Cellular Energetics and Photosynthesis

Cellular Energetics and Metabolism

Fermentation and the Evolution of Metabolism

• Early life evolved without molecular oxygen (O_2).
• Glycolysis was the primary (and possibly only) means of metabolizing sugar molecules.
• Glycolysis must be sufficient for some cells, as almost all unicellular organisms preferentially use it.
• Yeast cells preferentially use glycolysis even in the presence of oxygen; they only shift to using oxygen when glucose is limited.
• Oxygen can be toxic, causing damage to molecules through oxidation. Cells must carefully manage its use.

ATP Demand and Oxidative Phosphorylation

• When there's a greater demand for ATP, cells move beyond glycolysis.
• Complete oxidation of glucose yields carbon dioxide (CO2) and water (H2O).
• Substrate-level phosphorylation yields the equivalent of 4 ATPs per glucose molecule.
• NADH and FADH (plus two from glycolysis and two from pyruvate oxidation) are oxidized to release energy.
• A series of oxidation-reduction reactions occur in protein complexes in the microbial membrane to produce a proton gradient.
• This proton gradient powers ATP synthesis through the reverse action of the F-type ATPase (F-type pump).
• Proton pumps in the membrane use redox energy to pump protons; this is an active transport process.

Photosynthesis

• The reverse process, where water is split to produce oxygen, occurs in chloroplasts or independent photosynthetic bacteria like cyanobacteria.
• Photosynthesis occurs in two stages:
  • Light-dependent reactions (light reactions): Harness light energy to generate ATP and NADPH (no sugars are produced yet).

Metabolic Cycles

• Glycolysis is a linear pathway, whereas processes like the Krebs cycle are metabolic cycles.
• Advantages of metabolic cycles:
  • Allow for complex chemistry that might be difficult otherwise (e.g., oxidizing the acetyl group in acetyl CoA is difficult, but attaching it to oxaloacetate as citrate makes it easier).
  • Add extra steps that allow for more precise regulation. Every step (enzyme) can be regulated. The more steps, the more precise the regulation.

Calvin Cycle and Carbon Fixation

• Involves starting with five modules of ribulose-1,5-bisphosphate (15 carbons total).
• After carbon fixation, there is a three-carbon excess. One glyceraldehyde-3-phosphate molecule is removed from the cycle, leaving 15 carbons.
• The remaining 15 carbons are rearranged to regenerate three molecules of ribulose-1,5-bisphosphate, requiring an additional three ATPs to add the extra phosphate.

Energy Accounting in Catabolism and Anabolism

• The many more ATPs that we get out of the Krebs cycle come from NADH.
• There are 3 NADHs per turn of the Krebs cycle plus one FADH for a total of 4 per turn (8 total for 2 turns of the Krebs cycle).
• There are 2 NADHs from glycolysis.
• There are 2 NADHs from oxidizing pyruvate into acetyl CoA.
• Total: the equivalent of 12 NADHs.
• In the "dark reactions," 6 NADPHs are used per glyceraldehyde-3-phosphate. For two glyceraldehyde-3-phosphates, this is 12 NADPHs.
• The number of electrons coming out of the Krebs cycle and the oxidation of glucose and glycolysis is the same as the number put into the reduction of carbon dioxide.
• The extra 28 ATPs are accounted for by the 12 NADPHs used to reduce carbon dioxide.
• The real difference between catabolic and anabolic reactions is the difference between 9 ATPs (from anabolic) versus 4 ATPs (from catabolic).
• The large difference represents energy lost due to inefficiencies in the system.
• Cellular metabolism works by taking small steps catalyzed by enzymes to extract energy in manageable amounts and reduce activation energies.

Regulation of Metabolism

• Enzymes are highly regulated through allosteric regulation and feedback regulation.
• Metabolic cycles allow for very precise regulation.
• Cycles allow the intermediates of metabolism to be used for other things and allow other nutrients (carbohydrates, fats, amino acids) to feed into the same pathways.