BIO 121 Chapter 9

Metabolic pathways

- harvest energy from high-energy molecules such as glucose
- cellular respiration is critical and often interacts with other pathways
- comprises thousands of different chemical reactions that may be organized and regulated

Cellular respiration

- occurs through a long series of carefully controlled redox reactions (conserves energy/prevents mini explosions) that use the electrons of high-energy molecules to make ATP
- oxygen atoms are reduced to form water
- glucose + 6 oxygen gas + ADP + inorganic Phosphate —> 6 carbon dioxide + 6 water + ATP
- consists of 4 processes: glycolysis, pyruvate processing, Krebs cycle, and electron transport and oxidative phosphorylation

Glycolysis overview

- a series of 10 reactions that occurs in the cytosol of eukaryotes and prokaryotes
- net yield of 2 NADH, 2 ATP, 2 H2O, and 2 pyruvate for every glucose
- glucose + 2 ATP —> 2 (NADH + H+) + 4 ATP + 2 Pyruvate + 2 H2O

Phosphofructokinase (PFK)

- uses ATP to phosphorylate the end of fructose-6-phosphate to form fructose-1,6-bisphosphate
- increases potential energy

Pyruvate processing

- occurs in the matrix of the mitochondria or the cytosol of prokaryotes
- for eukaryotes, pyruvate is transported from the cytosol to the mitochondrial matrix
- catalyzed by pyruvate dehydrogenase, an enormous enzyme complex which is regulated by a negative feedback loop involving ATP
- 2 pyruvate + 2 NAD+ + 2 Coenzyme A —> 2 acetyl CoA + 2 CO2 + 2 NADH
- Decarboxylation: the carboxyl group on pyruvate (the 3rd carbon) is released as CO2

Kinase

- enzyme that catalyzes the transfer of a phosphate group from ATP to another molecule

Phosphotase

- enzyme that removes phosphate group

Krebs cycle (citric acid cycle)

- also occurs in the matrix of the mitochondria or the cytosol of prokaryotes
- 2 turns of the citric acid cycle for each glucose molecule
- Potential energy is released to reduce coenzymes
- The acetyl group (2C) from acetyl CoA is transferred to oxaloacetate (4C) to form citrate (6C); oxaloacetate is regenerated at the end (cycle)
- 8 reactions
- 2 acetyl coA —> 6 NADH + 6H+ + 2 FADH2 + 2 ATP + 4CO2

Electron transport and oxidative phosphorylation

- electron transport chain consisting of 4 main protein complexes establishes a proton gradient that is used to produce ATP
- uses NADH and FADH2 produced in previous steps to generate the protein gradient, which contributes to the phosphorylation of ADP
- uses O2 (oxygen gas) and produces ATP and water
- occurs across the inner membrane of the mitochondria or the plasma membrane + the periplasm of prokaryotes
- a small amount of energy is released in each reaction; each successive bond/molecule in the ETC holds less potential energy ; after the ETC, most of the chemical energy from glucose is accounted for by a proton electrochemical gradient
- primary goal: make ATP
- secondary goal: regenerate NAD+

Periplasm

- space between the cell wall and the plasma membrane

2 fundamental requirements of cellular life

- energy to generate ATP
- a source of carbon to use as raw materials for synthesizing macromolecules

Catabolic pathways

- involve the breakdown of molecules
- often harvest stored chemical energy to produce ATP

Anabolic pathways

- result in the synthesis of larger molecules from smaller components
- often use energy in the form of ATP

Homeostasis

- maintenance of a stable internal environment under different environmental conditions

Energy investment phase (glycolysis)

- reactions 1 through 5
- uses 2 ATP molecules
- regulation of the metabolic pathway occurs during this phase (reaction 3, regulation of phosphofructokinase)

Energy payoff phase (glycolysis)

- reactions 6 through 10
- NADH is made and ATP is produced by substrate-level phosphorylation

Substrate-level phosphorylation

- 1 way to make ATP
- the ONLY way to produce ATP through glycolysis
- enzyme facilitates the transfer of a phosphate group from a substrate to ADP

Glycolysis regulation

- regulated by feedback inhibition
- high levels of ATP inhibit the third enzyme/step of glycolysis (phosphofructokinase), which have two binding sites for ATP
- when ATP binds to the regulatory site of phosphofructokinase, the reaction rate slows dramatically

Regulation of pyruvate processing

- when products of glycolysis and pyruvate processing are abundant, pyruvate dehydrogenase is phosphorylated, inducing a conformational change in the enzyme and inhibiting its activity

Citric acid cycle regulation

- can be turned off at multiple points via several different mechanisms of feedback inhibitions
- regulated at steps 1, 3, and 4 by ATP and NADH
- reaction rates are high when ATP and NADH are scarce; rates are low when ATP or NAHD are abundant

Oxidation of NADH and FADH2

- oxidized by membrane complexes
- NADH is oxidized when combined with the inner membrane of the mitochondria; in prokaryotes, it is oxidized by the plasma membrane
- molecules in the inner mitochondrial membrane can cycle between oxidized and reduced states

ETC Protein complexes

- most are composed of easily-oxidized proteins
- some accept only electrons, while others accept electrons plus protons; each complex has differing redox potentials

Ubiquinone (coenzyme Q, or simply Q)

- lipid-soluble, non-protein
- critical component of the ETC
- reduced by complexes I and II; moves throughout the hydrophobic interior of the electron transport chain membrane, where it is oxidized by complex III

Redox potential

- ability to accept electrons
- High positive value = more potential to GAIN electrons
- strong negative value = more potential to LOSE electrons

Complex I (ETC)

- NADH dehydrogenase oxidizes NADH
- transfers 2 electrons through proteins containing FMN prosthetic groups and Fe-S cofactors to reduce an oxidized form of Q
- 4 protons pumped out of the matrix to the intermembrane space per pair of electrons

Complex II (ETC)

- Succinate dehydrogenase oxidizes FADH2
- transfers the two electrons through proteins containing Fe-S cofactors to reduce an oxidized form of Q
- this complex is also used in step 6 of the Krebs cycle
- does not produce sufficient energy to pump protons

Complex III

- cytochrome c reductase oxidizes Q
- transfers 1 electron at a time through proteins containing heme prosthetic groups and Fe-S cofactors to reduce an oxidized form of cytochrome c
- 4 protons for each pair of electrons is transported from the matrix to the intermembrane space

Cyt c (cyctochrome c)

- reduced by accepting a single electron from complex III
- moves along the surface of the ETC membrane, where it is oxidized by complex IV

Complex IV

- cytochrome c oxidase oxidizes cyt c
- transfers each electron through proteins containing heme prosthetic groups to reduce oxygen gas, which picks up two protons from the matrix to produce water
- 2 additional protons are pumped out of the matrix of the intermembrane space

ATP Synthesis (ETC)

- fueled by chemiosmosis; uses the established proton gradient to create ATP using ATP synthase

ATP synthase

- located in the inner mitochondrial membrane in eukaryotes, or the plasma membrane in prokaryotes
- creates energy from the proton motive force of the proton gradient to chemical bond energy in ATP
- is a rotary machine that makes ATP as it spins
- consists of 2 components—an ATPase "knob"/F1 unit, and a membrane-bound, proton-transporting base/F0 unit, which is a rotor that turns as protons flow through it—that are connected by a shaft and held in place by a stator
- the spinning F0 unit changes the conformation of the F1 unit so that it phosphorylates ADP to form ATP

Oxidative phosphorylation

- oxidative = FADH2 and NADH are being oxidized
- phosphorylation = ADP —> ATP
- different from substrate-level phosphorylation because instead of potential energy activating the enzyme, kinetic energy activates the enzyme (movement of protons down their gradient)
- yields ~24-28 ATP per glucose

Chemiosmotic hypothesis

- the linkage between electron transport and ATP production by ATP synthase is indirect
- the synthesis of ATP only requires a proton gradient

Aerobic respiration

- O2, which has a very high redox potential, is the final electron acceptor
- most efficient—CO2 (single-carbon compound) is the byproduct

Anaerobic respiration

- some other compound is the final electron acceptor
- has a lower energy yield compared to aerobic respiration because oxygen is super electronegative and has a high redox potential
- less efficient—some other carbon-containing (organic) molecule is the byproduct (ethanol, lactic acid, etc)
- seen in some prokaryotes

Fermentation

- a metabolic pathway that regenerates NAD+ from NADH
- the electron in NADH is transferred to pyruvate
- serves as an emergency backup for aerobic respiration when there is not enough oxygen
- incomplete oxidation of glucose; much less efficient than cellular respiration
- produces 2 ATP per glucose, compared with about 29 ATP per glucose in cellular respiration

Lactic acid fermentation

- fermentation in which the product is lactic acid
- occurs in humans in the absence of oxygen
- muscle cramps = the accumulation of lactic acid
- in humans, lactic acid fermentation results in the production of yogurt, cheese, etc
- produces only 2 ATP (by substrate-level phosphorylation)

Ethanol fermentation

- some yeast cells can perform alcohol fermentation
- pyruvate is converted to acetaldehyde and CO2
- acetaldehyde accepts electrons from NADH
- ethanol and NAD+ are produced

Faculative anaerobes

- organisms that can switch between fermentation and aerobic respiration
- only use fermentation if an electron acceptor is not available
- E.coli, yeast, etc

Glycolysis step 1

- hexokinase uses ATP to phosphorylate glucose, increasing its potential energy
- forms glucose-6-phosphate and ADP

Glycolysis Step 2

- phosphoglucose isomerase converts glucose-6-phosphate to fructose-6-phosphate (an isomer)

Glycolysis Step 3

- Phosphofructokinase uses ATP to phosphorylate the opposite end of fructose-6-phosphate, increasing its potential energy
- forms fructose-1,6-bisphosphate

Glycolysis Step 4

- fructose-bis-phosphate aldolase cleaves fructose-1,6-bisphosphate into 2 different 3-carbon sugars (DAP and G3P)

Glycolysis Step 5

- triose phosphate isomerase converts dihydroxyacetone phosphate (DAP) to glyceraldehyde-3-phosphate (G3P)
- reaction is fully reversible, but DAP-to-G3P reaction is favored because G3P can be immediately used as a substrate for step 6

Glycolysis Step 6

- glyceraldehyde-3-phosphate (G3P) dehydrogenase catalyzes a 2-step reaction
- first oxidizes G3P using the NAD+ coenzyme to produce NADH
- Energy from this reaction is used to attach an inorganic phosphate to the oxidized product to form 1,3-bisphosphoglycerate

Glycolysis Step 7

- phosphoglycerate kinase transfers a phosphate from 1,3-bisphosphoglycerate to ADP to make 3-phosphoglycerate and ATP (PRODUCES ATP—1 for each 3-carbon intermediate)

Glycolysis Step 8

- phosphoglycerate mutase rearranges the phosphate in 3-phosphoglycerate to form 2-phosphoglycerate

Glycolysis Step 9

- enolase removes a water molecule from 2-phosphoglycerate to form a C=C double bond and produce phosphoenolpyruvate

Glycolysis Step 10

- remaining phosphate groups are added to 2 ADP molecules to form 2 ATP and pyruvate
- pyruvate kinase transfers a phosphate fro phosphoenolpyruvate to ADP to make pyruvate and ATP

Electron Transport Chain Theoretical Yield

- 1 NADH = 3 ATP
- 1 FADH2 = 2 ATP (lower because complex II, where FADH2 is oxidized, has a lower redox potential than complex I, where NADH is oxidized)

ETC Actual Yield

- 1 NADH = ~2.25 ATP
- 1 FADH2 = ~1.25 ATP