Cellular Energetics and Metabolism

Cellular Energetics

• Cellular metabolism occurs in a series of small, enzyme-catalyzed steps.
• Enzymes break reactions into smaller pieces to capture energy.

Classes of Metabolism

• Catabolic reactions: Break down larger molecules into smaller ones to extract energy.
• Anabolic reactions: Build smaller molecules into larger ones, requiring energy input.

Catabolic Reactions

• Breakdown of glucose via glycolysis and the citric acid cycle (Krebs cycle).
• Glycolysis occurs in the cytosol.
• The citric acid cycle occurs in the mitochondria.

Compartmentalization of Metabolism

• Catabolic and anabolic reactions are separated, preventing futile cycles (building up and breaking down simultaneously).
• Carbon oxidation of glucose happens in glycolysis and the citric acid cycle.
• High-energy electrons are removed during oxidation.
• Energy from electrons is extracted through redox reactions, passed from one molecule to the next.
• This energy generates a proton gradient across the mitochondrial membrane.
• The proton gradient is then used to synthesize ATP via oxidative phosphorylation.

Complexity and Interconnectedness of Cellular Metabolism

• Metabolism involves approximately 500 interconnected chemical reactions.
• Glycolysis and the citric acid cycle are central to these reactions.
• Reactions influence many other reactions, even seemingly unrelated ones.
• Glycolysis affects fatty acid metabolism, amino acid metabolism, and the metabolism of other complex molecules.
• All reactions are equilibrium reactions. Changing reactant concentrations affects product concentrations, and vice versa.
• Changes at one point in metabolism can affect other points (butterfly effect).
• Regulation helps buffer and isolate changes.
• Nutrients can enter the central pathway from various points.
• Amino acids, fats, and other organic compounds can be metabolized if they can be converted to an intermediate in the central pathway.
• Metabolic effects can be difficult to observe because they distribute throughout the cell.
• Glucose can be metabolized through the Krebs cycle, pentose phosphate pathway, amino acid synthesis, etc.
• Acetyl CoA can be used for fatty acid synthesis, heme synthesis, nucleotide synthesis, etc.

Energy Transfer in Cells

• Cells must transfer energy from one source to another to do work.
• Energy for cellular work comes from the chemical breakdown of nutrients.
• Plants store sunlight energy in chemical molecules, which are then broken down.
• Harvesting energy requires nutrient oxidation.
• Oxidation reactions do not always release energy, but carbon oxidation does.
• Carbon is in a lower energy state when oxidized and a higher energy state when reduced.
• Oxidation occurs in small, enzyme-catalyzed steps to avoid large amounts of heat release.
• Energy is captured in chemical forms for later use.
• Enzymes reduce the activation energy required for reactions, allowing them to happen at ambient temperature.
• Enzymes couple the release of energy from catabolic reactions to the synthesis of molecules in anabolic reactions.
• Energetically unfavorable reactions are coupled to the release of energy from glucose oxidation.
• Energy is stored in ATP.

Enzyme-Managed vs. Non-Enzyme-Managed Oxidation of Glucose

• Direct burning of sugar (e.g., marshmallow in a campfire) is enzyme-independent.
• This process has a large activation energy and releases substantial heat and light.
• Cells cannot manage this process.
• In cells, glucose is combined with oxygen to produce carbon dioxide and water.
• The overall energy released is the same regardless of the path (thermodynamics).
• Enzyme-catalyzed reactions occur in small steps with small activation energies at ambient temperature.
• Small packets of energy are stored in chemical bonds.
• Capture is not 100% efficient (about 50% overall), with the rest released as heat to maintain body temperature.

Activated Carrier Molecules

• Specialized molecules capture energy in an intermediate form.
• ATP is the most famous example.
• Acetyl CoA is another example, storing oxidation energy in the bond between the acetyl group and coenzyme A.
• Activated carrier molecules serve as intermediaries between catabolic and anabolic reactions.
• Energy from catabolic reactions is stored in activated carrier molecules.
• Activated carrier molecules are involved in energetically unfavorable reactions.
• The energy stored in the carrier molecule is released and used for anabolic reactions.

Why Use Intermediates?

• Energy conversion always results in some energy loss as heat (second law of thermodynamics).
• The answer is economics (cellular and societal).
• In small economies, direct exchanges (barter system) can be made.
• Direct exchanges are efficient but problematic if immediate use is impossible or the society becomes too large.
• A common currency is the solution.
• Currency decreases complexity by providing a single conversion factor for all exchanges.
• The cellular equivalent of currency is ATP.
• ATP serves the function of dollars in economies.
• There are different denominations of currency (e.g., dollars and quarters).
• There are other currencies (e.g., euros and pesos).
• Cells have different denominations of currency.
• Some cells use a proton gradient to power certain parts of the cell (different currency).
• Currencies can be exchanged (proton gradient converted into ATP).
• Cells use a common currency to manage metabolism efficiently.

Glycolysis

• One molecule of glucose is converted into two molecules of pyruvate (a more oxidized sugar).
• There is a net production of two ATP molecules and two NADH molecules per glucose molecule.
• ATP is direct chemical power.
• NADH provides high-energy electrons for redox reactions (reducing power).
• All reactions occur in the cytosol.
• Glycolysis has three phases:
  • Investment phase: Two ATPs are invested to activate the glucose molecule.
  • Cleavage phase: Glucose is split into two molecules (no net energy change).
  • Energy generation phase: Oxidation generates four ATP molecules.

ATP Generation

• Glycolysis generates two ATP molecules per molecule of glucose (net).
• Four ATP molecules are generated, but two are initially invested.
• Investment and return: Profit is the total yield minus the investment.

Reactions

• Glucose is rearranged into fructose using two ATP molecules.
• Fructose is more symmetrical for splitting.
• The two molecules formed are dihydroxyacetone phosphate and glyceraldehyde three phosphate.
• Dihydroxyacetone phosphate is easily converted into glyceraldehyde three phosphate.
• The remaining reactions are run twice, once for each glyceraldehyde three phosphate molecule.
• An oxidation reaction releases enough energy to convert NADPH and ADP to ATP.
• The result is a more highly oxidized molecule called pyruvate.
• Four ATPs are produced, but two are invested, yielding a net of two ATPs.

Key Steps: Energy Generation

• An aldehyde is converted to a carboxylic acid (glyceraldehyde to pyruvate).
• NADH and ATP are generated.
• Generation of carrier molecules is energetically unfavorable, requiring energy input.
• The energy comes from the oxidation of a carbon, which is coupled to the reduction of NADH and the generation of ATP.
• The enzyme facilitates the transfer of energy from carbon oxidation to these two reactions.

Details of the Coupled Reactions

• Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) performs the first part of the reaction.
• The enzyme has a sulfhydryl group (cysteine side chain), forms a covalent bond with glyceraldehyde 3-phosphate at the aldehyde group.
• NAD+ acts as a cofactor.
• The enzyme removes two protons and two electrons, converting the group into a carbonyl, forming a thioester.
• The thioester is a high-energy bond.
• An inorganic phosphate breaks the bond, replacing sulfur with phosphorus which a nucleophilic attack on the thioester.
• A phosphorylated molecule which forms called 1,3-bisphosphoglycerate.
• Phosphoglycerate kinase hydrolyzes the anhydride bond, releasing energy, and transferring the phosphate to ADP to make ATP.
• Glyceraldehyde 3-phosphate, the phosphate on the three carbon, is converted to 3-phosphoglycerate.
• The process is done through a thioester and then a phosphoacid anhydride, capturing it in the form of ATP

Substrate-Level Phosphorylation

• A phosphate group is attached to an organic molecule (substrate) and then transferred to ADP to make ATP.
• This is distinguished from ATP synthesis by chemiosmosis.

Difference Between Oxidative Phosphorylation and Substrate-Level Phosphorylation

• In substrate-level phosphorylation, the phosphate is first attached to an organic molecule and then transferred to ADP.
• In oxidative phosphorylation, inorganic phosphate is directly attached to ADP with no intermediate through an ATP synthase complex

Further Rearrangement

• 3-phosphoglycerate is rearranged to allow the phosphate to be transferred to ADP to make ATP.
• The enzyme is called phosphoglycerate kinase.
• Kinases typically hydrolyze ATP and transfer a phosphate to an organic molecule.
• In this rare case, the reverse reaction (generation of ATP from ADP plus phosphate) is favored under cellular conditions.
• Oxidation of a carbon-hydrogen bond allows the generation of NADH and a high-energy phosphate.
• The high-energy phosphate is hydrolyzed to convert ADP to ATP.
• The hydrolysis of so this anhydride bond has more energy in it than the energy required to attach a phosphate to ADP.

Hierachy Of Phosphate Intermediates

• You can transfer from a higher energy phosphate, to a lower energy phosphate.

Creatine Phosphate

• This is another carrier which is often ignored
• Because as you synthesize ATP in the mitochondria, you have a problem that the ATP is stuck inside the mitocondrial matrix
• In under high ATP demand it's rate limited.
• Taking ATP and converting it into creatine phosphate is independent of the ADP ATP exchange.
• When you're running away from a leopard your muscles can continue to synthesize ATP at a rapid rate.
• There's lots of evolutionary adaptations to get around the membrane barriers and the rate barriers.

After Glycolysis

• Pyruvate is generated with two ATP molecules per glucose.
• Yeast cells can live off of this.
• Muscle cells need more energy.
• Pyruvate needs to be further oxidized.
• Two NADH molecules are also generated.
• These can be oxidized back to NAD in the presence of oxygen.
• There is no transporter across the mitochondrion for NADH, but a workaround is figured out.
• If there is no molecular oxygen, NAD cannot be reoxidized. If you don't have an NAD cofactor, you're stuck.
• If there's no oxygen, you have to convert that NADH back to NAD via fermentation.

Fermentation

Happy Form

• The first form is what I call the happy form of fermentation.You generate CO2 and Ethanol.
• Carbon dioxide is removed from pyruvate, evaporating away (no oxidation involved).
• Acetaldehyde is produced.
• Acetaldehyde is reduced by electrons from NADH to generate ethanol.
• This happens, for example, with when Yeast tries to reconvert NADH back to NAD for Beer

Unhappy Form

• Our cells can't do yeast's happy form of fermentation, The carbon dioxide would build up in your blood.
• Instead of converting pyruvate into acetaldehyde, electrons are directly put back onto pyruvate to generate lactate.
• Lactate causes pain when exercising and may be converted into Pyruvate allowing glycolysis to happen in absence of Oxygen.
• These electrons don't go back exactly where they came off (a waste of energy).