer
Nitric Oxide Is Derived from
arginine
What enzyme reduces N2 to NH3? How many ATP per N2?
A
Nitrogenase
16
–
60
Q
What makes Nitrogen fixation difficult?
A
N2 is inert
structure of a nucleotide
base sugar phosphate
What are purine nucleotides initially derived from?
A
Purines are initially formed as ribonucleotides rather than as free bases.
The ribonucleotides form IMP which then synthesize AMP and GTP and finally
purine biosynthesis steps:
Ribose-5-Phosphate to IMP synthesis
Synthesis of AMP from IMP
Synthesis of GMP from IMP
Q
IMP is the precursor of both?
A
Inosine Monophosphate yields Adenine and Guanine ribonucleotides, AMP and GMP
What occurs in the salvage pathways?
RNA → adenine, guanine, hypoxanthine
bases reconverted to nucleotide in salvage pathways
pyrimidine ring coupled to ribose after synthesis (in contrast to purine synthesis)
Difference between purine and pyrimidine nucleotide synthesis regarding the ring.
A
In contrast to purine nucleotide synthesis, the pyrimidine ring is coupled to the ribose-5-phosphate moiety after the ring has been synthesized.
What are pyrimidine ribonucleotides, UTP and CTP derived from?
A
UMP is the precursor
How does DNA chemically differ from RNA?
thymine
deoxyribose instead of ribose
How are deoxyribonucleotides synthesized?
A
Deoxyribonucleotides are synthesized from their corresponding ribonucleotides by the reduction of their C2′ position rather than by their de novo synthesis from deoxyribose-containing precursors.
Ribonucleotide Reductase uses a free radical mechanism to Convert Ribonucleotides to Deoxyribonucleotides
uses NDP as substrate
Ribonucleotide Reductase Converts NDPs to dNDPs
(Enzymes that catalyze the formation of deoxyribonucleotides by the reduction of the corresponding ribonucleotides are named ribonucleotide reductases (RNRs). There are three classes of RNRs, which differ in their prosthetic groups, although they all replace the 2′-OH group of ribose with H via a free-radical mechanism involving a thiyl radical)
Here we discuss the mechanism of Class Ia RNRs, which have an Fe-containing prosthetic group and which occur in all eukaryotes and many aerobic bacteria (Class Ib RNRs have a similar mechanism but have an Mn-containing prosthetic group)
Class Ia RNRs reduce ribonucleoside diphosphates (NDPs) to the corresponding deoxyribonucleoside diphosphates (dNDPs). T
How is Thymine (dTTP) synthesized?
A
The dTTP substrate for DNA synthesis is derived from dUTP, which is hydrolyzed to dUMP by dUTP diphosphohydrolase (dUTPase):
dUTP + H2O → dUMP + PPi
The dUMP is then methylated to generate dTMP by thymidylate synthase:
dUMP + N5 ,N10 -methylene-THF → dTMP + dihydrofolate
Finally, the dTMP is phosphorylated to form dTTP by nucleoside monophosphate kinase and nucleoside diphosphate kinase:
dTMP → dTDP → dTTP
What is the reason for the energetically wasteful process of dephosphorylating dUTP and rephosphorylating dTMP?
is that cells must minimize their concentration of dUTP in order to prevent incorporation of uracil into their DNA (the enzyme system that synthesizes DNA from dNTPs does not efficiently discriminate between dUTP and dTTP; Section 25-2A).
appears to waste energy
necessary to keep dUTP concentration low
DNA polymerase does not discriminate efficiently between dUTP and dTTP
Summary of the Formation of Deoxyribonucleotides
A
Deoxyribonucleoside diphosphates (dNDPs) are synthesized from the corresponding NDPs in a free radical-mediated oxidation reaction catalyzed by ribonucleotide reductase, which contains a binuclear Fe(III) prosthetic group, a tyrosyl radical, and three redox-active sulfhydrylgroups. Enzyme activity is regenerated through disulfide interchange with thioredoxin.
Ribonucleotide reductase is regulated by allosteric effectors, which ensure that deoxynucleotides are synthesized in the amounts and ratios required for DNA synthesis.
dTMP is synthesized from dUMP by thymidylate synthase. The dihydrofolate produced in the reaction is converted back to tetrahydrofolate by dihydrofolate reductase (DHFR).
What are purines broken down into?
Uric Acid
excretion of excess nitrogen as uric acid instead of urea conserves water
What is The Purine Nucleotide Cycle and what does it generate?
A
This pathway functions in muscle to prime the citric acid cycle by generating fumarate.
-The deamination of AMP to IMP, when combined with the synthesis of AMP from IMP, has the net effect of deaminating aspartate to yield fumarate.
-Has an important metabolic role in skeletal muscle.
-Muscle replenishes its citric acid cycle intermediates with fumarate generated in the purine nucleotide cycle.
The synthesis and degradation of AMP in the purine nucleotide cycle yield the citric acid cycle intermediate fumarate in muscles.
Slide:
* important metabolic role in muscle
muscle activity requires increase in activity of citric acid cycle
muscle lacks many enzymes for anaplerotic reactions
uses fumarate generated in the purine nucleotide cycle
elevated blood levels of uric acid can cause?
→ formation of (nearly insoluble) crystals of sodium urate
→ crystals deposited in joints
→ gout
Whats gout and how do you treat it
Gout Is Caused by an Excess of Uric Acid.
Gout can be treated by administering the xanthine oxidase inhibitor allopurinol.
Allopurinol consequently alleviates the symptoms of gout by decreasing the rate of uric acid production while increasing the levels of the more soluble hypoxanthine and xanthine.
Characteristics of brain tissue
A
consumes 20% of O 2 taken up in resting state
ATP needed for Na+ ,K+ -ATPase for maintaining membrane potential in neurons
steady supply of glucose (or ketone bodies) from blood required
dysfunction if blood glucose levels < 50 % of normal (~ 5 mM)
What tissue can carry out all the reactions?
Liver
Nevertheless, about 60% of all metabolic enzymes, representing essential “housekeeping” functions, are expressed at some level in all tissues in the human body but liver is the most metabolically active tissue, followed by adipose tissue and skeletal muscle.
What 5 mammalian organs are we going over? How are they connected?
A
-brain, muscle, adipose tissue, liver, and kidney.
-connected via bloodstream
Muscle’s major fuels are?
glucose (from glycogen), fatty acids, and ketone bodies.
Characteristics of the muscle
stores glycogen (1 – 2% of muscle mass)
(stores glucose in the form of glycogen)
glycogen is not as efficient as triacylglycerides in storing energy. however, glycogen can be mobilized more rapidly than fat and because glucose can be metabolized anaerobically, fatty acids not
ATP used for muscle contraction (myosin)/Muscle contraction is driven by ATP hydrolysis (Section 7-2) and therefore requires either an aerobic or an anaerobic ATP regeneration system.
(Can work aerobically or anaerobically. Anaerobic needs glucose, not fat)
muscle cannot export what?
muscle doesn’t participate in what?
-In muscle, glycogen is converted to glucose-6-phosphate (G6P) for entry into glycolysis. Muscle cannot export glucose, however, because it lacks glucose-6phosphatase.
-Furthermore, although muscle can synthesize glycogen from glucose, it does not participate in gluconeogenesis because it lacks the required enzymatic machinery. Consequently, muscle carbohydrate metabolism serves only muscle.
ATP is used for?
What is a major app source
ATP used for muscle contraction (myosin)
respiration (citric acid cycle and oxidative phosphorylation) major ATP source
at rest, skeletal muscle uses how much of O2 taken up by body
A
Skeletal muscle at rest uses ∼30% of the O 2consumed by the human body. A muscle’s respiration rate may increase in response to a heavy workload by as much as 25-fold
Function of the adipose tissue? Where do the fatty acids come from?
A
The function of adipose tissue is to store and release fatty acids as needed for fuel as well as to secrete hormones involved in regulating metabolism.
stores fat/triglycerides; releases it when needed
150 lb person – 30 lb fat (sufficient energy for ~ 3 months)
Liver functions
A
The liver maintains the proper levels of circulating fuels for use by the brain, muscles, and other tissues. It is uniquely situated to carry out this task because all the nutrients absorbed by the intestines except fatty acids are released into the portal vein, which drains directly into the liver.
* The liver makes all types of fuel available to other tissues.
One of the liver’s major functions is to act as a blood glucose “buffer.”
Fuel:
makes ketone bodies but does not use them s fuel
amino acids used as fuel
* when other fuels are scarce (muscle protein degradation)
main source of acetyl-CoA?
A
fatty acids
When the demand for metabolic fuels is high, fatty acids are degraded to acetyl-CoA
The liver also converts fatty acids to ketone bodies a
muscle fuel
amino acids used as fuel source
immediately after feeding
when other fuels are scarce (muscle protein degradation)
kidney function, function during starvation?
kidney excretes urea, NH3, H+, ketone bodies
during starvation, kidneys supply up to 50% of the body’s glucose
Kidney Filters Wastes and Maintains Blood pH
Compare Glucokinase and Hexokinase
higher affinity for glucose
B) inhibited by glucose-6-phosphate
C) occurs in liver
D) occurs in muscle
E) higher K M for glucose
glucokinase glucokinase glucokinase glucokinase glucokinase
hexokinase hexokinase hexokinase hexokinase hexokinase
The hexokinases in most cells obey Michaelis–Menten kinetics, have a high glucose affinity (K M < 0.1 mM), and are inhibited by their reaction product (G6P).
occurs in the liver
Glucokinase, in contrast, has much lower glucose affinity (reaching half-maximal velocity at ∼5 mM) and displays sigmoidal kinetics. Consequently, glucokinase activity increases rapidly with blood [glucose] over the normal physiological range (Fig. 22-4). Glucokinase, moreover, is not inhibited by physiological concentrations of G6P.
occurs in the muscle
food absorption after meal:
proteins: - broken down into amino acids - absorbed - (in liver) used for protein biosynthesis, or oxidized to gain energy (no storage depot)
carbohydrates: - broken down into monosaccharides - absorbed - converted to glycogen (in liver and muscle), or oxidized to gain energy
fat: - fatty acids absorbed in intestinal mucosa and incorporated into chylomicrons (as triacylglycerides) - mostly taken up by adipose tissue, stored in adipocytes
what is diabetes mellitus
not sufficient insulin released, or
insulin fails to stimulate target cells sufficiently
[glucose]blood elevated, glucose excreted in urine
insulin-dependent take-up of glucose into cells impaired
ketone body levels become abnormally high (“ketosis”)
pH of blood decreases; H+ excreted, together with Na+, K+, Pi, H2O, resulting in dehydration, decrease in blood volume
Type 1 diabetes vs Type 2 diabetes
1.not sufficient insulin released
insulin-dependent (type I, or juvenile-onset) diabetes
pancreas lacks or has defective b cells (often caused by autoimmune response)
insulin has to be provided by injection
- insulin fails to stimulate target cells sufficiently
non-insulin-dependent (type II, or maturity-onset) diabetes
lack of insulin receptors ([insulin] high), cells are “insulin-resistant”
