Ch. 7 How Cells Harvest Energy
Pyruvate oxidation and Krebs cycle products and reactants (per molecule of glucose)
- 6 CO₂ - 8 NADH - 2 FADH₂ - 2 GTP (= 2 ATP)
What do different types of allosteric regulators do and what are they called?
- Allosteric regulators bind to non-active sites of enzymes and change the conformation of the active site. - They can either increase or decrease the activity of the enzyme. - called a Positive Regulator if it increases activity - called a Negative Regulator if it decreases activity
Acetyl-CoA has many roles
- Almost all catabolized molecules are turned into acetyl-CoA - Also used in anabolic metabolism, building fatty acids - Which role, depends on ATP concentration
Pyruvate Oxidation
- Between Glycolysis and Krebs - Releases CO₂ - Reduces NAD⁺ to NADH - Remaining compound attached to coenzyme A; entire unit called acetyl-CoA.
Mitochontrial Intermembrane Space
- Between inner, outer membranes - Composition of ions and small molecules is the same as the cytosol's
Mitochondrial Matrix
- Contains Krebs cycle enzymes - Pyruvate gets brought into the matrix
8,9. Regeneration of Oxaloacetate, Fourth Oxidation
- Fulmarate is oxidized to Malate, then to oxaloacetate - Reduces an NAD⁺ to NADH
Actual ATP yield for Eukaryotes
- Inner mitochondrial membrane "leaky" - Proton gradient used for other things as well → measured values closer to 2.5xNADH, 1.5xFADH₂ - Actual yield ~30 ATP/glucose
5. Second Oxidation
- Loses another carbon as CO₂ w/ help from multienzyme complex - 4-carbon Succinyl joins CoA to form succinyl-CoA - - Reduces an NAD⁺ to NADH
Mitochontrial Outer Membrane
- More typical protein % - Contains porins
Progression along the ETC
- NADH passes electrons to complex 1. - Energy from the electrons is used to pump H⁺ out of the matrix. - FADH₂ is oxidized at complex 2, skips complex 1; electrons from it thus result in less ATP - Ubiquinone takes electrons from complexes 1 and 2 to complex 3, which pumps more H⁺. - Cytochrome C carries electrons from complex 3 to complex 4; another H⁺ pumped. - Cytochrome oxidase complex forms water O₂ + 4 H⁺ → 2 H₂O : End
Mitochontrial Inner Membrane
- Principle site of ATP generation - >70% protein (a lot for a membrane) - Impenetrable to ions and small molecules except at transporters
A small number of key intermediates connect metabolic pathways
- Pyruvate - Acetyl Co-A Allows the interconversions of fats/sugars/etc.
4. First Oxidation
- Reduces an NAD⁺ to NADH - Loses a carbon as CO₂ - Forms 5-carbon α-ketoglutarate.
7. Third Oxidation
- Succinate oxidized to Fumarate - Not enough energy to reduce NAD⁺, so FADH₂ made instead. - FADH₂ can only contribute electrons to the electron transport chain in the membrane
6. Substrate-Level Phosphorylation
- Succinyl-CoA breaks apart to form Succinate - Energy release helps make GTP (→ATP)
What still needs to be done at the end of the Krebs cycle
- need to get NADHs back to NAD⁺ - need to get FADH₂ back to FAD - still need to transfer energy in cofactors to ATP
What coordinates the catabolic and biosynthetic pathways?
- the amount of enzymes present (long-term) - the activity of allosteric enzymes (short-term)
For organisms that do not undergo aerobic respiration, they compensate by...
... having glycolysis proceed much faster, so that they can still produce enough ATP to function.
Glucose reactants/products
1 glucose molecule → 2 pyruvates 2 NAD⁺ → 2 NADH 2 ATP → 2 ADP 4 ADP → 4 ATP → 2 H₂O Total: 2 NADH, 2 ATP, 2 H₂O
Nine reactions of Krebs
1. Condensation 2,3. Isomerization 4. First Oxidation 5. Second Oxidation 6. Substrate-Level Phosphorylation 7. Third Oxidation 8,9. Regeneration of Oxaloacetate, Fourth Oxidation
Glycolysis
1st step, occurs in the cytoplasmic fluid. It is the multistep chemical breakdown of a molecule of glucose into two molecules of pyruvate (net gain of 2 ATP)
Theoretical ATP yield for Eukaryotes
2 from Glycolysis SLP 6 from Glycolysis Chemiosmosis (3×2 NADH) 6 from Pyruvate Oxidation Chemiosmosis (3×2 NADH) 2 from Krebs SLP (2×GTP) 18 from Krebs Chemiosmosis (3×6 NADH) 4 from Krebs Chemiosmosis (2×2 FADH₂) Total = 38 ATP; true for Proks, but for Euks 2 ATP needed to transport NADH from cytoplasm to matrix → theoretically, 36 ATP produced.
The average adult neededs
2200 kcal of energy per day
Citric acid cycle (Kreb cycle)
2nd step, occurs in the matrix of mitochondria and supplies most of the NADH molecules that carry energy to the electron transport chains. The metabolic cycle fueled by acetyl CoA formed after glycolysis in cellular respiration. chemical reactions complete the metabolic breakdown of glusoce molecules to carbon dioxide
Cellular respiration can produce...
38 ATP molecules for each glucose molecule, representing about 40% of the energy in glucose
Oxidative Phosphorylation
3rd step. The production of ATP using energy derived from the redox reactions of an electron transport chain~ involves the electron transport chain and a process known as chemiosmosis. NADH and FADH2 shuttle elctrons to the electron transport chain embedded in the inner mitochondrion membrane. Energy released by the downhill fall of electrons from NADH and FADH2 to O2 to phosphorylate ADP
Glycolysis step 6-9
4 ATP and 2 pyruvate are produced
C6H12O6 (glucose)+ 6 O2 (oxygen) >>>
6 CO2 (carbon dioxide) + 6 H2O (water) + ATPs
ATP Synthase Structure
A "rotor" within the membrane connected by a narrow stalk to a catalytic head sticking out into the matrix. Movement of H⁺ through it drives physical rotation, changing conformation of domains on the complex.
Redox reaction/ Oxidation-Reduction reaction
A chemical reaction in which electrons are lost from one substance (oxidation) and added to another (reduction). O & R always occur together
ATP
A cluster of several membrane proteins that function in chemiosmosis with adjacent electron transport chains, using the energy of a hydrogen ion concentration gradient to make ATP
NAD+ (nicotinamide adenine dinucleotide)
A coenzyme that can accept electrons during the redox reactions of cellular metabolism. An organic molecule that cells make from the vitamin niacin.
Glycolysis step 1-3
A fuel molecule is energized using 2 ATP
Limiting Step
A key step in a reaction that if altered could change the entire pathway's speed. A "chokepoint". ex. feedback inhibition of glycolysis by ATP; phosphofructokinase inhibited.
Glycolysis step 5
A redox reaction generates NADH
Electron transport chain
A series of electron carrier molecules that shuttle electrons during the redox reactions that release energy used to make ATP; located in the inner membrane of the mitochondria, the thylakoid membranes of chloroplasts, and the plasma membranes of prokaryotes
The electron transport chain involves...
A series of redox reactions in which electrons pass from carrier to carrier down to oxygen
Glycolysis begins with
A single molecule of glucose and concludes with two molecules of pyruvate. As these reaction occur, the cell reduces two molecules of NAD+, forming two molecules of NADH, and produces two molecules of ATP by substrate-level phosphorylation
Glycolysis Step 4
A six-carbon intermedicate splits into two three-carbon intermediates
Multienzyme complex
A unit containing multiple enzymes; pyruvate oxidation is catalyzed by one within the mitochondria. Contains pyruvate dehydrogenase, one of the largest enzymes known.
Three segments of Krebs
A: Acetyl-CoA plus oxaloacetate. Produces 6-carbon citrate molecule. B: Citrate rearrangement and decarboxylation. Reduces citrate to 5, then 4 carbons. Produces 2 NADH and 1 GTP. C: Regeneration of oxaloacetate. Produces 1 NADH, 1 FADH₂.
Regulation of Aerobic Respiration - Glycolysis
ATP and citrate are allosteric inhibitors of an enzyme in glycolysis, phosphofructokinase. When ATP is in excess or Krebs is making more citrate than is consumed, glycolysis is slowed.
Citric acid cycle step 1
Acetyl CoA stokes the furnace
Reactants/Products of Krebs
Acetyl-CoA + H₂O → 3 NADH + 1 GTP + 1 FADH₂
Efficiency of catabolism of glucose
Aerobic respiration captures ~32% of a glucose's energy (compared to ~25% for a car engine).
Cellular respiration is the complete oxidation of glucose.
Aerobic respiration uses oxygen as the final electron acceptor for redox reactions. Anaerobic respiration utilizes inorganic molecules as acceptors, and fermentation uses organic molecules.
Dehydrogenase
An enzyme that catalyzes a chemical reaction during which one or more hydrogen atoms are removed from a molecule (NADH & FADH)
Facultative anaerobe
An organism that makes ATP by aerobic respiration if oxygen is present, but that switches to fermentation when oxygen is absent.
Obligate anaerobes
An organizm that only carries out fermentation; such organisms cannot use oxygen and also may be poisoned by it.
Aerobic respiration utilized oxygen
Ancient, purple, nonsulfur bacteria evolved to not photosynthesize at all, instead subsisting only off sequestered molecules → mitochondria descendants of those cells, now found in all euk cells.
Glucose becomes CO₂ and potential energy.
As a glucose molecule is broken down to CO₂, some of its energy is preserved in 4 ATPs,10 NADH, and 2 FADH₂.
Chemiosmosis
As a result of the ETC, the mitochondrial matrix is negative compared to the intermembrane space; hydrogens want to go in, and can go through a transmembrane enzyme called ATP synthase. By going through, they drive the production of ATP. Because this drive is similar to osmosis, it is called chemiosmosis.
Evolution of glycolysis occurred early on
As proteins evolved catalytic functions, became possible to extract more energy from molecules. Must have evolved early on b/c present in all organisms today.
Earliest lifeforms degraded carbon-based molecules present in the environment
Believed to have metabolized abiotically produced molecules. Then, began to store energy in bonds of ATP.
Respiration of fatty acids vs ATP
Carbon for carbon, fats will yield more energy than carbs, and are lighter to boot, hence their use as storage.
Energy of Carriers
Carriers are of successively lower energy as energy is lost from the previous carrier in driving the proton pumps.
Catabolism of Proteins and Fats
Catabolism of proteins removes amino groups. A small number of key intermediates connect metabolic pathways.
Overview of Respiration
Cells oxidize organic compounds to drive metabolism.
1. Condensation
Citrate formed from Acetyl-CoA and oxaloacetate. Inhibited by high levels of ATP, at which point Acetyle-CoA goes into fat synthesis.
2,3. Isomerization
Citrate needs to be rearranged so it can react better later; forms isocitrate.
Components of the Electron Transport Chain
Complex 1 (transmembrane) Complex 2 (integral) Complex 3 (trans) Complex 4 (trans) Ubiquinone (carrier) Cytochrome C (carrier)
Key players in the process of oxidizing glucose
Dehydrogenase and NAD+ are used to shuttle electrons in redox reactions
Catabolism of proteins removes amino groups
Depending on what amino acids are broken down, different substances present at different stages are made; they then enter glycolysis or Krebs.
Why are catabolic and biosynthetic pathways coordinated?
Don't want to spend more energy than necessary (ex. break down only to build up again)
Electron carriers play a critical role in energy metabolism.
Electron carriers can be reversibly oxidized and reduced. For example, NAD⁺ is reduced to NADH by acquiring two electrons; NADH supplies these electrons to other molecules to reduce them.
Kilocalories
Energy units, 1 kilocalorie can raise the temp. of water by 1C
Chemiosmosis
Energy-coupling mechanics that uses the energy of hydrogen ion (H+) gradients across membranes to phosphorylate ADP; powers most ATP synthesis in cells ~ during oxidative phosphorylation
Location of the Electron Transport Chain
Eukaryotes - inner mitochondrial membrane Prokaryotes - cytoplasmic membrane
Catabolism of fatty acids produces acetyl groups in a process called β oxidation
Fatty acids are oxidized in the matrix of the mitochondria; enzymes remove 2-carbon acetyl groups until the entire fatty acid has been converted into acetyl groups. They are then combined with coenzyme A to form acetyl Co-A.
Fermentation uses organic compounds as electron acceptors.
Fermentation is the regeneration of NAD⁺ by oxidation of NADH and reduction of an organic molecule. In yeast, pyruvate is decarboxylated, then reduced to ethanol. In animals, pyruvate is reduced directly to lactate.
The Krebs Cycle
Following the electrons in the reactions reveals the direction of transfer.
Cellular respiration provides energy...
For body maintenance and the energy for voluntary activities
Pyruvate is groomed
For the citric acid cycle. It is made into acetyl CoA
Regulation of Aerobic Respiration
Glucose catabolism is controlled by the concentration of ATP molecules and intermediates in the Krebs cycle.
The two main steps of Glycolysis
Glucose priming Cleavage and rearrangement
G3P
Glyceraldehyde-3-phosphate
Glycolysis: Splitting Glucose
Glycolysis converts glucose into two 3-carbon molecules of pyruvate. Each molecule of glucose yields two net ATP molecules.
Lactic Acid Fermentation
Glycolysis produces ATP and NADH. Lactate dehydrogenase takes Hs from NADH and give it to the pyruvates to form lactate and NAD⁺.
Ethanol Fermentation
Glycolysis produces ATP and NADH. Pyruvates produced lose CO₂ to become acetaldehyde. Acetaldehyde takes Hs from NADH to become ethanol, and NADHs are oxidized back to NAD⁺.
Regulation of Aerobic Respiration - Krebs
High levels of ATP will slow several steps in the Krebs catabolic pathway.
Oxidation Without O₂
In the absence of oxygen other final electron acceptors can be used for respiration. Methanogens use carbon dioxide. Sulfur bacteria use sulfate. Fermentation uses organic compounds.
Where Glycolysis Occurs
In the cytoplasm; works for all organisms.
The electron transport chain produces a proton gradient.
In the inner mitochondrial membrane, NADH is oxidized to NAD⁺ by NADH dehydrogenase. Electrons move through ubiquinone and the bc₁ complex to cytochrome oxidase, where they join with H⁺ and O₂ to form H₂O. This results in three protons being pumped into the intermembrane space. For FADH₂, electrons are passed directly to ubiquinone. Thus only two protons are pumped into the intermembrane space.
Krebs Cycle Location
In the matrix of the mitochondria for eukaryotes. In the cytoplasm and plasma membrane of prokaryotes.
NADH must be recycled into NAD⁺ to continue respiration.
In the presence of oxygen, NADH passes electrons to the electron transport chain. In the absence of oxygen, NADH passes the electrons to an organic molecule such as acetaldehyde (fermentation).
Evolution of Metabolism
Major milestones are recognized in the evolution of metabolism; the order of events is hypothetical. The earliest life forms degraded carbon-based molecules present in the environment. The evolution of glycolysis also occurred early. Anoxygenic photosynthesis allowed the capture of light energy. Oxygen-forming photosynthesis used a different source of hydrogen. Nitrogen fixation provided new organic nitrogen. Aerobic respiration utilized oxygen.
Metabolism harvests energy in stages.
Mitochondria of eukaryotic cells move electrons in steps via the electron transport chain to capture energy efficiently.
Citric acid cycle step 2-3
NADH, ATP, and CO2 are generated during redox reactions
New nitrogen fixation provided new organic nitrogen
Nitrogen fixation = getting nitrogen from N₂ gas; important step in evolution, as nitrogen needed to make proteins.
Does the Krebs cycle produce ATP?
Not directly - it produces cofactors that help to make ATP.
In cellular respiration...
O2 is consumed as glucose is broken down to CO2 and H2O; the cell captures the energy released in ATP
Intermediate
One of the compounds that form between the inital reactant and the final product in a metabolic pathway, such as between glucose and pyruvate in glycolysis.
Oxygen-forming photosynthesis uses a different source of hydrogen
Organisms evolved that substituted use of H₂S in photosynthesis for H₂O; produced oxygen gas. Became dominant.
ATP is synthesized by substrate-level phosphorylation.
Oxidation of G3P transfers electrons to NAD⁺, yielding NADH. After four more reactions, the final product is two molecules of pyruvate. Glycolysis produces 2 net ATP, 2 NADH, and 2 pyruvate.
Porins
Passive holes in the mitochontrial outer membrane that are made out of β-strands to form a β-barrel.
Anoxygenic photosynthesis allowed capture of light energy
Photosynthesis that used H₂S evolved. Uses light to pump protons.
Priming changes glucose into an easily cleaved form.
Priming reactions add two phosphates to glucose; this is cleaved into two 3-carbon molecules of glyceraldehyde 3-phosphate (G3P).
ATP synthase is a molecular rotary motor.
Protons diffuse back into the mitochondrial matrix via the ATP synthase channel. The enzyme uses this energy to synthesize ATP.
Regulation of Aerobic Respiration - Pyruvate Oxidation
Pyruvate dehydrogenase, which converts pyruvate to acetyl-CoA, is inhibited by NADH.
The Oxidation of Pyruvate to Produce Acetyl-CoA
Pyruvate is oxidized to yield 1 CO₂, 1 NADH, and 1 acetyl-CoA. Acetyl-CoA enters the Krebs cycle as 2-carbon acetyl units.
Citric acid cycle step 4-5
Redox reactions generate FADH2, NADH (6 total) and ATP (2 total)
Purpose of steps after Glycolysis
Release energy from pyruvates Replace NAD⁺ Transfer NADH to ATP
Evolution of Glycolysis
Second half older; production of G3P newer.
Cells make ATP by two fundamentally different mechanisms.
Substrate-level phosphorylation transfers a phosphate directly to ADP. Oxidative phosphorylation generates ATP via the enzyme ATP synthase, powered by a proton gradient.
Cleavage and rearrangement, reactants/products
The 6-carbon product of glucose priming is split, with one product being G3P and another being converted to G3P in another step. Each G3P then donates 2 e⁻s and 1 H⁺ to oxidize NAD⁺, and then later produces two ATPs.
Reduction
The addition of electron to another substance
Glycolysis
The breakdown of glucose into two pyruvates; an example of substrate-level phosphorylation.
Oxidative Phosphorylation
The chemiosmosis-driven phosphorylation that creates ATP.
Alcohol fermentation
The conversion of pyruvate from glycolysis to carbon dioxide and ethyl alcohol
Lactic acid fermentation
The conversion of pyruvate to lactate with no releases of carbon dioxide
Oxidative phosphorylation (basics)
The energy is derived from redox reactions of the electron transport chain is used to phosphorylate ADP (makes 34 ATP)
In photosynthesis...
The energy of sunlight is used to rearrange the atoms of CO2 and H2O to produce glucose and O2
Acetyl CoA
The entry compound for the citric acid cycle in cellular respiration; formed from a frament of pyruvate attached to a coenzyme
The Krebs cycle extracts electrons and synthesizes one ATP.
The first reaction is an irreversible condensation that produces citrate; it is inhibited when ATP is plentiful. The second and third reactions rearrange citrate to isocitrate. The fourth and fifth reactions are oxidations; in each reaction, one NAD⁺ is reduced to NADH. The sixth reaction is a substrate-level phosphorylation producing GTP, and from that ATP. The seventh reaction is another oxidation that reduces FAD to FADH₂. Reactions eight and nine regenerate oxaloacetate, including one final oxidation that reduces NAD⁺ to NADH.
First Committed Step
The first step in a pathway that could be shut off that won't interfere with the production of other molecules but is as early on as possible to not waste energy.
Cristae
The folds in the mitochondria that makes its inner membrane's surface area larger.
Substrate-level phosphorylation
The formation of ATP by an enzyme directly transferring a phosphate group to ADP from an orgainc molecule
The Electron Transport Chain and Chemiosmosis
The gradient forms as electrons move through electron carriers. Chemiosmosis utilizes the electrochemical gradient to produce ATP.
Dehydrogenation
The loss of a hydrogen atom.
Oxidation
The loss of electrons from one substance
Deamination
The removal of amines, sp. so that proteins can be catabolised.
Proton Gradient
The result of the ETC's pumping; what drives chemiosmosis.
Oxidative Phosphorylation
The synthesis of ATP using the enzyme ATP Synthase, which uses energy from a proton (H⁺) gradient to power production. The gradient is formed by high-energy electrons from the oxidation of glucose passing down an electron transport chain, which are at the end, with their energy depleted, donated to oxygen - hence oxidative phosphorylation.
Energy Yield of Aerobic Respiration
The theoretical yield for eukaryotes is 36 molecules of ATP per glucose molecule. The actual yield for eukaryotes is 30 molecules of ATP per glucose molecule.
The first step
The transfer of electrons from an organic molecule to NAD+ to form NADH
ATP plays a central role in metabolism.
The ultimate goal of cellular respiration is synthesis of ATP, which is used to power most of the cell's activities.
Glucose Priming, reactants/products
Three reactions prime glucose so that it can be more easily cleaved into 2 pyruvates. This step uses 2 ATP.
Substrate-Level Phosphorylation
When ATP is formed by transferring a phosphate group directly to ADP from a phosphate-bearing intermediate or substrate.
Feedback Inhibition
When an allosteric regulator is a product of a later reaction in a pathway. ex. glycolysis regulated by ATP; if lots of ATP, wasteful to do glycolysis; pathway slowed by rate limiting step.
Anaerobic Respiration
When the final, electron-accepting step in oxidative phosphorylation is a nonorganic molecule other than oxygen.
Fermentation
When the final, electron-accepting step in oxidative phosphorylation is an organic molecule.
Aerobic Respiration
When the final, electron-accepting step in oxidative phosphorylation is oxygen.
Why is the Krebs cycle dependent on oxygen?
While it does not require oxygen directly, it is coupled to a third pathway that does require oxygen (electron transport chain).
Acetyl-CoA has many roles.
With high ATP, acetyl-CoA is converted into fatty acids.
FAD (flavin adenine dinucleotide)
a compound that acts as a hydrogen acceptor in dehydrogenation reactions
Acetyl CoA (acetyl coenzyme A)
a copmound that is synthesized by cells and that plays a major role in metabolism
Oxaloacetic Acid
a four-carbon compound of Krebs cycle that combines with Acetyl CoA to form citric acid
Krebs Cycle
a series of biochemical reactions that convert pyruvic acid into carbon dioxide and water; it is the major pathway of oxidation in animal, bacterial, and plant cells, and it releases energy
Citric Acid
a six-carbon compound formed in the Krebs cycle
Kilocalories
a unit of energy equal to 1,000 calories
NAD+ (nicotinamide adenine dinucleotide)
an organic molecule that serves as an electron carrier by being oxidized to ___ and reduced to NADH
Anaerobic
describes a process that does not require oxygen
Some allosteric regulators can turn "up" one reaction and turn "down" a different reaction
i.e. it acts positively on one pathway and negatively on another
Pyruvate Oxidation Rxn
pyruvate + NAD⁺ + CoA → acetyl-CoA + NADH + CO₂ + H⁺
Glycolysis
the anaerobic breakdown of glucose to pyruvic acid, which makes a small amount of energy available to cells in the form of ATP
Alcoholic Fermentation
the anaerobic process by which yeasts and other microorganisms break down sugars to form carbon dioxide and ethanol
Fermentation
the breakdown of carbohydrates by enzymes, bacteria, yeasts, or mold in the absence of oxygen
Lactic Acid Fermentation
the chemical breakdown of carbohydrates that is called ______ as the main end product
Mitochondrial Matrix
the fluid that is inside the inner membrane of a mitochondrion
Cellular Respiration
the process by which cells obtain energy from carbohydrates; atmospheric oxygen combines with glucose to form water and carbon dioxide
Aerobic Respiration
the process in which pyruvic acid is broken down and NADH is used to make a large amount of ATP; the part of respiration that is carried out in the presence of oxygen
NADH
the reduced form of NAD+; an electron-carrying molecule that functions in cellular respiration
Pyruvic Acid
the three-carbon compound that is produced during glycolysis and needed for both the aerobic and anaerobic pathways of cellular repiration that follow glycolysis
Hydrolysis of 1 molecule of ATP produces ? energy
ΔG = -7.3 kcal/mol