Biochemistry Chapter 3: Metabolism

Chapter 3: Metabolism

• This chapter covers metabolism, which encompasses all biochemical reactions necessary for life.
• Energy is conserved by converting it into a usable form.
• Cells generate Adenosine Triphosphate (ATP) to store and utilize energy in cellular processes.

3.1 Defining the Requirements for Life

• Metabolism is the sum total of all biochemical reactions within a cell.
• Metabolism includes catabolic & anabolic pathways.

Anabolism and Catabolism

• Catabolic pathways release energy by breaking down larger molecules into smaller ones.
• Anabolic pathways use energy to synthesize larger molecules from smaller ones.
• Energy released in catabolic pathways fuels anabolic processes.

3.1 Defining the Requirements for Life - Energy Sources

• Organisms can obtain energy from chemicals (chemosynthesis) or light (photosynthesis).
• Chemoorganotrophs: Use organic molecules as energy sources.
• Chemolithotrophs: Use inorganic molecules as energy sources.
• Phototrophs: Use light as energy sources.

3.4 Cellular Energy Conservation

• Adenosine Triphosphate (ATP) is the principal energy currency in cells.
• ATP stores energy in high-energy phosphate bonds.
• Several other chemicals also store energy in bonds, but ATP is the primary molecule for energy transfer

3.4 Cellular Energy Conservation - Energy Rich Compounds

• Several compounds contain energy in their phosphate or sulfur bonds.
• Not all phosphate bonds have high energy content.
• Examples discussed: Phosphoenolpyruvate, ATP, Acetyl Phosphate, Glucose 6-phosphate, and Acetyl-CoA.
• The chapter discusses specific energy values using AG° values.

II. Catabolism: Chemoorganotrophs

• Subsections (3.6-3.9) cover specific catabolic pathways used by chemoorganotrophs for energy production.
• These include Glycolysis, Citric Acid Cycle, Glyoxylate Cycle, Fermentation pathways, Respiration pathways, and the role of electron carriers.

3.6 Glycolysis

• Glycolysis is a crucial universal pathway for glucose catabolism.
• This process oxidizes glucose to pyruvate.
• It is a two-stage process.

3.6 The Citric Acid Cycle

• Pyruvate is oxidized to CO2 in the Citric Acid Cycle (CAC).
• The CAC produces important precursor molecules for biosynthesis.
• This pathway can process various carbon substrates.

3.6 The Glyoxylate Cycle

• The glyoxylate cycle is an alternative to the CAC, used for oxidizing C₂ compounds (like acetate).

3.7 Principles of Fermentation

• Fermentation involves substrate-level phosphorylation for ATP production.
• It maintains redox balance by reducing oxidized compounds.
• It usually involves excretion of the products.

3.8 Principles of Respiration: Electron Carriers

• Respiration breaks down glucose to make ATP.
• Electrons move from reduced donors to external acceptors (e.g., oxygen).
• Reoxidation of NADH and FADH₂ occurs during electron transport.
• Electron transport occurs in the cytoplasmic membrane
• Creates a proton motive force for ATP synthesis.

3.8 Principles of Respiration: Electron Carriers - Other Electron carriers

• Specific electron carriers like NADH dehydrogenases, flavoproteins, cytochromes, and quinones are involved in electron transport chains.

3.9 Principles of Respiration: Generating a Proton Motive Force

• Electron transfer during respiration is exergonic.
• It drives proton pumping across membranes.
• This creates a proton motive force, which is used by ATP synthase to generate ATP.

Cellular Respiration Summary

• Cellular respiration involves glycolysis, pyruvate oxidation/citric acid cycle, and oxidative phosphorylation.
• These steps produce ATP.

3.10 Anaerobic Respiration and Metabolic Modularity

• Microorganisms can adapt metabolic pathways to utilize various electron donors.
• Aerobic respiration is more efficient than anaerobic respiration.
• Oxygen availability influences the kinds of metabolic processes.

3.11 Chemolithotrophy and Phototrophy

• Phototrophy is energy capture via light.
• Phototrophs use light energy to synthesize ATP.

IV. Biosynthesis

• This section deals with the synthesis of molecules vital for life.
• The sections include Autotrophy,sugars, amino acids, nucleotides, and lipids.

3.12 Autotrophy and Nitrogen Fixation

• Microorganisms obtain nitrogen from ammonia, and some fix atmospheric nitrogen gas to produce ammonium.

3.14 Amino Acids and Nucleotides

• Amino acid and nucleotide biosynthesis occurs via varied multistep pathways.
• Amino acid precursors arise from intermediates in central metabolic pathways.

3.15 Fatty Acids and Lipids

• Fatty acids can be saturated or unsaturated.
• Varying carbon chain lengths are observed across different bacteria species.