2.3-2.4

Cellular Synthesis, Degradation, and Enzymatic Kinetics

• Dehydration Synthesis Reactions:

  • Cellular synthesis reactions that build larger macromolecules from smaller subunits (monomers) are classified as dehydration synthesis reactions.

  • Mechanism: When two monomers are joined together, one monomer releases a hydroxyl group ($\text{-OH}$) and the second monomer releases a hydrogen atom ($\text{-H}$).

  • Byproduct: The released hydroxyl group and hydrogen atom combine to form a molecule of water ($\text{H}_2\text{O}$).

  • Summary: Water is removed from the reactants in order to covalently link monomers into a polymer chain.

• Hydrolysis Reactions (Degradation):

  • Metabolic reactions that break complex molecules down into smaller components are termed degradation or hydrolytic reactions.

  • Etymology: "Hydro" refers to water, and "lysis" denotes splitting or breaking apart.

  • Mechanism: A water molecule ($\text{H}_2\text{O}$) is added to the system. One monomer in the polymer chain accepts a hydroxyl group ($\text{-OH}$), while the adjacent monomer accepts a hydrogen atom ($\text{-H}$).

  • Summary: The addition of water splits the covalent bond linking the monomers, operating as the exact reverse process of dehydration synthesis.

• Factors Influencing Chemical Reaction Rates:

  • Temperature: Increasing temperature increases molecular kinetic energy, generally accelerating reaction rates.

  • Pressure: Lowering the ambient pressure in a system decreases the reaction rate because molecules disperse. Raising pressure forces reactant molecules closer together, increasing collision frequency and reaction rate.

• Enzyme Function and Energy Dynamics:

  • Biochemical Identity: Enzymes are specialized biological molecules, predominantly composed of proteins.

  • Catalytic Activity: Enzymes act as biological catalysts that accelerate chemical reaction rates without being consumed.

  • Activation Energy: Enzymes function by lowering the activation energy—the initial energy barrier required for reactants to reach a spontaneous transition state.

  • Analogy: Reaching activation energy is analogous to pushing a object over the top of a hill; once the summit is cleared, the reaction proceeds spontaneously.

• Definition of Organic Compounds:

  • An organic compound is defined by the presence of carbon ($\text{C}$) covalently bonded to at least one hydrogen atom ($\text{-H}$).

  • Inorganic Counterexample: Carbon dioxide ($\text{CO}_2$) contains carbon, but lacks hydrogen, classifying it as inorganic.

  • Simplest Organic Compound: Methane ($\text{CH}_4$) represents the simplest complete organic molecule. It features a central carbon atom displaying tetravalence (four valence electrons) bonded covalently to four surrounding hydrogen atoms.

Organic Compounds, Water Properties, and Respiratory Physiology

• Cohesion and Adhesion in Water:

  • Cohesion: The attraction of water molecules to other water molecules mediated through intermolecular hydrogen bonds.

  • Adhesion: The attraction of water molecules to other polar or charged surfaces. The slightly negative oxygen atom of water is electrostatically attracted to positively charged surfaces, while the slightly positive hydrogen atoms are attracted to negatively charged surfaces.

• Surface Tension Physics and Biomechanical Impacts:

  • Intermolecular hydrogen bonding across the surface layer of a body of water creates high surface tension, causing the liquid surface to resist external forces much like a solid sheet.

  • Diving Physics: Entering a body of water requires breaking surface hydrogen bonds. Divers minimize body surface area exposure by entering strictly vertically (feet-first or head-first). A "belly flop" exposes maximal body surface area, requiring an enormous quantity of hydrogen bonds to break simultaneously upon impact.

  • Competitive Diving Evaluation: Olympic divers are scored in part on splash minimization; less splash signifies a precise, perpendicular entry that displaced minimal water volume.

• Physiological Role of Surface Tension in Breathing (Ventilation):

  • Pleural fluid surface tension causes the outer membrane of the lungs to adhere directly to the internal surface of the thoracic cavity wall.

  • Inhalation Mechanism: During inhalation, intercostal muscles between the ribs lift the thoracic cage upward and outward, while the diaphragm contracts downward.

  • Volume Expansion: Surface tension prevents the lungs from detaching from the expanding chest wall. As the thoracic wall expands, it pulls the lungs outward, increasing total pulmonary volume.

  • Pressure Gradients: The increase in lung volume creates a negative pressure relative to external atmospheric pressure, pulling ambient air into the respiratory passages.

  • Dry Cavity Hypothetical: If the thoracic cavity were dry and devoid of surface-tension-mediated fluid adhesion, expanding the chest wall would fail to enlarge lung volume, preventing pulmonary ventilation.

Specific Heat Dynamics and Climatological Thermodynamics

• Heat Sink Properties and Specific Heat Definition:

  • Water functions as an environmental heat sink, absorbing and releasing massive quantities of heat energy with minimal changes in its own measured temperature.

  • Specific Heat Definition: The precise quantity of heat energy required to raise the temperature of $1\,\text{g}$ of a substance by $1^\circ\text{C}$, or conversely, the energy released when $1\,\text{g}$ cools by $1^\circ\text{C}$.

  • Microscopic Mechanism: Temperature measures molecular kinetic motion. Water possesses a high specific heat because absorbed thermal energy is initially consumed breaking and reforming hydrogen bonds continuously. Only after substantial energy input breaks these interactions do individual water molecules accelerate their kinetic motion to register a measurable temperature increase.

• Regional Climate Moderation Examples:

  • Portland, Oregon vs. Portland, Maine: Both cities lie at similar northern latitudes, yet experience vastly different winter climates.

  • Portland, Oregon Winter: Average high temperatures sit around $38^\circ\text{F}$, with average lows in the high $20\text{s}^\circ\text{F}$ (a mild winter relative to latitude).

  • Portland, Maine Winter: Average high temperatures remain in the lower $20\text{s}^\circ\text{F}$, with average lows dropping to around $10^\circ\text{F}$ or below.

• Meteorological Mechanisms of Temperature Control:

  • Prevailing Air Patterns: Continental US weather patterns move predominantly from west to east, driven by cold Arctic air streams from the north and warm air streams from the south.

  • Pacific Ocean Convection (West Coast): During summer, the Pacific Ocean absorbs vast amounts of heat. In winter, cold Arctic air moving eastward over the warm Pacific Ocean receives transferred thermal energy via convection. The warmed air blows across Portland, Oregon, maintaining mild winter temperatures.

  • Continental Tundra Dynamics (East Coast): Cold Arctic air traveling toward Portland, Maine travels across Canadian land masses and tundra. Because soil moisture in the tundra is frozen (permafrost), the land cannot transfer thermal heat to the air mass. The cold air remains freezing as it reaches the East Coast. Ocean warmth off the East Coast is blown away from land by west-to-east winds.

  • Midwest Severe Winters: The interior Midwest experiences severe winters because incoming Arctic air masses travel exclusively over cold, frozen land without interacting with warm oceanic heat sinks.

  • South Texas / Laredo Microclimates: Cold atmospheric fronts traveling south through Texas (causing snow in San Antonio or Cotulla) often stall or retreat before reaching Laredo. Tropical high-pressure systems sitting over South Texas force low-pressure cold air fronts upward and northward, preserving elevated regional temperatures.

Aqueous Solutions, Colloidal Suspensions, and Emulsification Mechanisms

• Solvent Capabilities and Limitations:

  • Water is the essential medium for life and acts as a versatile biological solvent, but it is not a universal solvent. If water dissolved all substances, living organisms (which consist of approximately $70\%$ water) would instantly dissolve their own cell membranes and structural proteins.

  • Solution Structure: A solution consists of a liquid solvent containing fully dissolved solute particles.

  • Polarity Rules: Water is polar and readily dissolves other polar substances (such as sugars, ionic salts, and hydrophilic proteins).

• Processing Nonpolar Lipids (Emulsification):

  • Lipids (fats, oils, steroids) are nonpolar and hydrophobic; they do not dissolve in water.

  • Bile Salts: The liver synthesizes and secretes bile salts into the digestive tract to act as emulsifiers.

  • Mechanism of Emulsification: Emulsifying agents do not alter the chemical polarity of lipids. Instead, they possess dual affinity: one domain binds to nonpolar lipids while another domain binds to polar water molecules. This prevents nonpolar lipids from coalescing and keeps them suspended within an aqueous fluid.

  • Everyday Emulsifier Analogies:

    • Soap: Acts as an emulsifier to bind nonpolar grease to polar wash water.

    • Salad Vinaigrettes: Mixing oil and vinegar forms a temporary mixture that separates rapidly. Adding an emulsifying agent like Dijon mustard or egg yolk creates a stable emulsion that resists separation.

  • Lipid Transport in Circulation: Nonpolar steroid hormones require amphipathic transport proteins to travel through aqueous blood plasma without separating out. Dietary fats absorbed in the intestine enter lymphatic lacteals before entering the main bloodstream.

• Dissociation of Ionic Salts:

  • When solid ionic crystals (such as sodium chloride, $\text{NaCl}$) are added to water, water molecules dissolve the crystal by forming hydration shells around individual ions.

  • Dissociation: Water splits the ionic lattice into discrete sodium ions ($\text{Na}^+$) and chloride ions ($\text{Cl}^-$).

  • Significance: Ions retain their full electrostatic charge in solution, acting as electrolytes essential for generating action potentials and electrical signals across cell membranes.

• Classifications of Biological Liquid Mixtures:

  • Solution: A homogeneous mixture where polar solutes completely dissolve into individual molecules or ions within the solvent.

  • Colloid: A stable mixture containing large macromolecular particles (such as suspended proteins) that remain dispersed throughout the liquid without settling.

  • Suspension: A heterogeneous mixture containing large particulate components suspended in a liquid. If left unagitated, suspended particles settle out over time due to gravity.

  • Blood Composition: Whole blood is a suspension. Blood cells (red blood cells, white blood cells, platelets) do not dissolve in aqueous blood plasma because cell membranes are composed of nonpolar phospholipid bilayers. Centrifuging a blood sample separates the cell suspension from the liquid plasma.

Acid-Base Chemistry, Dissociation Dynamics, and Environmental Acidification

• Digestive Metabolism and Hangover Physiology:

  • Digestive catabolism relies on hydrolytic reactions, requiring systemic water to break nutrient bonds.

  • Alcohol consumption causes systemic dehydration.

  • Consuming dense foods while dehydrated forces the body to divert remaining systemic water toward digestive hydrolysis, worsening cellular dehydration.

  • Treatment: Consuming water paired with dissociated electrolytes (such as Pedialyte) restores hydration and cellular ion balance.

• Autoionization of Water and the pH Scale:

  • Water molecules spontaneously undergo reversible autoionization:         $\text{H}_2\text{O} \rightleftharpoons \text{H}^+ + \text{OH}^-$

  • A water molecule that loses a proton becomes a negatively charged hydroxide ion ($\text{OH}^-$).

  • The released proton binds to another water molecule to form a positively charged hydronium ion ($\text{H}_3\text{O}^+$), represented in chemical notation simply as a hydrogen proton ($\text{H}^+$).

  • pH Scale Range: Ranges from $0$ to $14$.

    • $\text{pH } 7.0$: Neutral state (pure water), where the ratio of $\text{H}^+$ protons to $\text{OH}^-$ ions is exactly equal ($1:1$).

    • $\text{pH } < 7.0$: Acidic state, where $\text{H}^+$ protons outnumber $\text{OH}^-$ ions.

    • $\text{pH } > 7.0$: Basic or Alkaline state, where $\text{OH}^-$ ions outnumber $\text{H}^+$ protons.

  • Logarithmic Nature: The pH scale is logarithmic. A single whole-unit shift on the pH scale represents a tenfold change in $\text{H}^+$ concentration, representing thousands-fold shifts in actual proton activity across multi-unit ranges.

• Acidic pH Values and Chemical Corrosiveness:

  • Milk, Urine, Saliva: Slightly acidic, ranging from $\text{pH } 6.3$ to $\text{pH } 6.6$

  • Black Coffee: Acidic, at $\text{pH } 5.0$

  • Soda and Tomato Juice: Highly acidic, ranging from $\text{pH } 2.5$ to $\text{pH } 3.5$ (tomatoes sit at ~$\text{pH } 2.5$ and frequently trigger gastroesophageal acid reflux).

  • Battery Acid / Hydrochloric Acid: Extremely corrosive, sitting at $\text{pH } 0.0$

  • Corrosive Mechanism: Concentrated acids act as corrosive agents because excess $\text{H}^+$ protons disrupt intermolecular hydrogen bonding within organic materials, degrading their structural integrity.

  • Polytetrafluoroethylene / Styrofoam Degradation: Squeezing highly acidic citrus (lime juice) onto a Styrofoam plate causes the acid to visibly eat away and degrade the polymer matrix.

  • Tissue Dissolution Realities: Dissolving organic tissue (such as human remains) using strong acids like hydrofluoric acid or hydrochloric acid is extremely slow and inefficient. Concentrated industrial acids are strictly regulated by chemical manufacturers with monitored supply chains, preventing off-the-shelf bulk purchases at retail stores.

• Atmospheric Pollution, Acid Rain, and Ocean Acidification:

  • Normal Rainwater: Unpolluted rain is naturally slightly acidic (around $\text{pH } 5.6$) because ambient atmospheric carbon dioxide ($\text{CO}_2$) reacts with atmospheric water vapor ($\text{H}_2\text{O}$) to form weak carbonic acid ($\text{H}_2\text{CO}_3$).

  • Acid Rain: Defined as precipitation dropping below $\text{pH } 5.6$ (typically $\text{pH } 4.6$ or lower).

  • Cause: Excess industrial emissions of carbon dioxide significantly increase atmospheric carbonic acid concentrations.

  • Ecological Damage: Acid rain disrupts cellular hydrogen bonds within plant foliage, causing severe forest degradation and plant death.

  • Ocean Acidification: Oceans absorb excess atmospheric $\text{CO}_2$, forming carbonic acid and lowering ocean water pH.

  • Coral Bleaching: Corals are sessile, colonial animals related to jellyfish that secrete calcium carbonate ($\text{CaCO}_3$) to build hard exoskeletons. Ocean acidification kills the living coral animal colonies. The dead colonies leave behind white calcium carbonate skeletons, resulting in coral bleaching.

Physiological Buffering Systems, Blood Homeostasis, and Caustic Reactivity

• Alkaline pH Examples and Blood Homeostasis:

  • Seawater: Slightly alkaline, at $\text{pH } 8.0$

  • Baking Soda: Alkaline, at $\text{pH } 9.5$ (used to neutralize acid spills).

  • Human Blood Plasma: Strictly maintained at $\text{pH } 7.4$

• Pathologies of Blood pH Imbalance:

  • Blood Alkalosis: Occurs if blood plasma pH rises above $\text{pH } 7.4$ to values such as $\text{pH } 7.5$ or $\text{pH } 7.6$. Left uncorrected, severe alkalosis causes death.

  • Blood Acidosis: Occurs if blood plasma pH drops below $\text{pH } 7.4$ to values such as $\text{pH } 7.3$ or $\text{pH } 7.2$. Left uncorrected, severe acidosis causes death.

• The Bicarbonate Buffer System:

  • Carbon dioxide ($\text{CO}_2$) produced as metabolic waste during cellular respiration dissolves into blood plasma, forming bicarbonate ions ($\text{HCO}_3^-$).

  • Buffer Function: Bicarbonate ions function as biological buffers that resist shifts in systemic pH.

  • Mechanism: If blood plasma becomes too acidic, bicarbonate ions accept excess $\text{H}^+$ protons. If blood plasma becomes too alkaline, the system donates $\text{H}^+$ protons, keeping physiological blood pH stable at $\text{pH } 7.4$

• Caustic Bases and Reactivity:

  • High Alkaline Extreme: Drain cleaners and caustic lye/salts sit at the upper limit of the scale (up to $\text{pH } 14.0$

  • Caustic Reactivity: High-pH bases disrupt hydrogen bonds in organic tissue as aggressively as strong acids, rapidly dissolving biological matter.

  • Retail Availability: Unlike strictly controlled industrial acids, commercial caustic bases (such as household drain cleaners) can be purchased in volume across multiple retail stores without special regulatory accounting.