Chapter 6: Metabolism: Fueling Cell Growth

All cells need carbon and energy:
- Harvest energy to power reactions.
- Use carbon to synthesize cellular components.
Definitions of Metabolism:
- Metabolism: Sum of all chemical reactions within a cell.
- Catabolism: Breaking down complex molecules into simpler ones.
- Anabolism: Building up complex molecules from simpler ones.

Energy: Capacity to do work.
- Potential energy: Stored energy.
- Kinetic energy: Energy of motion.
Types of Reactions:
- Exergonic reactions: Energy is released.
- Endergonic reactions: Energy input is required to proceed.

Metabolic pathways: Series of reactions that convert a starting compound into a product.
- Linear metabolic pathway: A straight series of reactions.
- Branched metabolic pathway: Contains branches for different products.
- Cyclical metabolic pathway: Cycles back to initiate new reactions.

Role of Enzymes:
- Enzymes speed up rates of reaction by lowering activation energy.
- Diagram depicts energy levels of reactants and products in the presence and absence of enzymes.

Energy sources and terminal electron acceptors:
- Electronegativity: Some atoms and molecules have a greater tendency to attract electrons.
- Energy released: Occurs when electrons move from a low-affinity molecule (e.g., glucose) to a high-affinity molecule (e.g., O2).

Electron carriers: Molecules that transport electrons in metabolic pathways.
- Examples include NAD+/NADH, NADP+/NADPH, and FAD/FADH2.
- They facilitate electron transfer and, as a result, raise the energy level of recipient molecules.

Definition: Intermediates of catabolism that can be used in anabolism.
- Serve as carbon skeletons for building macromolecules such as amino acids, nucleic acids, lipids, and carbohydrates.

Central metabolic pathways:
- Glycolysis: Converts 1 glucose into 2 pyruvates, yielding a net of 2 ATP and 2 NADH.
- Investment phase: Two phosphate groups are added to glucose, splitting it into two 3-carbon molecules.
- Pay-off phase: 3-carbon molecules are converted to pyruvate, generating a total of 4 ATP and 2 NADH.
- Tricarboxylic Acid (TCA) Cycle: Completes the oxidation of glucose.
- Produces 2 CO2, 2 ATP, 6 NADH, and 2 FADH2.

Process: Uses reducing power to generate a proton motive force.
Electrons originate from NADH and FADH2:
- Travel through a series of complexes in the inner mitochondrial membrane.
Production of ATP: The proton motive force drives ATP synthase to produce ATP from ADP and inorganic phosphate.

Characteristics:
- Prokaryotes show remarkable variation, often utilizing different sets of electron carriers compared to eukaryotic cells.
E. coli example:
- Capable of aerobic respiration and produces several variants based on environmental oxygen levels.

Cofactors and coenzymes:
- Some enzymes require additional non-protein molecules called cofactors (e.g., Mg, Zn).
- Coenzymes are organic molecules that assist enzymes, such as FAD, NAD+, and NADP+.
Factors affecting enzyme activity:
- Optimal temperature, pH, and salt concentration can greatly influence enzyme speed and efficiency.

Non-competitive inhibition:
- Involves an allosteric site where regulatory molecules can enhance or inhibit enzyme activity based on feedback mechanisms.
Competitive inhibition:
- Inhibitor resembles the substrate and competes for the active site, blocking substrate binding.
- Example: Sulfa drugs inhibit folic acid synthesis in bacteria.

Definition: Utilizes organic compounds as terminal electron acceptors.
Examples: Produce end products such as lactic acid, ethanol, and other organic acids.

Energy Sources:
- Chemotrophs: Obtain energy from chemical compounds.
- Phototrophs: Obtain energy from light.
Carbon Sources:
- Chemoheterotrophs: Use organic compounds as a carbon source.
- Chemoautotrophs: Use inorganic compounds and fix CO2.
- Photoautotrophs: Use light to fix CO2 and produce organic compounds.

General Process:
- Plants, algae, and some bacteria convert light energy into chemical energy stored as glucose.
- Divided into two stages:
- Light Reactions: Capture energy and produce ATP and NADPH.
- Dark Reactions (Calvin Cycle): Use ATP and NADPH to synthesize glucose from CO2.

Process description:
- Involves photosystems I and II that work together to produce ATP and NADPH while releasing oxygen from water splitting.

Calvin Cycle:
- Incorporates CO2 into organic molecules and allows for the synthesis of sugars such as fructose.
- Stages:
1. Incorporation of CO2 into ribulose-1,5-bisphosphate.
2. Conversion of 3-phosphoglycerate to glyceraldehyde-3-phosphate.
3. Regeneration of ribulose-1,5-bisphosphate.

Amino Acid Synthesis:
- Precursors such as oxaloacetate are used to synthesize amino acids.
- Aromatic amino acids such as tryptophan act as feedback inhibitors in their respective biosynthetic pathways
- Pathways lead to the synthesis of various amino acids that serve in cellular functions.

Metabolism: The sum of all chemical reactions in a cell.
Catabolism: Reactions that break down molecules to release energy.
Anabolism: Reactions that use energy to build cell components.
Energy Types:
- Exergonic: Reactions that release energy.
- Endergonic: Reactions that require energy input.

Enzymes: Act as biological catalysts that speed up reactions by lowering the activation energy.
ATP: The main energy currency of the cell.
Electron Carriers: Molecules like $NADH$ , $NADPH$ , and $FADH_{2}$ that move high-energy electrons around.

Glycolysis: The process of splitting $1$ glucose molecule into $2$ pyruvate molecules. It nets $2$ $ATP$ and $2$ $NADH$ .
TCA (Krebs) Cycle: Takes the products of glycolysis and fully oxidizes them, releasing $CO<em>{2}$ and generating more electron carriers ( $NADH$ and $FADH</em>{2}$ ) plus $2$ $ATP$ .
Electron Transport Chain (ETC): Found in the cell membrane (prokaryotes) or mitochondria (eukaryotes). It uses electrons from carriers to create a proton gradient that drives the production of a large amount of $ATP$ .

Fermentation: Used when oxygen (or other terminal electron acceptors) is unavailable. It recycles $NAD^{+}$ by dumping electrons onto organic molecules, resulting in products like lactic acid or ethanol.
Photosynthesis: Bases life on light energy.
- Light Reactions: Capture light to produce $ATP$ and $NADPH$ .
- Calvin Cycle: Uses that energy to turn $CO_{2}$ into organic sugars.

By Energy Source:
- Chemotrophs: Get energy from chemical compounds.
- Phototrophs: Get energy from light.
By Carbon Source:
- Autotrophs: Use inorganic $CO_{2}$ to build molecules.
- Heterotrophs: Use organic carbon (from other organisms).