Metabolism & Cellular Respiration Notes

Metabolism Overview

General Overview

• Cells harvest chemical energy stored in organic molecules to generate ATP via catabolic pathways.
• Electron transfer during chemical reactions is the basis for this process.
• Relocation of electrons releases energy stored in organic molecules, which is then used to synthesize ATP.
• Cells must continuously generate ATP from ADP to do work.
• ATP is used in anabolic pathways and to drive movement.
• Catabolic pathways break down complex molecules into cellular building blocks, releasing energy and heat.
• Anabolic pathways use energy (ATP) to build macromolecules from cellular building blocks.

Relocation of Electrons and Redox Reactions

• Electron transfers are called oxidation-reduction reactions (redox reactions).
• Oxidation: loss of electrons.
• Reduction: gain of electrons.
• Oxidation and reduction always occur together.
• The electron donor is the reducing agent, reducing the electron acceptor.
• The electron acceptor is the oxidizing agent, oxidizing the electron donor.
• Some redox reactions involve a change in electron sharing in covalent bonds instead of full electron transfer.
• Oxygen atoms are highly electronegative and attract electrons.
• The partial "gain" of electrons by oxygen and the partial "loss" by their bonding partners constitutes a redox reaction.
• Oxidation can occur by:
  • Removing a hydrogen atom.
  • Adding an oxygen atom.
  • Direct electron transfer involving metal ions.

Catabolic Pathways and Electron Carriers

• Catabolic pathways are oxidative pathways.
• Electrons given up are relocated to other molecules, which are reduced (e.g., NAD^+ is converted to NADH).
• NADH is then re-oxidized to produce ATP.
• This can occur anaerobically or aerobically via the electron transport chain (requires oxygen – cellular respiration).
• Enzymes called dehydrogenases remove a pair of hydrogen atoms (2 electrons and 2 protons) from the substrate.
• The 2 electrons and 1 proton are transferred to NAD^+ forming NADH.
• The other proton is released as a hydrogen ion (H^+) into the surrounding solution.
• NADH passes electrons to the electron transport chain where they are transferred in a series of redox reactions, each releasing a small amount of energy.
• O2, the final electron acceptor, captures the electrons and the hydrogen nuclei (H^+), forming H2O.
• The energy yielded is used to regenerate ATP.

Glycolysis Overview

• Glycolysis is nearly universal in living cells.
• Its regulation is well understood.
• Glycolysis plays a central metabolic role in generating both energy and metabolic intermediates for other pathways.
• Early prokaryotes likely used glycolysis to produce ATP before oxygen accumulated in the atmosphere.
• Used in both cellular respiration and fermentation, it is the most widespread metabolic pathway on Earth.
• Glycolysis is a metabolic heirloom from early cells that continues to function in fermentation and cellular respiration.

Glycolysis Process

• Glycolysis is a 10-step pathway.
• 1 molecule of glucose is converted to 2 molecules of pyruvate.
• It has 2 distinct phases:
  • Energy investment phase (5 reactions – 2 ATP used; 6C molecule is split into 2 3C sugar phosphates).
  • Energy generation (payoff) phase (5 reactions – 2 triose phosphates are converted to energy-rich compounds; these transfer 4 phosphates to ADP).
• Net yield: 2 ATP, 2 moles of pyruvate, and 2 reducing equivalents (NADH).
• The fate of pyruvate depends on whether conditions are aerobic or anaerobic.

Glycolysis Equation

• Glucose + 2 ADP + 2 NAD + 2 Pi \rightarrow 2 Pyruvate + 2 ATP + 2 NADH + 2H^+ + 2 H2O

• ATP consumed per glucose: 2 (hexose stage).

• ATP produced per glucose: 4 (triose stage).

• Net ATP production per glucose: 2.

• All of the carbon originally present in glucose is accounted for in the two molecules of pyruvate.

• Glycolysis does not release any CO2, and occurs whether or not O2 is present.

Fermentation

• Glycolysis is an ancient metabolic pathway that probably evolved before photosynthetic organisms contributed oxygen to Earth’s atmosphere, thus had to function under anaerobic conditions.
• For the pathway to continue operating anaerobically, NADH must be re-oxidized to NAD^+ by transferring electrons to an electron acceptor to maintain a steady-state concentration of NAD^+.
• Fermentations use a common strategy to regenerate oxidized NAD^+.
• A fermentation is an energy-yielding metabolic pathway with no net change in the oxidation state of the products compared to that of the substrates, because pyruvate is reduced in the final step, resulting in no net oxidation of glucose.

Different Fermentation Processes

• Dozens of different fermentation processes have been discovered in different organisms, many of which play major roles in the food and chemical industries.
• Alcoholic fermentation by yeasts is an important process in brewing, wine-making, and baking, generating ethanol and CO_2.
• In baking, the CO_2 causes bread to rise while the ethanol evaporates.
• Other useful fermentations lead to acetic acid (vinegar manufacture) and propionic acid (Swiss cheese manufacture).

Alcohol Fermentation

• In alcohol fermentation, pyruvate is converted to ethanol in two steps.
• The first step releases CO_2 from pyruvate.
• The second step produces NAD^+ and ethanol.

Lactic Acid Fermentation

• In lactic acid fermentation, pyruvate is reduced directly by NADH to form lactate and NAD^+.
• There is no release of CO_2 in lactic acid fermentation.
• Lactic acid fermentation by fungi and bacteria is used to make cheese and yogurt.

Other Fates of Pyruvate

Aerobic Respiration

• When oxygen is present, the pyruvate in eukaryotic cells enters a mitochondrion, where the oxidation of glucose is completed.
• In aerobically respiring prokaryotic cells, this process occurs in the cytosol.

Anaerobic Respiration

• Takes place in certain prokaryotic organisms that live in environments without oxygen.
• These organisms have an electron transport chain but do not use oxygen as a final electron acceptor.
• Some “sulfate-reducing” marine bacteria use SO4^{2-}, resulting in hydrogen sulfide (H2S) production instead of water.

Anaerobes

• Obligate anaerobes:

  • Only fermentation or anaerobic respiration.
  • Cannot survive in the presence of oxygen.

• Facultative anaerobes:

  • Examples are yeasts and many bacteria (consume sugar much faster when fermenting than when respiring).
  • On a cellular level, muscle cells behave as facultative anaerobes, forming lactic acid when not sufficient oxygen for aerobic respiration.

• A complex series of fermentation and aerobic respiration carried out by yeasts and bacteria on cacao beans is responsible for chocolate production.

• Though previously thought that human muscle cells produced lactate only when O_2 was in short supply, recent research indicates a more complicated story.

  • One type of skeletal muscle (red) oxidizes glucose completely to CO_2; the other (white) produces lactate even under aerobic conditions.
  • The term fermentation is no longer used because lactate production isn't solely anaerobic.

Aerobic Respiration and Pyruvate Oxidation

• Most of the energy from glycolysis remains stockpiled in the 2 molecules of pyruvate.
• Pyruvate enters the mitochondrion via active transport.
• Pyruvate is converted to acetyl CoA by a multienzyme complex that catalyzes 3 reactions.

Pyruvate to Acetyl CoA Conversion

• Pyruvate is converted to acetyl coenzyme A (acetyl CoA) before entering the citric acid cycle.
• Pyruvate dehydrogenase catalyzes three reactions:
  1. Oxidation of pyruvate’s carboxyl group, releasing the first CO_2 of cellular respiration.
  2. Reduction of NAD^+ to NADH.
  3. Combination of the remaining two-carbon fragment with coenzyme A to form acetyl CoA.

Stages of Cellular Respiration

• Harvesting energy from glucose by cellular respiration has three stages:
  1. Glycolysis breaks down glucose into two molecules of pyruvate.
  2. Pyruvate oxidation and the citric acid cycle complete the breakdown of glucose to CO_2.
  3. During oxidative phosphorylation, the electron transfer chain and chemiosmosis facilitate the synthesis of most of the cell’s ATP.
• Oxidative phosphorylation generates almost 90% of the ATP and is powered by redox reactions.
• Some ATP is also formed in glycolysis and the citric acid cycle by substrate-level phosphorylation.
• Substrate-level phosphorylation occurs when an enzyme transfers a phosphate group directly from a substrate to ADP.
• For each molecule of glucose degraded to CO2 and H2O by cellular respiration, up to 32 molecules of ATP are produced.

Citric Acid Cycle (Krebs Cycle)

• The citric acid cycle oxidizes organic fuel derived from pyruvate, generating 1 ATP, 3 NADH, and 1 FADH_2 per turn.
• Another 2 CO_2 are produced as a waste product.
• Because 2 pyruvate are produced per glucose, the cycle runs twice per glucose molecule consumed.

Process Overview

• 2C compound + 4C compound = 6C compound

• During the cycle 2 carbons are lost as CO_2.

• The citric acid cycle has eight steps, each catalyzed by a specific enzyme.

• First, the acetyl group of acetyl CoA joins the cycle by combining with oxaloacetate, forming citrate.

• The next seven steps decompose the citrate back to oxaloacetate, making the process a cycle.

• The NADH and FADH_2 produced by the cycle carry electrons to the electron transport chain.

• Molecules of NADH and FADH_2 produced during glycolysis and the citric acid cycle account for most of the energy extracted from glucose.

• NADH and FADH_2 donate electrons to the electron transport chain, which powers ATP synthesis via oxidative phosphorylation.

• During oxidative phosphorylation, chemiosmosis couples electron transport to ATP synthesis.

Electron Transport Chain

• Molecules of the electron transport chain are embedded in the inner mitochondrial membrane in eukaryotic cells.
• The membrane is folded into cristae to increase surface area for electron transport chains.
• In prokaryotes, the electron transport chain is embedded in the plasma membrane.
• Most of the molecules in the electron transport chain are proteins, which exist in multi-protein complexes.
• NADH and FADH_2 donate electrons to different electron acceptors early in the chain.
• Electrons are passed through a number of carrier molecules including several cytochromes (proteins with heme groups containing an iron atom).
• Electron carriers alternate between reduced and oxidized states as they accept and donate electrons.
• Electrons drop in free energy as they are transferred down the chain, finally passing to O2 to form H2O.
• The electron transport chain breaks the large free-energy drop from glucose to O_2 into smaller steps, releasing energy in manageable amounts.
• No ATP is produced directly by the chain.
• If NADH transferred electrons directly to oxygen, energy would be released in one explosive reaction.
• Instead, cellular respiration uses an electron transport chain to break the fall of electrons to O_2 into several energy-releasing steps.
• An electron transport chain consists of a series of molecules built into the inner membrane of the mitochondria (or plasma membrane of prokaryotes).
• Certain electron carriers in the electron transport chain accept and release H^+ along with the electrons.
• Maintaining the H^+ gradient couples redox reactions of the electron transport chain to ATP synthesis.
• The H^+ gradient is referred to as a proton-motive force, emphasizing its capacity to do work.

ATP Production Accounting

• During cellular respiration, most energy flows in this sequence:
  • glucose → NADH → electron transport chain → proton-motive force → ATP
• About 34% of the energy in a glucose molecule is transferred to ATP, making about 32 ATP.
• The rest of the energy is lost as heat.
• There are three reasons why the exact number of ATP produced is not known:
  1. Photophosphorylation and the redox reactions are not directly coupled; the ratio of NADH to ATP molecules is not a whole number.
  2. ATP yield varies depending on whether electrons are passed to NAD^+ or FAD.
  3. The proton-motive force is also used to drive other kinds of work.

Chemiosmosis and ATP Synthase

• The energy released as electrons are passed down the electron transport chain is used to pump H^+ from the mitochondrial matrix to the intermembrane space.
• H^+ then moves down its concentration gradient back across the membrane, passing through the protein complex ATP synthase.
• H^+ moves into binding sites on the rotor of ATP synthase, causing it to spin in a way that catalyzes phosphorylation of ADP to ATP.
• This is an example of chemiosmosis, the use of energy in a H^+ gradient to drive cellular work.

Connections to Other Metabolic Pathways

• Glycolysis and the citric acid cycle are major intersections to various catabolic and anabolic pathways.
• Catabolic pathways funnel electrons from many kinds of organic molecules into cellular respiration.
• Glycolysis can use many carbohydrates, including starch, glycogen, and several disaccharides.
• Proteins used for fuel must be digested to amino acids and their amino groups must be removed in a process called deamination.
• Nitrogenous waste is excreted as ammonia (NH_3), urea, or other products.
• Fats are digested to glycerol (used to produce compounds needed for glycolysis) and fatty acids.
• Fatty acids are broken down by beta oxidation and yield acetyl CoA, NADH, and FADH_2.
• An oxidized gram of fat produces more than twice as much ATP as an oxidized gram of carbohydrate.

Biosynthesis (Anabolic Pathways)

• Organisms use small molecules from food to build macromolecules, such as proteins from amino acids.
• These small molecules may come directly from food, from glycolysis, or from the citric acid cycle.

Regulation of Cellular Respiration

• Feedback inhibition is the most common mechanism for metabolic control because it prevents wasteful production.
• If ATP concentration drops, respiration speeds up; if there is plenty of ATP, respiration slows down.
• Catabolism is controlled by regulating the activity of enzymes at strategic points in the pathway.