Biochemistry Study Notes: Enzyme Activity, Metabolic Pathways, Diffusion & Membrane Transport sep 5

Enzyme Structure and Active Sites

• The function of an enzyme is dictated by its structure
• Each enzyme has a characteristic 3D shape or conformation
• Pockets in the enzyme serve as active sites

Enzyme Activity Rate

• Activity is measured by the rate at which substrate is converted to product
• Influences on rate include:
  • Temperature
  • pH
  • Concentration of cofactors and coenzymes
  • Concentration of enzyme and substrate
  • Possible stimulatory or inhibitory effects of products on enzyme function

Effects of Temperature

• Increasing temperature raises reaction rate up to a point
• The rate increases until a few degrees above body temperature
• Beyond this point, the enzyme becomes denatured and loses activity

Effects of pH

• Enzymes have a pH optimum where activity is peak
• pH changes cause conformational changes in enzymes
• The optimum pH reflects the environment in which the enzyme operates (e.g., stomach, saliva, small intestine)

Metabolic Pathways

• Most reactions are linked in a chain or web called a metabolic pathway
• Pathways begin with an initial substrate and end with a final product
• Many enzymatic steps occur along the way
• Example schematic (conceptual):
  • Initial substrate A → (Enz1) → B → (Enz2) → C → (Enz3) → D → (Enz4) → E → (Enz5) → F (final product)
  • Intermediates are produced along the way

Branched Metabolic Pathways

• Few metabolic pathways are strictly linear; most have branches
• Branching produces several possible end products
• Example schematic (conceptual):
  • A → Enz1 → Intermediates → Enz2 → B
  • Branches: Enz4' and Enz5' lead to final products F' and E'
  • Additional branches: Enz4, Enz5 lead to D, C, and E

End Product Inhibition

• End product inhibition occurs when the final product inhibits an enzyme earlier in the pathway
• This regulatory mechanism helps control flux through the pathway
• Inhibition occurs as the final product accumulates, shifting pathway dynamics

Glycolysis – Key Steps and Enzymes

• Glucose → Glucose-6-phosphate via Hexokinase
• Glucose-6-phosphate → Fructose-6-phosphate via Phosphoglucose isomerase
• Fructose-6-phosphate → Fructose-1,6-bisphosphate via Phosphofructokinase
• Fructose-1,6-bisphosphate → Dihydroxyacetone phosphate (DHAP) + Glyceraldehyde-3-phosphate (G3P) via Aldolase
• DHAP ↔ G3P interconversion via Triose phosphate isomerase
• G3P → 1,3-bisphosphoglycerate via Glyceraldehyde-3-phosphate dehydrogenase (NAD+ → NADH + H+)
• 1,3-bisphosphoglycerate → 3-phosphoglycerate via Phosphoglycerate kinase (ATP production)
• 3-phosphoglycerate → 2-phosphoglycerate via Phosphoglycerate mutase
• 2-phosphoglycerate → Phosphoenolpyruvate (PEP) via Enolase
• PEP → Pyruvate via Pyruvate kinase (ATP production)
• Key energy carriers noted in the diagram:
  • NAD+ to NADH at the G3P dehydrogenase step
  • ATP and ADP changes at steps involving phosphoglycerate kinase and pyruvate kinase
• Overall implication: glycolysis converts glucose to pyruvate with generation of energy carriers (ATP, NADH)

Membrane and Epithelial Transport

• (Content references membrane transport topics; see diffusion and transport sections below for details)

Body Fluids Distribution

• 67% of body water is intracellular (inside cells; intracellular compartment)
• 33% is extracellular
  • Of extracellular water, 7% is in blood plasma
  • 26% is interstitial fluid (tissue fluid) that connects intracellular fluid with the blood plasma
• These distributions reflect compartmentalization vital for physiological processes

Entropy (ΔS)

• Entropy is the amount of disorder a reaction creates
• Entropy increases as systems become more disordered
• Notation: ΔS; ΔS > 0 indicates increased disorder

Exergonic and Endergonic Processes

• Exergonic processes are energy-yielding and occur spontaneously: $riangle G < 0$
• Endergonic processes require energy and do not occur spontaneously under the specified conditions: $riangle G > 0$

Magnitude and Direction of Diffusion

• Diffusion magnitude and direction depend on concentration gradient
• Definitions:
  • Compartment 1 (high solute concentration) to Compartment 2 (low solute concentration)
  • One-way flux and net flux arise from the gradient
• Equilibrium is reached when concentrations are equal; no net diffusion
• Notation: Net flux represents the overall movement after considering opposing forces

Diffusion of a Solute

• Higher concentration → lower concentration leads to net diffusion (a)
• Equal concentrations lead to no net diffusion (b)

Osmosis

• Movement of water across a selectively permeable membrane
• Water moves from areas of higher water concentration (lower solute concentration) to lower water concentration (higher solute concentration)
• Illustrated with a concentrated sugar solution and a dilute sugar solution across a selective membrane

Diffusion Across a Membrane (Dye Diffusion Demonstration)

• Diffusion of dye molecules across a membrane demonstrates passage through or around the membrane
• Equilibration occurs when concentrations on both sides are equal

Cellular Membranes

• Structure includes lipid bilayer, embedded proteins, and carbohydrate chains on the extracellular surface
• Inside the cell is the cytoplasm

Diffusion Factors

• Gradient magnitude drives diffusion: bigger gradient → faster diffusion
• Temperature: higher temp → greater kinetic energy and diffusion rate
• Surface area: more surface area → greater rate of diffusion
• Permeability: depends on solute size (smaller diffuses more easily)
• Solute polarity/charge: “like dissolves like” affects solubility and diffusion across membranes

Plasma Membrane Transport

• The plasma membrane is selectively permeable
• It allows some molecules to cross while excluding others

Passive vs. Active Transport

• Passive Transport
  • Gradient is favorable
  • If the membrane is permeable, diffusion occurs via SIMPLE diffusion
  • If the membrane is non-permeable, diffusion occurs via FACILITATED diffusion (carriers or channels)
• Active Transport
  • Moves substances against a gradient
  • Requires ATP hydrolysis
  • Requires a facilitator (carrier or pump) to move the molecule