Chapter 4 & 5 Notes

Chapter 4: Energy and Cellular Metabolism

Energy

• Energy is the capacity to do work. There are three types of work:

  • Chemical work: Making and breaking of chemical bonds.

  • Transport work: Movement of ions, molecules, and larger particles through cell membranes, creating concentration gradients.

  • Mechanical work: Movement, such as organelles moving within a cell, cilia and flagella beating, and muscle contraction.

Forms of Energy

• Kinetic Energy: Energy in motion.

• Potential Energy: Stored energy.

• Energy Conversion: Energy can be converted from potential to kinetic and vice versa.

• Potential energy is stored in concentration gradients and chemical bonds.

• Stored potential energy transforms into kinetic energy for chemical, transport, or mechanical work.

Chemical Reactions

• Activation Energy: Energy required for a reaction to proceed.

  • Low activation energy: Spontaneous reaction.

  • High activation energy: Slow or no reaction.

• Reaction Rate: Speed of a reaction.

• Coupling: Using energy released from exergonic reactions to fuel endergonic reactions.

Enzymes

• Enzymes speed up reaction rates by lowering the activation energy.

• They bind to substrates, bringing them into the optimal position for reaction.

• Enzymes are biological catalysts and are not changed in the process.

• Most enzymes are proteins.

Metabolism

• Metabolism encompasses all chemical reactions in an organism.

• Catabolic Reactions: Breakdown of biomolecules, producing energy.

• Anabolic Reactions: Synthesis of large biomolecules, utilizing energy.

ATP Production

• Aerobic Pathways: Yield the most ATP and require oxygen.

  • Carbohydrates enter as glucose.

  • Lipids enter as fatty acids.

  • Proteins enter as amino acids.

Glycolysis

• $Glucose \rightarrow 2 \text{ Pyruvate } + 2 \text{ ATP } + 2 \text{ NADH } + 2 \text{ H}_2\text{O}$

• Glycolysis does not require oxygen and occurs in the cytosol.

Pyruvate Metabolism

• Anaerobic Metabolism (no oxygen):

  • $2 \text{ Pyruvate } + 2 \text{ NADH } \rightarrow 2 \text{ Lactate}$

  • Net energy yield: 2 ATP (no NADH).

• Aerobic Metabolism (sufficient oxygen):

  • 2Pyruvate + 2O2 > 2Acetyl CoA + 2NADH + 2CO2

Citric Acid Cycle

• $2 \text{ Acetyl CoA } + 4 \text{ O}<em>2 + 2 \text{ H}</em>2\text{O } \rightarrow 6 \text{ NADH } + 2 \text{ FADH}<em>2 + 2 \text{ ATP } + 4 \text{ CO}</em>2$

Electron Transport Chain

• High-energy electrons from glycolysis are captured by NADH and FADH2.

• Energy released pumps $H^+$ from the mitochondrial matrix into the intermembrane space.

• Electrons combine with $H^+$ and oxygen to form water.

• Potential energy in the $H^+$ gradient is converted to kinetic energy via ATP synthase, producing ATP.

Metabolism Summary

• Each NADH yields 2.5 ATP.

• Each FADH2 yields 1.5 ATP.

• Total ATP production from aerobic metabolism: 4 ATP + (10 NADH x 2.5 ATP) + (2 FADH2 x 1.5 ATP) = 32 ATP.

Lipid Synthesis

• Most lipids are synthesized in the smooth ER and cytosol.

• Glycerol can be made from glucose through glycolysis.

• Two-carbon acyl units from acetyl CoA are linked by fatty acid synthetase to form fatty acids.

• One glycerol plus three fatty acids make a triglyceride.

Protein Synthesis

• The genetic code of DNA is converted into a functional protein.

• Four nitrogenous bases code for 20 amino acids.

• Transcription factors bind and activate the promoter region.

• RNA polymerase binds and unwinds DNA.

• mRNA is created from the sense strand.

• mRNA is processed via RNA interference and alternative splicing.

Transcription and Translation

• Transcription: DNA to mRNA.

• Translation: mRNA to protein, involving tRNA and ribosomes.

Post-translational Modification

• Protein folding, tertiary structure, cross-linkage.

• Strong covalent bonds.

• Cleavage.

• Addition of other molecules or groups.

• Assembly into polymeric proteins.

Key Concepts

• Energy types (chemical, transport, mechanical work).

• Kinetic vs. potential energy.

• Enzymes and activation energy.

• Endergonic vs. exergonic reactions.

• Reactants, substrates, and products.

• Metabolism (catabolic vs. anabolic reactions).

• Aerobic and anaerobic metabolism.

• Protein synthesis (transcription, translation).

• Nucleotide pairings (DNA: A=T, G=C; RNA: A=U, G=C).

Chapter 5: Membrane Dynamics

Mass Balance and Homeostasis

• Law of Mass Balance: Any gain of a substance must be offset by an equal loss to maintain a constant amount.

• Homeostasis ≠ equilibrium.

• Osmotic Equilibrium: Total solute concentration is equal on both sides of the cell membrane.

• Chemical Disequilibrium: Unequal distribution of solutes (e.g., $K^+$ high inside, $Na^+$ high outside).

• Electrical Disequilibrium: Unequal distribution of ions, creating a slight negative charge inside the cell.

Diffusion

• Passive process, requiring no ATP.

• Movement from high to low concentration (down the concentration gradient).

• Net movement until equilibrium is reached.

• Rapid over short distances, slower over long distances.

• Directly related to temperature; diffusion increases at higher temperatures.

• Inversely related to molecular size.

• Occurs in open systems or across a partition.

• Ion movement depends on the electrochemical gradient.

Lipophilic Molecules

• Hydrophilic substances (lipophobic) do not dissolve in lipids and do not cross the cell membrane.

• Hydrophobic substances (lipophilic) can cross the lipid cell membrane.

Fick's Law of Diffusion

• $\text{Rate of diffusion} = \frac{\text{Surface area} \cdot \text{Concentration gradient} \cdot \text{Membrane permeability}}{\text{Membrane thickness}}$

• $\text{Membrane permeability} \propto \frac{\text{Lipid solubility}}{\text{Molecular size}}$

Membrane Proteins

• Structural proteins maintain cell shape.

• Enzymes catalyze chemical reactions.

• Membrane receptor proteins facilitate chemical signaling.

• Transporters move molecules across membranes.

  • Channel proteins create water-filled passageways.

  • Carrier proteins bind to the substrate, aiding transport by changing conformation.

Membrane Transporters

• Channel Proteins: Create a water-filled pore.

  • Gated channels (chemically, voltage, or mechanically gated).

  • Open channels.

• Carrier Proteins: Never form an open channel.

  • Uniport carriers: Transport one substance.

  • Symport carriers: Transport two substances in the same direction.

  • Antiport carriers: Transport two substances in opposite directions.

Gating of Channel Proteins

• Chemically gated: Controlled by intracellular messengers or extracellular ligands.

• Voltage-gated: Controlled by the electrical state of the cell.

• Mechanically gated: Controlled by physical changes like temperature or tension.

Facilitated Diffusion

• Uses a “facilitator” but has the same properties as simple diffusion.

• No energy required, stops at equilibrium.

• Examples: Sugars and amino acids using GLUT transporter.

Primary Active Transport

• Uses ATP to move solutes against their concentration gradient.

• Creates disequilibrium.

• Example: $Na^+\text{-}K^+\text{-ATPase}$

Secondary Active Transport

• Uses the kinetic energy of one molecule moving down its concentration gradient to push another against its gradient.

• Example: SGLT (Sodium Glucose Linked Transporter).

Vesicular Transport

• Used for macromolecules that are too large for protein channels.

• Phagocytosis: Cells engulf particles into phagosomes.

• Endocytosis: Membrane surface indents and forms vesicles.

  • Active process requiring ATP.

  • Can use caveolae or receptor-mediated clathrin-coated pits.

Receptor-Mediated Endocytosis and Exocytosis

• Ligand binds to membrane receptor.

• Receptor-ligand migrates to clathrin-coated pit.

• Vesicle loses clathrin coat.

• Receptors and ligands separate.

• Ligands go to lysosomes or Golgi for processing.

• Transport vesicle and cell membrane fuse (membrane recycling).

Transcytosis

• Proteins too large to enter transporters.

• Plasma proteins are concentrated in caveolae.

• Vesicles cross the cell with help from the cytoskeleton.

• Vesicle contents are released into interstitial fluid by exocytosis.

Transepithelial Transport

• Movement across epithelial cells using active and passive transport.

• Involves transport proteins like the $Na^+\text{-glucose}$
  symporter and GLUT transporter.

• Example: Glucose transport in the kidney or intestine.

Osmosis

• Movement of $H_2O$ across a membrane in response to a concentration gradient.

• Water follows solutes to dilute the more concentrated solution.

• Osmolarity: Describes the number of particles in solution.

  • 2 OsM is hyperosmotic to 1 OsM.

  • 1 OsM is hyposmotic to 2 OsM.

  • 1 OsM is isosmotic to 1 OsM.

• Water moves from hyposmotic to hyperosmotic.

Tonicity

• Describes the volume change of a cell placed in a solution.

• Describes the solution relative to the cell.

Electricity Review

• Law of conservation of electrical charges: The net charge produced is zero.

• Opposite charges attract, like charges repel.

• Separating charges requires energy.

• Conductor: Material through which charges move freely (e.g., water).

• Insulator: Material in which charges cannot move freely (e.g., phospholipid bilayer).

Membrane Potential

• Resting membrane potential is mostly due to $K^+$.

• A cell's resting membrane potential is ~ -70 mV.

• The $Na^+/K^+$ pump is important in maintaining the resting membrane potential.

Pancreatic Insulin Secretion

• Decrease in ATP opens $K^+\text{ ATPase}$ channels, maintaining resting membrane potential.

• Closing of $K^+\text{ ATPase}$ channels prevents $K^+$ leakage, which depolarizes the cell.

• Voltage-gated $$Ca^{++}$ channels open.

Key Concepts

• Law of mass balance, chemical disequilibrium, electrical disequilibrium, osmotic equilibrium.

• Transporters (carriers, channels, gated channels).

• Principles of diffusion, Fick’s law of diffusion.

• Simple diffusion and facilitated diffusion.

• Vesicular transport.

• Primary and secondary active transport.

• Exocytosis, endocytosis, phagocytosis.

• Osmosis and tonicity; water moves from hypo- to hyperosmotic solutions.

• Resting membrane potential, depolarization, repolarization, hyperpolarization.

• Conductors and insulators.

• Insulin release as an example.