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Lecture Summary: Metabolism Review, Fermentation, Photosynthesis & Introduction to Anabolism

Course Logistics

Enzymes & Metabolic Regulation (Review + Deeper Connections)

What Enzymes Do

• Function of Enzymes:

  • Enzymes lower the activation energy of chemical reactions, facilitating their progress.

  • Composition:

  • Most enzymes are proteins; however, some are ribozymes (catalytic RNA).

  • Naming Convention:

  • Often end with the suffix -ase.

  • The first part of the name may indicate the substrate (e.g., sucrase acts on sucrose).

Types of Enzyme Inhibition

1. Competitive Inhibition

   • Inhibitor binds to the active site of the enzyme.

   • Can be overcome by increasing the substrate concentration.

   • Changes the apparent affinity of the enzyme (denoted as K_m), but does not affect the maximum velocity (denoted as V_max).

2. Noncompetitive (Allosteric) Inhibition

   • Inhibitor binds to a site other than the active site.

   • Alters the shape of the enzyme.

   • Cannot be overcome by increasing substrate concentration.

   • Reduces maximum velocity (V_max).

Feedback Inhibition (Key Concept)

• Cells regulate metabolism by allowing end products to inhibit earlier steps.

  • Benefits of Feedback Inhibition:

  • Prevents waste of resources.

  • Maintains energy balance.

  • Efficient allocation of cellular resources.

Regulation of Glycolysis (Example)

• Key Regulatory Enzymes:

  • Phosphofructokinase (PFK)

  • Pyruvate kinase

• Regulatory Logic:

  • High levels of AMP (indicating low energy) activate glycolysis.

  • High levels of ATP (indicating high energy) inhibit glycolysis.

  • High levels of citrate or acetyl-CoA also inhibit glycolysis.

  • Outcome of Regulation:

  • If a cell has sufficient ATP or downstream metabolic intermediates, it slows down energy production.

Catabolism Overview

• Metabolic Pathway:

  • Glycolysis → Krebs Cycle → Electron Transport Chain (ETC)

• Energy Generation Types:

  1. Substrate-Level Phosphorylation:

  • Occurs during glycolysis and the Krebs cycle.

  • Involves direct transfer of a phosphate group to ADP from a substrate.

  1. Oxidative Phosphorylation:

  • Occurs in the electron transport chain (ETC).

  • A proton gradient powers ATP synthase to produce ATP.

Electron Transport Chain (ETC)

• Process Overview:

  • NADH and FADH₂ donate electrons.

  • Electrons traverse through membrane complexes.

  • Protons are pumped outside, generating a proton gradient.

  • Protons return through ATP synthase.

  • Oxygen acts as the final electron acceptor (in aerobic respiration).

  • Water is produced as a byproduct of this process.

Important Clarification

• ATP synthase is reversible.

• If detached from its membrane, ATP synthase hydrolyzes ATP instead of synthesizing it.

• Iron, found in heme groups, is critical for the functioning of cytochromes, highlighting the importance of trace metals.

What Happens Without Oxygen?

• In the absence of oxygen:

  • The electron transport chain ceases to operate.

  • NADH accumulates without a way to oxidize it.

  • Glycolysis halts due to a lack of NAD⁺.

  • Cells revert to fermentation.

Fermentation

• Key Principle:

  • Fermentation does not produce extra ATP beyond what glycolysis yields.

  • Its primary purpose is to regenerate NAD⁺.

Types of Fermentation

1. Lactic Acid Fermentation

   • Conversion: Pyruvate → Lactate

   • Regens NAD⁺.

   • Occurs in human muscle cells when oxygen levels drop.

   • Results in acidic byproducts that can contribute to muscle fatigue.

2. Alcohol Fermentation

   • Conversion: Pyruvate → Ethanol + CO₂

   • Carried out by Saccharomyces cerevisiae (yeast)

   • CO₂ causes bubbling in beer and wine production.

   • Ethanol becomes toxic at high concentrations, demonstrating a limit to fermentation process.

Fermentation in Food Examples

• Sake:

  • Involves the mold Aspergillus oryzae.

• Soy Fermentation:

  • Often involves Bacillus subtilis.

• Potential Health Effects of Fermented Foods:

  • May influence inflammation.

  • Could interact with the immune system.

  • Have the potential to alter the microbiome, and ongoing research is examining these effects.

Photosynthesis (Introduction)

Evolutionary Origin

• Chloroplasts are believed to have evolved from ancient cyanobacteria through a process called endosymbiosis, which accounts for their double membrane structure.

Light-Dependent Reactions

• Occur in the thylakoid membrane.

• Light energy excites electrons, leading to a series of events:

  • A proton gradient is established.

  • ATP and NADPH are produced.

  • Oxygen gas is released as a byproduct during oxygenic photosynthesis.

Light-Independent Reactions (Calvin Cycle)

• Utilize ATP and NADPH produced in the light-dependent reactions.

• The primary function is the fixation of CO₂ into glucose.

  • Characterized as an anabolic process.

Oxygenic vs. Anoxygenic Photosynthesis

• Oxygenic Photosynthesis:

  • Produces oxygen (O₂).

  • Found in:

  • Cyanobacteria

  • Plants

  • Algae

• Anoxygenic Photosynthesis:

  • Does NOT produce oxygen (O₂).

  • Utilizes alternative electron donors (e.g., hydrogen sulfide, H₂S).

  • Common in:

  • Purple sulfur bacteria

  • Green sulfur bacteria

• Important Evolutionary Note:

  • Anoxygenic photosynthesis is believed to have evolved first, while oxygenic photosynthesis transformed Earth's atmosphere by introducing free oxygen.

Transition to Anabolism

• Prior Discussion:

  • Focused on catabolic pathways (breaking down molecules).

• Current Discussion:

  • Explore how cells utilize resources to build complex molecules.

• Anabolism:

  • Requires energy in the form of ATP.

  • Responsible for the synthesis of:

  • DNA

  • RNA

  • Proteins

  • Lipids

  • Peptidoglycan

  • Polysaccharides

  • Amino acids

Chromosome Partitioning in Bacteria

• Pre-Division Events:

  • DNA replicates prior to cell division.

  • Chromosomes must segregate appropriately between daughter cells.

• Key System:

  • parS: a specific DNA sequence on the chromosome.

  • ParB: a protein that binds to parS.

  • ParA: a protein that facilitates movement of chromosomes to opposite poles during cell division.

• Model Organism:

  • Caulobacter crescentus is often used for studying chromosome partitioning.

  • This ensures that each daughter cell receives one complete chromosome.

Big Conceptual Connections

1. Metabolism is highly interconnected.

2. Catabolism provides:

   • ATP

   • Reducing power

   • Precursors necessary for anabolic processes.

3. Feedback inhibition helps to integrate the cellular energy status.

4. Availability of oxygen can shift metabolic strategies within cells.

5. Both photosynthesis and respiration utilize similar electron transport chain logic.

6. Evolution provides a connection linking chloroplasts and bacteria.

Additional Points/Emphasis

• Fermentation does NOT generate additional ATP beyond glycolysis.

• ATP synthase is normally ATP-generating due to the proton gradient, but it is reversible.

• Eukaryotic photosynthesis is solely oxygenic.

• Anoxygenic photosynthesis is believed to precede oxygenic photosynthesis in evolutionary history.

• Fermentation's primary function is to regenerate NAD⁺, rather than producing ATP.