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).