BIO 110 CHAPTER 2

Atoms are the particles that make up elements; all atoms of a given element have the same chemical and physical properties.
Subatomic particles: protons (positive), neutrons (neutral), electrons (negative).
Protons and neutrons in the nucleus; electrons form a cloud around the nucleus.
Protons determine the unique chemical properties of each element.
There are $118$ known elements; $92$ occur naturally.
Hydrogen, Carbon, and Nitrogen make up $96\%$ of matter in living organisms.
Trace elements are required; essential elements constitute roughly $\frac{1}{5}$ to $\frac{1}{4}$ of natural elements.

Matter occupies space and has mass; it cycles within a system, and energy flows through a system.
Matter is different from energy; life requires both cycling of matter and flow of energy.
Elements are pure substances; compounds are substances made of two or more elements in a specific ratio with chemical bonds.
Compounds have properties different from the elements that compose them (e.g., table salt, NaCl, has properties not found in Na or Cl).
Living organisms are built from a small fraction of all elements.
We encounter compounds in daily life, not just elements; essential and trace elements vary by species.

A molecule’s shape is determined by chemical bonding; shape drives function (structure–function relationship).
Bond types: covalent (single, double, polar, nonpolar), ionic, hydrogen, and Van der Waals forces.
Covalent bonds: sharing a pair of valence electrons; single covalent bond is one pair, double bond is two pairs.
Polar covalent: unequal sharing due to differing electronegativity; nonpolar covalent: equal sharing (same element).
Example: H–H is a nonpolar covalent bond.
Ionic bonds: attraction between oppositely charged ions (cations and anions); salts form via ionic bonding (e.g., NaCl).
Hydrogen bonds: weak, noncovalent attractions between a hydrogen and electronegative atoms (usually N or O).
Van der Waals forces: weak interactions when atoms/molecules are very close.
Serotonin example: its specific structure binds to its receptor like a key fits a lock; binding enables the biological effect.

Water is polar: results from a polar covalent bond where O attracts electrons more strongly than H.
Water’s four key life-supporting properties:
- Adhesion and cohesion
- Temperature regulation
- Expansion on freezing (ice floats)
- Solvent capabilities (aqueous solutions)
Adhesion: water’s attraction to polar substances (e.g., cell walls) aiding transport and countering gravity.
Cohesion: water–water attraction supporting transport in organisms (e.g., plants).
Temperature regulation: water’s high specific heat buffers temperature changes in environments.
Expansion on freezing: ice is less dense than liquid water, so ice floats and aquatic life persists beneath.
Solvent property: polarity allows water to dissolve many substances; hydrophilic solutes interact with water, hydrophobic solutes do not; aqueous solutions consist of water as solvent.

Biological reactions are reversible and involve changes in matter’s composition.
Photosynthesis (in chloroplasts): light reactions in thylakoid membranes convert light energy to ATP and NADPH; Calvin Cycle uses NADPH to reduce CO₂ to glucose and other carbohydrates.
Cellular respiration (Krebs cycle): in mitochondria; generates ATP for cellular energy.
In summary: atoms, molecular structure, bonding, and reactions underpin biology.