Chapter 8

🧪 Metabolism

Metabolism is defined as all the chemical reactions of the cell, including making proteins, DNA, RNA, and new cells through mitosis, binary fission, or budding.

Catabolic vs Anabolic Reactions

  • Catabolic reactions involve tearing down large molecules into smaller subunits, also known as decomposition.

  • Anabolic reactions involve building up or synthesizing molecules, like anabolic steroids used by athletes to build muscle.

Aerobic vs Anaerobic Reactions

  • Aerobic reactions require oxygen, although they don't necessarily use it directly.

  • Anaerobic reactions do not require oxygen, even if oxygen is present.

Redox Reactions

  • Redox (reduction and oxidation) reactions involve the transfer of electrons.

    • Reduction: A compound or atom receives electrons, becoming more negatively charged.

    • Oxidation: A compound or atom gives away electrons, becoming less negatively charged or more positively charged.

🦠 Classifying Organisms by Energy and Carbon Sources

Organisms can be classified based on their energy and carbon sources:

Category

Energy Source

Carbon Source

Examples

Chemoautotrophs

Chemical

Inorganic compounds

Hydrogen, sulfur, iron, nitrogen, and carbon monoxide oxidizing bacteria

Chemoheterotrophs

Chemical

Organic compounds

Animals, most fungi, protozoans, and bacteria

Photoautotrophs

Light

Inorganic

Plants, algae, cyanobacteria, green and purple sulfur bacteria

Photoheterotrophs

Light

Organic

Green and purple non-sulfur bacteria, and helobacterium

⚙ Enzymes

Enzymes are proteins that catalyze reactions by acting on substrates to create products. Enzymes are not consumed in the reaction, but they can wear out and need replacement. Their function is influenced by physical factors like temperature, pH, and concentration.

Enzyme Structure and Function

  • Substrates: Chemical reactants that an enzyme acts upon.

  • Active Site: The location on the enzyme where substrates bind. It is specifically shaped to interact with the substrate.

  • Products: Chemical products made by enzyme-substrate interactions.

When a substrate binds to the active site of an enzyme, it causes a conformation change, which is a change in shape. This change either binds substrates together or breaks them apart. After the products are created, they are released, and the enzyme returns to its original state.

Cofactors and Coenzymes

These are helper molecules that make an enzyme functional. Not all enzymes require them.

  • Apoenzyme: An enzyme without its cofactor or coenzyme (incomplete).

  • Holoenzyme: An enzyme with its necessary cofactor or coenzyme (complete).

The binding of a cofactor or coenzyme causes a conformation change that makes the active site the correct shape for the substrate.

🚧 Enzyme Regulation

Competitive Inhibition

A competitive inhibitor binds to the active site of an enzyme, preventing the substrate from binding and thus preventing the reaction.

Non-competitive (Allosteric) Inhibition

An inhibitor binds to an allosteric site (a site other than the active site) on the enzyme. This binding causes a conformation change in the enzyme, altering the shape of the active site and preventing the substrate from binding effectively.

Allosteric Activation

A regulatory molecule binds to the allosteric site to change the conformation of the enzyme, creating an active site that is functional.

Feedback Inhibition

In a metabolic pathway, the end product of the pathway inhibits an earlier enzyme in the pathway, preventing the overproduction of the end product. In this process, a substrate binds to the active site of an enzyme, and the enzyme and substrate interact, resulting in a product, also known as an intermediate substrate.

Metabolism of Carbohydrates (Catabolism of Carbohydrates, lipids, proteins)

Overview

Metabolism involves the chemical reactions in cells, including ATP production from carbohydrates. Key processes are glycolysis, the Krebs cycle (TCA cycle), and electron transport, with fermentation as an alternative pathway.

Key Molecules

  • NAD+ (Nicotinamide Adenine Dinucleotide): Can accept electrons, functioning as an electron carrier.

  • NADP+ (Nicotinamide Adenine Dinucleotide Phosphate): Similar to NAD+, used in photosynthesis.

  • FAD (Flavin Adenine Dinucleotide): Another electron carrier, uncharged, therefore not short an electron.

  • ATP (Adenosine Triphosphate): Primary energy molecule in cells, consisting of three phosphates with high-energy bonds.

  • GTP (Guanosine Triphosphate): Similar function to ATP.

Glycolysis

  • Glycolysis is primarily the Embden-Meyerhof pathway, converting glucose into 2 ATP and 2 NADH in a net reaction (after burning 2 ATP).

  • Anaerobic Process: Does not require oxygen, but can occur in its presence.

  • Substrate-level phosphorylation occurs here.

Krebs Cycle (Citric Acid Cycle)

  • Follows glycolysis, beginning with a transition reaction from pyruvic acid.

  • Produces additional NADH, FADH2, and ATP per pyruvate (doubling with 2 pyruvates).

  • Requires oxygen to be present, even though it does not utilize it directly.

Electron Transport Chain (ETS)

  • The final aerobic step of respiration requiring oxygen as the final electron acceptor.

  • Enzyme Cytochrome Oxidase transfers electrons to oxygen, while ATP synthase synthesize ATP through oxidative phosphorylation.

Anaerobic Catabolism

  • Anaerobic organisms undertake a similar process to glycolysis, Krebs, and ETS but use another compound as the final electron acceptor instead of oxygen.

  • Fermentation is a key anaerobic pathway yielding alcohol or acid as end products when oxygen is absent.

Catabolism of Lipids and Proteins

  • Cells can catabolize lipids and proteins, particularly in the absence of carbohydrates.

  • Intermediate metabolites from the breakdown can be diverted into glycolysis or the Krebs cycle.

Photosynthesis

  • The process of converting light energy into chemical energy stored in sugars, the reverse of cellular respiration, having light and dark reactions.

Bioremediation

  • Microbes can process carbon-containing compounds and toxins, aiding in environmental restoration by breaking down harmful substances such as hydrocarbons, cyanide, and heavy metals.


Glycolysis Overview (Glycolysis visual)

Glycolysis is a catabolic, anaerobic reaction that breaks down one molecule of glucose (a six-carbon compound) into energy-rich products.

Key Steps in Glycolysis:

  1. Starting Molecule: Glucose (C6H12O6)

    • Contains 6 carbons, 12 hydrogens, and 6 oxygens.

  2. Preparation Phase: Adding Phosphates

    • Two ATP are consumed to add phosphate groups to glucose, converting it to a six-carbon, two-phosphate molecule. This step requires energy (ATP) to activate glucose for further breakdown.

  3. Splitting the Molecule: Cleavage

    • The six-carbon, two-phosphate molecule is split into two three-carbon, one-phosphate molecules, making it easier to add phosphates and generate ATP.

  4. NAD+ Involvement: Electron Carrier Contribution

    • NAD+ (Nicotinamide Adenine Dinucleotide) comes in to accept electrons (from a hydrogen), becoming NADH. This process also allows the addition of a free phosphate to form a two-phosphate, three-carbon compound.

  5. ATP Generation: Substrate-Level Phosphorylation

    • Two ADP molecules each receive a phosphate group from the now two-phosphate, three-carbon compound, producing two ATP.

    • At the end of glycolysis, two pyruvic acid molecules are generated.

Glycolysis Yield:

  • Total Yield:

    • 4 ATP produced (2 net after 2 ATP used in the initial phase)

    • 2 NADH generated

    • 2 H+ ions produced

    • 2 Pyruvic acid molecules created.


Krebs Cycle Overview (Krebs Visual)

The Krebs cycle, also known as the Citric Acid Cycle or TCA Cycle, begins where glycolysis left off with pyruvic acid. It consists of two parts: the feeder chain and the cycle itself.

Starting Molecule: Pyruvic Acid

  • Pyruvic acid is a three-carbon compound that enters the Krebs cycle.

  • NAD+ comes in, takes two electrons and a hydrogen, liberating a hydrogen ion (H+), which destabilizes pyruvic acid and allows CO2 to be released as a waste product.

  • As a result of this reaction, pyruvic acid is converted to acetic acid (a two-carbon compound).

Formation of Acetyl CoA

  • Acetic acid binds with coenzyme A to form acetyl CoA, which is crucial for the cycle.

  • The combination of acetyl CoA and a four-carbon compound called oxaloacetic acid forms citric acid (six-carbon compound).

Citric Acid to CO2

  1. NAD+ enters again, takes two hydrogens/electrons, and liberates another H+, releasing CO2 and converting citric acid to a five-carbon compound.

  2. NAD+ comes in a third time, facilitating another release of CO2 and converting the five-carbon compound to a four-carbon compound.

  3. ADP combines with a free phosphate to produce ATP (not from the substrate).

FAD Interaction

  • FAD enters next and takes two electrons (and their accompanying hydrogens) leaving a modified four-carbon compound behind.

  • Water is then added for further modifications.

  • Finally, NAD+ comes back to facilitate the last conversion back to oxaloacetic acid, completing the cycle.

Overall Yield (per Pyruvic Acid)

  • 1 ATP (produced directly)

  • 4 NADH

  • 1 FADH2

Since each glucose molecule produces two pyruvic acids, the total yield for one glucose molecule becomes:

  • 2 ATP

  • 8 NADH

  • 2 FADH2

This cycle continues as long as pyruvic acid is available, ensuring sustained ATP production.

Electron Transport Chain Overview (ETS visual)

The electron transport chain (or system) is a key component of aerobic respiration and occurs in the inner membrane of the mitochondria (or in the cell membrane for prokaryotes). It primarily involves the transfer of electrons and the creation of a proton gradient used to synthesize ATP.

Structure of the Electron Transport Chain

  • Cell Wall: Represents the boundary of the cell.

  • Cell Membrane: A phospholipid bilayer that contains embedded proteins called cytochromes which are essential for electron transfer.

Key Steps in the Electron Transport Chain:

  1. Electron Donation from NADH and FADH2:

    • NADH donates electrons to the first cytochrome, resulting in the excitation and transfer of these electrons through a series of cytochromes.

    • FADH2 also delivers its electrons to the chain, resulting in the release of hydrogen ions (H+) into the periplasmic space, contributing to a proton gradient.

    • The process involves redox reactions where an electron carrier gets reduced by receiving electrons and oxidized when passing the electrons to the next carrier.

  2. Formation of Hydrogen Ion Gradient:

    • As electrons are passed through the cytochromes, hydrogen ions are pumped into the periplasmic space, creating a gradient and an acidic environment.

  3. ATP Synthesis via ATP Synthase:

    • Hydrogen ions flow back into the cell through ATP synthase, an enzyme that synthesizes ATP from ADP and inorganic phosphate (P). For every two hydrogen ions that pass through ATP synthase, one ATP molecule is produced.

Roles of Oxygen in the Electron Transport Chain:

  • Final Electron Acceptor:

    • Oxygen plays a crucial role as the final electron acceptor in the chain. It reacts with electrons and hydrogen ions at the end of the transport chain to form water (H2O).

    • Oxygen is diatomic (O2), meaning it consists of two oxygen atoms sharing electrons. The electron transport process would halt without oxygen to accept these electrons.

Summary of Outputs from Electron Transport Chain:

  • Water: Formed when oxygen reacts with electrons and hydrogen ions, enabling continuation of metabolic processes.

  • ATP: Generated as hydrogen ions flow back into the cell through ATP synthase.

This final step of aerobic respiration highlights why oxygen is vital for ATP production and why breathing is essential for organisms that rely on aerobic respiration.

Photosynthesis Overview (Photosynthesis)

Equation for Photosynthesis

  • Raw Materials: H2O + CO2

  • Products: O2 + C6H12O6 (glucose)

  • The process is usually presented as CO2 + H2O yielding O2 + C6H12O6, but the arrangement here represents the actual events.

The Role of Sunlight

  • Sunlight provides photons which fuel the process of photosynthesis, particularly during the Photosystem phase.

  • In the photosystem, water (H2O) is split into oxygen (O2) and hydrogen (H+).

  • The hydrogen is then used in a process similar to the electron transport chain, producing NADPH and ATP as products.

  • The release of O2 is a byproduct of this reaction.

The Calvin Cycle (Dark Reactions)

  • This phase does not require sunlight directly but needs the products from the photosystem.

  • Key inputs are CO2, ribulose bisphosphate, NADPH, and ATP from the photosystem.

  • The combination of these materials in the Calvin Cycle results in the formation of glucose (C6H12O6).

Summary of Photosynthesis Chemistry

  • The complete reaction is represented as:

    • H2O + CO2 yields O2 + C6H12O6

  • Photosynthesis creates glucose, which can later be converted into ATP via glycolysis, Krebs cycle, electron transport, and fermentation.

Final Note

  • While ATP is not a direct product of photosynthesis, the glucose produced can be converted into ATP, linking photosynthesis to energy production.