Metabolism Overview Notes

Metabolism Overview

Module 1

  • Jan Reynald Shane A. Coquilla, MD, MPH
  • 2015
  • Mapúa Malayan Colleges Mindanao
  • CHM060: Biomolecules
  • CAS

Diagram Key

  • Carbohydrates
  • Lipids
  • Amino Acids
  • Nucleotides
  • Heme
  • Vitamins
  • Multiple Steps
  • Multiple Cycles
  • Crosses Membrane (Outer Mitochondrial Membrane)
  • Crosses Membrane (Inner Mitochondrial Membrane)

Pathways of Human Metabolism

  • Version 1.36
  • Includes various metabolic pathways such as:
    • Glycolysis and Gluconeogenesis
    • Fatty Acid Synthesis
    • Fatty Acid Oxidation
    • Ketone Body Metabolism
    • Heme Synthesis
    • Pentose Phosphate Pathway
    • Aromatic Amino Acid Metabolism
    • Single-Carbon Metabolism and Sulfur-Containing Amino Acids
    • Citric Acid Cycle (Tricarboxylic Acid Cycle)
    • Heme Degradation
    • Branched-Chain Amino Acid Breakdown
    • Ammonium Capture and Release
    • Electron Transport Chain
    • Nucleotide Breakdown
    • Urea Cycle
    • Purine Synthesis
    • Pyrimidine Synthesis
    • Deoxyribonucleotides
    • Base Salvage
    • Nucleoside Salvage

Metabolism Functions

  • Obtain chemical energy by capturing solar energy or degrading energy-rich nutrients.
  • Convert nutrient molecules into the cell’s own characteristic molecules.
  • Polymerize monomeric precursors into macromolecules.
  • Synthesize and degrade biomolecules required for specialized cellular functions.

Two Groups of Organisms Based on Carbon Source

  • Autotrophs:
    • Use CO_2 from the atmosphere as their sole carbon source.
  • Heterotrophs:
    • Cannot use atmospheric CO_2.
    • Obtain carbon from complex organic molecules like glucose.

Catabolism

  • Degradative process.
  • Organic nutrient molecules are broken down into smaller, simpler end products.
  • Releases energy in the form of:
    • ATP
    • Reduced electron carriers (NADH, NADPH, and FADH2 ).
    • Heat

Anabolism

  • Also known as biosynthesis.
  • Precursors are built into larger, more complex molecules.
  • Requires energy in the form of:
    • ATP
    • NADH
    • NADPH
    • FADH2

Energy Conversion

  • Oxidation reactions yield energy.
  • Electrons are captured by:
    • NADH
    • FADH2
  • Electron transport and oxidative phosphorylation lead to:
    • Production of ATP, which provides energy for anabolic pathways.

Redox Reactions

  • Oxidation reactions release energy.
  • Electrons are captured by:
    • NADH
    • FADH2
  • Electron transport & oxidative phosphorylation:
    • Production of ATP
    • ATP provides energy for anabolic pathways

Metabolic Pathways

  • Catabolic Pathway: Convergent
  • Anabolic Pathway: Divergent
  • Linear
  • Branched
  • Cyclic

Common Intermediates

  • Metabolic pathways must converge.
    • Glucose
    • Amino acids
    • Triacylglycerols
  • Intermediates you will often encounter:
    • Glyceraldehyde-3-phosphate
    • Pyruvate
    • Acetyl-CoA
    • Oxaloacetate
    • Alanine
    • Fatty acids
    • CO_2

Redox Reactions (Oxidations of Carbon)

  • All are 2 electron oxidations.
  • Most are reversible.
  • Examples:
    • Alkane (Methane: CH_4)
    • Alcohol (Methanol: CH_3OH)
    • Aldehyde/Ketone (Formaldehyde: \frac{H}{H}C=O)
    • Carboxylic Acid (Formic acid: \frac{H}{OH}C=O)
    • Carbon Dioxide (CO_2)

Redox Reactions in Biochemistry

  • Most involve redox of carbon.
  • Example: Oxidation of ethanol (Fewer C-H bonds, more C-O bonds)
  • Need something to receive the electrons.
  • H3C\frac{H}{OH} + 2e^- + 2H^+ \rightarrow H3C\frac{H}{H}C=O

Electron Transfer Agents

  • NAD+/NADH: 2 electron redox agent. Found in catabolic pathways.
    • NAD^+ + 2e^- + H^+ \rightarrow NADH
  • NADP+/NADPH: 2 electron redox agent. Anabolic pathways.

Electron Transfer Agents: FAD & FMN

  • FAD & FMN: 1 or 2 electron oxidizing agent.
  • FADH2 & FMNH2: 1 or 2 electron reducing agent.
  • FAD + 2e^- + 2H^+ \rightarrow FADH_2

Redox Pairs

  • Oxidation of ethanol coupled to reduction of NAD^+
    • H3C\frac{H}{OH} + NAD^+ \rightarrow H3C\frac{H}{H}C=O + NADH + H^+

Metabolic Pathway Regulation

  • Regulation from within and outside the cell.
  • Availability of substrate: Reaction depends on the substrate concentration.
  • Allosteric regulation: Metabolic metabolite or coenzyme (e.g., amino acids or ATP) signals the cell’s internal metabolic state.