Fundamental Chemistry and Water in Biology: Study Notes for BIOL 141

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Elements Essential for Life

The Four Major Elements

Living organisms are primarily composed of a small number of elements. Four elements make up approximately 96% of the mass of living matter.

Oxygen (O)
Carbon (C)
Hydrogen (H)
Nitrogen (N)

These elements are fundamental to the structure and function of biological molecules such as proteins, nucleic acids, carbohydrates, and lipids.

Example: Water (H2O) contains hydrogen and oxygen; proteins contain all four elements.

Atomic Structure and Properties

Atomic Number and Mass Number

Atoms are characterized by their atomic number and mass number:

Atomic Number: The number of protons in the nucleus of an atom. Determines the element's identity.
Mass Number: The sum of protons and neutrons in the nucleus.

Example: For an element X with atomic number 75 and mass number 78:

Atomic number = 75
Mass number = 78

Chemical Bonds in Biology

Covalent Bonds and Electronegativity

Chemical bonds are essential for the formation of biological molecules. Covalent bonds involve the sharing of electrons between atoms.

Nonpolar Covalent Bond: Electrons are shared equally between atoms with similar electronegativity.
Polar Covalent Bond: Electrons are shared unequally due to a difference in electronegativity, resulting in partial charges.

Electronegativity: The tendency of an atom to attract electrons. For example, in ammonia (NH3):

Nitrogen (N) electronegativity = 3.04
Hydrogen (H) electronegativity = 2.20
Difference = 0.84 (polar covalent bond)

Example: In NH3, nitrogen is more electronegative than hydrogen, resulting in polar covalent bonds.

The Scientific Method in Biology

Steps of the Scientific Method

The scientific method is a systematic approach to investigating biological phenomena.

Make an observation: Notice something specific in nature.
Form a question: Ask a question based on the observation.
Form hypotheses: Propose possible explanations.
Design an experiment: Plan a way to test the hypothesis.
Make a prediction and test the hypothesis: Predict outcomes and perform experiments.
Get a result: Analyze data to support or contradict the hypothesis.

Example: "Seeds will grow faster at 35°C" is a testable hypothesis.

Properties of Water

Importance and Structure of Water

Water is vital for life, covering most of Earth's surface and making up a large portion of living cells.

Water (H2O) is a polar molecule due to the higher electronegativity of oxygen compared to hydrogen.
Oxygen attracts shared electrons more strongly, resulting in partial negative (O) and partial positive (H) charges.

Example: Water's polarity allows it to form hydrogen bonds with other water molecules.

Hydrogen Bonds

Hydrogen bonds are weak, temporary bonds between polar molecules, often involving oxygen or nitrogen bound to hydrogen.

Hydrogen bonds are responsible for many of water's unique properties.
They constantly break and reform, lasting only fractions of a second.

Example: Hydrogen bonding gives water high surface tension and allows for cohesion and adhesion.

Cohesion and Adhesion

Cohesion: Water molecules stick to each other due to hydrogen bonding.
Adhesion: Water molecules stick to other surfaces.

Example: Water droplets forming on a leaf demonstrate cohesion; water climbing up plant vessels shows adhesion.

Water as the Universal Solvent

Water dissolves many substances due to its polarity.

Solution: Homogeneous mixture of substances.
Solute: The substance dissolved.
Solvent: The dissolving agent (water in biological systems).

Example: Table salt (NaCl) dissolves in water to form a salt solution.

Hydrophilic, Hydrophobic, and Amphipathic Molecules

Hydrophilic: Substances with an affinity for water; dissolve easily (e.g., ions, polar molecules).
Hydrophobic: Substances that repel water; do not dissolve (e.g., nonpolar molecules).
Amphipathic: Molecules with both polar and nonpolar regions (e.g., fatty acids, phospholipids).

Example: Phospholipids form cell membranes due to their amphipathic nature.

Dissociation of Water and pH

Water Ionization

Water can dissociate into ions:

Hydrogen ion (H+)
Hydroxide ion (OH-)

The reaction is:

At equilibrium in pure water, the concentrations of H+ and OH- are equal, resulting in a neutral solution (pH = 7).

Acids, Bases, and pH Scale

Acids and bases alter the concentration of H+ and OH- ions in solution.

Acid: Increases H+ concentration (e.g., HCl dissociates to H+ and Cl-).
Base: Reduces H+ concentration, often by increasing OH- (e.g., NaOH dissociates to Na+ and OH-).

The pH scale measures H+ concentration:

Pure water: , so pH = 7.

Acidic solutions: pH < 7 (higher H+ concentration)
Basic solutions: pH > 7 (lower H+ concentration)

Each unit change in pH represents a tenfold change in H+ concentration.

Buffers in Biological Systems

Buffers help maintain stable pH in biological systems by binding excess H+ or OH- ions.

Example: Bicarbonate (HCO3-) acts as a buffer in blood, soaking up excess H+ ions and minimizing pH changes.

Amphipathic Molecules and Biological Structures

Role in Cell Membranes

Amphipathic molecules, such as phospholipids, have both hydrophilic (water-attracting) and hydrophobic (water-repelling) regions.

Hydrophilic head interacts with water.
Hydrophobic tail avoids water.

This dual nature allows them to form bilayers, which are the basis of cell membranes and vesicles.

Example: The lipid bilayer of cell membranes is formed by amphipathic phospholipids.

Summary Table: Water and Its Properties

Property	Description	Biological Importance
Polarity	Unequal sharing of electrons; partial charges	Allows hydrogen bonding, solvent abilities
Hydrogen Bonding	Weak bonds between water molecules	High surface tension, cohesion, adhesion
Solvent Properties	Dissolves polar and ionic substances	Facilitates biochemical reactions
Dissociation	Forms H+ and OH- ions	Basis for pH and acid-base balance
Buffering	Resists changes in pH	Maintains homeostasis in organisms

Additional info: Some context and terminology have been expanded for clarity and completeness, including definitions and examples of acids, bases, buffers, and amphipathic molecules.