Biology I - Chapter 3

Polarity and Hydrogen Bonding in Water

Water ( $\text{H}_2\text{O}$ ) molecules consist of two hydrogen atoms bonded to an oxygen atom by polar covalent bonds.
Oxygen is more electronegative than hydrogen, resulting in a partial negative charge ( $\delta-$ ) near the oxygen region and partial positive charges ( $\delta+$ ) near the hydrogen regions.
The polar nature of water allows molecules to form fragile, transient hydrogen bonds with up to four neighbouring water molecules.

Hydrogen bonding between water molecules

Emergent Properties of Water

Cohesion and Adhesion:
- Cohesion occurs when hydrogen bonds hold water molecules together, assisting in pulling water upward through plant vessels.
- Adhesion is the attraction between water and different substances, such as plant cell walls.
Surface Tension:
- Surface tension measures the force required to stretch or break the surface of a liquid.
- Water has an unusually high surface tension due to cohesive hydrogen bonding at the surface.

Spider on water surface demonstrating surface tension

Moderation of Temperature:
- Kinetic energy is the energy of motion; heat is the total kinetic energy of molecular motion, while temperature measures the average kinetic energy.
- Specific heat is defined as the heat required to change the temperature of $1\,\text{g}$ of a substance by $1\,^\circ\text{C}$ . Water has a high specific heat ( $1\,\text{cal/g/}^\circ\text{C}$ or $4.184\,\text{J/g/}^\circ\text{C}$ ), resisting temperature fluctuations because heat is absorbed to break hydrogen bonds and released when they form.
- Heat of vaporization ( $\approx 580\,\text{cal}$ per gram at room temperature) powers evaporative cooling, stabilizing temperature in organisms and aquatic bodies.
Expansion Upon Freezing:
- Water reaches its maximum density at $4\,^\circ\text{C}$ .
- At $0\,^\circ\text{C}$ , water locks into a crystalline lattice where each molecule forms stable hydrogen bonds with four partners, making ice $\approx 10\%$ less dense than liquid water.
- Floating ice insulates liquid water below, preventing aquatic ecosystems from freezing solid.

Solvent Properties of Water

A solution is a homogeneous mixture containing a solvent (dissolving agent) and a solute (dissolved substance); water is the solvent in an aqueous solution.
Water dissolves ionic compounds by forming hydration shells around individual ions, and dissolves polar molecules through hydrogen bonding.
Hydrophilic vs. Hydrophobic:
- Hydrophilic substances have an affinity for water (dominated by polar or ionic bonds).
- Hydrophobic substances lack an affinity for water (nonpolar compounds, such as oils).
- A colloid is a stable suspension of fine particles in a liquid.
Quantitative Measures:
- Molecular mass is the sum of the masses of all atoms in a molecule.
- One mole (mol) equals $6.02 \times 10^{23}$ molecules (Avogadro's number), where $6.02 \times 10^{23}\,\text{daltons} = 1\,\text{g}$ .
- Molarity ( $\text{M}$ ) is the number of moles of solute per liter of solution.

Acids, Bases, and the pH Scale

Water molecules reversibly dissociate: $\text{H}_2\text{O} \rightleftharpoons \text{H}^+ + \text{OH}^-$ (forming hydronium $\text{H}_3\text{O}^+$ and hydroxide $\text{OH}^-$ ).
In neutral water at $25\,^\circ\text{C}$ , $[\text{H}^+] = [\text{OH}^-] = 10^{-7}\,\text{M}$ .
Acids increase the $\text{H}^+$ concentration of a solution; bases decrease $\text{H}^+$ concentration directly (accepting $\text{H}^+$ ) or indirectly (releasing $\text{OH}^-$ ).
pH Scale:
- In any aqueous solution at $25\,^\circ\text{C}$ , $[\text{H}^+][\text{OH}^-] = 10^{-14}$ .
- $\text{pH} = -\log[\text{H}^+]$ .
- Neutral solutions have $\text{pH} = 7$ ; acidic solutions have $\text{pH} < 7$ ; basic solutions have $\text{pH} > 7$ .
- Each pH unit represents a tenfold change in $\text{H}^+$ concentration.

pH scale and relative concentrations of hydrogen and hydroxide ions

Buffers:
- Buffers maintain cellular pH stability by reversibly binding and releasing $\text{H}^+$ ions.
- An important biological buffer is carbonic acid: $\text{H}_2\text{CO}_3 \rightleftharpoons \text{HCO}_3^- + \text{H}^+$ .

Environmental Acidification

Ocean Acidification:
- Combustion of fossil fuels increases atmospheric $\text{CO}_2$ , about $25\%$ of which is absorbed by oceans.
- Dissolved $\text{CO}_2$ forms carbonic acid ( $\text{H}_2\text{CO}_3$ ), lowering ocean pH.
- $\text{H}^+$ ions combine with carbonate ions ( $\text{CO}_3^{2-}$ ) to form bicarbonate ( $\text{HCO}_3^-$ ), reducing carbonate availability for calcification ( $\text{CaCO}_3$ ) by corals and shelled organisms.

Acid Precipitation:
- Burning fossil fuels emits sulfur oxides and nitrogen oxides that react with atmospheric water, producing rain, snow, or fog with a $\text{pH} < 5.2$ , which damages aquatic life and soil chemistry.

Polarity and Hydrogen Bonding in Water

Polar Covalent Bonds: Water ( $\text{H}_2\text{O}$ ) consists of two hydrogen atoms bonded to an oxygen atom by polar covalent bonds. Oxygen is more electronegative than hydrogen, pulling shared electrons closer to itself.
- Analogy: Think of a water molecule like a Mickey Mouse head—the oxygen "face" carries a partial negative charge ( $\delta-$ ), while the hydrogen "ears" carry partial positive charges ( $\delta+$ ).
Hydrogen Bonding: The polar nature allows water to form fragile, transient hydrogen bonds with up to four neighboring water molecules.
- Analogy: Like runners high-fiving during a marathon—these bonds constantly break and re-form (lasting only a few trillionths of a second).
Emergent Properties of Water (Acronym: CASE):
- C - Cohesion & Adhesion:
- Cohesion: Water molecules sticking to each other via hydrogen bonds.
  - Analogy: Friends holding hands in a group hug chain.
- Adhesion: Water molecules sticking to other polar surfaces (e.g., plant cell walls).
  - Analogy: Tape sticking to a wall or water clinging to paper towels.
- Surface Tension: Measure of how difficult it is to stretch or break the liquid surface. Water's surface tension acts like an invisible stretchy skin or trampoline (allowing insects like water striders to walk on water).
- A - Ability to Moderate Temperature:
- High Specific Heat: Water absorbs or releases large amounts of heat with minimal temperature change ( $1\,\text{cal/g/}^\circ\text{C}$ ).
  - Analogy: Water acts as a thermal sponge or temperature shock absorber.
- Evaporative Cooling: As liquid evaporates, molecules with the highest kinetic energy depart.
  - Analogy: Sweating during exercise—the hottest molecules leave, cooling down the remaining surface.
- S - Solvent Versatility:
- Water is a versatile solvent dissolving hydrophilic ("water-loving", polar/ionic) solutes by surrounding them in a hydration shell.
  - Analogy: Water molecules act like polite party hosts surrounding individual guest ions (like $\text{Na}^+$ and $\text{Cl}^-$ ) to keep them comfortably separated.
- Hydrophobic ("water-fearing", nonpolar) substances like oil repel water because they cannot form hydrogen bonds.
- E - Expansion Upon Freezing:
- At $0\,^\circ\text{C}$ , water locks into a rigid 3D crystalline lattice, holding molecules further apart than in liquid form.
- Ice is about $10\%$ less dense than liquid water at $4\,^\circ\text{C}$ , allowing ice to float.
  - Analogy: Ice forms an insulating thermal blanket over lakes, preventing entire bodies of water from freezing solid.

Acids, Bases, and the pH Scale

Dissociation of Water: Water reversibly dissociates into ions: $\text{H}2\text{O} \rightleftharpoons \text{H}^+ + \text{OH}^-$ (forming hydronium $\text{H}3\text{O}^+$ and hydroxide $\text{OH}^-$ ).
- In neutral water at $25\,^\circ\text{C}$ , $[\text{H}^+] = [\text{OH}^-] = 10^{-7}\,\text{M}$ .
Acids and Bases:
- Acids: Increase the $\text{H}^+$ concentration of a solution (e.g., $\text{HCl} \rightarrow \text{H}^+ + \text{Cl}^-$ ).
- Bases: Decrease $\text{H}^+$ concentration directly (accepting $\text{H}^+$ ) or indirectly (releasing $\text{OH}^-$ ).
- Memory Trick: Acids Add $\text{H}^+$ ; Bases Bind $\text{H}^+$ .
The pH Scale:
- Formula: $\text{pH} = -\log[\text{H}^+]$ . In aqueous solution at $25\,^\circ\text{C}$ , $[\text{H}^+][\text{OH}^-] = 10^{-14}$ .
- Memory Trick: "A" comes before "B" on the number line— $\text{pH} < 7$ is Acidic, $\text{pH} = 7$ is Neutral, and $\text{pH} > 7$ is Basic.
- Analogy: The pH scale is logarithmic like the Richter scale for earthquakes. Each $1$ -unit change represents a $10\times$ difference in $\text{H}^+$ concentration (e.g., pH $3$ is $1,000\times$ more acidic than pH $6$ , not $3\times$ !).
Buffers: Substances that minimize drastic pH changes by accepting $\text{H}^+$ when in excess and donating $\text{H}^+$ when depleted (e.g., carbonic acid $\text{H}2\text{CO}3$ buffer in human blood).
- Analogy: A buffer acts like a chemical shock absorber or sponge.

Environmental Acidification

Ocean Acidification:
- Fossil fuel combustion increases atmospheric $\text{CO}_2$ , $\sim 25\%$ of which dissolves into oceans.
- Chemical path: $\text{CO}2 + \text{H}2\text{O} \rightarrow \text{H}2\text{CO}3$ (carbonic acid), lowering ocean pH.
- Extra $\text{H}^+$ reacts with carbonate ions ( $\text{CO}3^{2-}$ ) to form bicarbonate ( $\text{HCO}3^-$ ).
- Consequence: Reduces available carbonate required for calcification ( $\text{CaCO}_3$ ) by reef-building corals and shelled organisms.
- Analogy: Ocean acidification steals the construction bricks (carbonate ions) marine creatures need to build their houses (shells and reefs).
Acid Precipitation: Rain, snow, or fog with $\text{pH} < 5.2$ caused by sulfur and nitrogen oxides reacting with water, damaging aquatic ecosystems and altering soil chemistry.