Energy in Biological Molecules

Chemical Bonds and Energy

Biological molecules such as glucose store energy in their chemical bonds, which is essential for cellular processes.

• Potential Energy: The energy stored in the C-H bonds of glucose is potential energy, which can be released during cellular respiration.

• Kinetic Energy: The energy of motion, not stored in chemical bonds.

• Solar Energy: Energy from sunlight, captured during photosynthesis.

• Gravitational Energy: Energy due to position in a gravitational field, not relevant to chemical bonds.

• Example: When glucose is metabolized, the potential energy in its bonds is converted to ATP, the cell's energy currency.

Metabolic Pathways and Regulation

Feedback Inhibition

Metabolic pathways are regulated to maintain homeostasis and efficiency in the cell.

• Feedback Inhibition: A process where the end product of a metabolic pathway inhibits an enzyme involved earlier in the pathway, thus regulating its own production.

• Key Point: This prevents the overaccumulation of products and conserves resources.

• Example: The synthesis of isoleucine from threonine is regulated by feedback inhibition.

Spontaneous Reactions and Entropy

Spontaneous reactions in biology are governed by the laws of thermodynamics.

• Entropy (S): A measure of disorder or randomness in a system.

• Key Point: Most spontaneous reactions increase the entropy of the system.

• Equation: for spontaneous processes.

Enzyme Function and Inhibition

Noncompetitive Inhibition

Enzymes can be regulated by inhibitors that affect their activity.

• Noncompetitive Inhibitor: Binds to an allosteric site (not the active site), causing a conformational change in the enzyme.

• Effect: This change prevents the substrate from binding effectively to the active site.

• Key Point: Noncompetitive inhibition does not compete with the substrate for the active site.

Activation Energy and Enzymes

Enzymes lower the activation energy required for biological reactions.

• Transition State: The high-energy state that reactants must reach for a reaction to proceed.

• Activation Energy (Ea): The energy required to reach the transition state.

• Effect of Enzymes: Enzymes lower the activation energy, increasing the rate of reaction.

Cellular Respiration and Metabolism

Krebs Cycle (Citric Acid Cycle)

The Krebs cycle is a series of reactions that generate energy through the oxidation of acetyl-CoA.

• Oxidative Decarboxylation: Steps in the cycle where carbon atoms are removed as CO2 and electrons are transferred to NAD+ or FAD.

• Key Reactions:

  • Citrate to alpha-ketoglutarate

  • Alpha-ketoglutarate to succinyl CoA

Electron Transport and Magnetite Production

Some bacteria use the electron transport chain for cellular respiration and can produce magnetite.

• Key Evidence: Inhibiting electron transport enzymes prevents magnetite production, supporting the link between respiration and magnetite synthesis.

ATP Formation: Oxidative vs. Substrate-Level Phosphorylation

Cells generate ATP through two main mechanisms.

• Substrate-Level Phosphorylation: Direct transfer of a phosphate group to ADP to form ATP, occurs in glycolysis and the Krebs cycle.

• Oxidative Phosphorylation: ATP is produced using energy from the electron transport chain and chemiosmosis.

• Key Features:

  • Substrate-level phosphorylation produces less ATP than oxidative phosphorylation.

  • ATP is formed during glycolysis by substrate-level phosphorylation.

  • Oxidative phosphorylation's mechanism is chemiosmosis.

Photosynthesis

Light Reactions and Calvin Cycle

Photosynthesis consists of light-dependent and light-independent reactions.

• Light Reactions: Convert solar energy to chemical energy (ATP and NADPH).

• Calvin Cycle: Uses ATP and NADPH to reduce CO2 to sugars.

• Key Point: ATP and NADPH from light reactions are used in the Calvin cycle for carbon fixation.

Electromagnetic Spectrum and Photosynthesis

Photosynthetic organisms use specific wavelengths of light for energy.

• Visible Light: The part of the spectrum used in photosynthesis (approximately 400–700 nm).

• Other Regions: Infrared and ultraviolet are not efficiently used for photosynthesis.

Carbon Fixation Pathways in Plants

Plants use different pathways to fix carbon, depending on their environment.

• C3 Plants: Use Rubisco to fix CO2 directly in the Calvin cycle.

• C4 and CAM Plants: Use alternative enzymes for initial CO2 fixation before the Calvin cycle.

• Key Point: C4 and CAM plants do not use Rubisco for the initial fixation of carbon.

Overview of Photosynthesis Events

• Light is absorbed by photosynthetic pigments.

• Light energy is converted to chemical energy (ATP and NADPH).

• CO2 is fixed into sugars by the Calvin cycle.

Comparing Cellular Respiration and Photosynthesis

Similarities and Differences

• Redox Reactions: Both processes involve oxidation-reduction reactions.

• Energy: Both synthesize and utilize energy, but only photosynthesis is anabolic (building up), while respiration is catabolic (breaking down).

• Key Point: Not both are anabolic; cellular respiration is catabolic.

DNA Replication and Repair

DNA Synthesis Directionality

DNA is synthesized in a specific direction during replication.

• 5' to 3' Direction: Both leading and lagging strands, as well as Okazaki fragments, are synthesized in this direction.

Griffith's Experiment and Transformation

Griffith's experiment demonstrated the transfer of genetic material between bacteria.

• Key Finding: Mixing live R strain with heat-killed S strain led to the death of mice, indicating transformation.

Enzymes in DNA Replication

• DNA Polymerase: Main enzyme responsible for synthesizing new DNA strands.

• Other Enzymes: DNA helicase (unwinds DNA), DNA ligase (joins fragments), DNA gyrase (relieves supercoiling).

DNA Repair Mechanisms

Cells have mechanisms to repair DNA damage caused by environmental factors.

• Pyrimidine Dimers: Lesions formed by UV-induced covalent bonding between adjacent thymine or cytosine bases.

• Repair: Nucleotide excision repair mechanisms remove and replace damaged DNA.

Monomers of Nucleic Acids

• Nucleotide: The monomer unit of nucleic acids (DNA and RNA), consisting of a phosphate group, a sugar, and a nitrogenous base.