Science & The Nature of Biology

What is Science?

Science is a systematic approach to understanding the natural world through observation, experimentation, and evidence-based reasoning.

• Science: The agreement that arguments are won with evidence.

• Evidence: Repeatable, measurable observations of the natural world.

• Consensus: Science progresses as agreement is reached among scientists.

• Example: Scientists no longer debate whether the Earth is flat, which allows them to study new problems.

Rules for Doing Science

• Rely only on cold evidence, not what people tell you.

• No "magic"—only natural explanations.

• Take nobody's word for it (test ideas yourself).

Science vs. Non-Science

• Science: Explains phenomena through natural causes and evidence.

• Non-science: Relies on magic or untestable explanations.

• Scientific worldview: Assumes that material phenomena can be explained.

Origin of Matter

• Big Bang: 13.8 billion years ago, all matter was created.

• Within 1 second: Protons, neutrons, electrons formed.

• 3-20 minutes: Hydrogen and helium nuclei formed.

• Atoms formed ~380 million years later.

• "We are 1% hydrogen by weight," meaning that part of you is as old as the universe.

Course Goals (Thinking Like a Biologist)

• Use a mechanical perspective: Life explained by atoms and energy.

• Understand how "stupid molecules" make life without violating the 2nd Law of Thermodynamics.

• Recognize that function arises from structure.

• Appreciate scales of time/space in biology.

Atoms, Elements & Isotopes

Matter & Atoms

All matter is composed of atoms, which are the smallest units of matter that retain the properties of an element.

• Atoms: Smallest unit of matter; consists of protons, neutrons, and electrons.

• Protons (p): Positively charged particles.

• Neutrons (n): Neutral particles.

• Electrons (e-): Negatively charged particles, found in a "cloud" around the nucleus.

• Atomic mass: Protons + neutrons.

Elements

• Element: Substance with only one type of atom.

• Atomic number: Number of protons.

• Atomic mass: Protons + neutrons.

Isotopes

Isotopes are atoms of the same element with different numbers of neutrons.

• Stable isotopes: Do not decay.

• Radioisotopes: Decay, releasing energy and particles (radioactivity).

• Uses: Radioactive isotopes can be used to date fossils and rocks, and in medicine (e.g., radioactive glucose to detect cancer).

• Half-life: Time it takes for half of a radioactive sample to decay.

Elements of Life

• Only ~25% of natural elements are essential for life.

• CHNOPS: Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur = ~96% of living matter.

• Trace elements: Needed in very small amounts (e.g., iodine, iron).

• Example: Iodine deficiency affects thyroid; iron deficiency causes anemia.

Compounds & Chemical Bonds

Compounds

Compounds are substances composed of two or more elements in a fixed ratio, with properties different from the individual elements.

• Compound: Substance of two or more elements in a fixed ratio (e.g., NaCl, H2O).

• Compounds have emergent properties different from their constituent elements.

• Example: Na (toxic gas) + Cl (toxic gas) = NaCl (edible salt).

Valence Electrons & Stability

• Valence electrons: Outer shell electrons; determine reactivity.

• Atoms with incomplete shells are unstable; seek bonds to achieve stability.

Types of Bonds

• Ionic bond: Electrons transferred from one atom to another, forming ions (e.g., NaCl).

• Covalent bond: Electrons shared between atoms.

• Single bond: 1 pair shared; Double bond: 2 pairs shared.

• Polar covalent: Unequal sharing, partial charges (e.g., H2O).

• Nonpolar covalent: Equal sharing.

• Hydrogen bond: Weak attraction between polar molecules.

Electronegativity

• Ability of an atom to attract shared electrons.

• Important for DNA, proteins, and water properties.

Polarity, Water & Its Properties

Polarity of Water

Water is a polar molecule due to the unequal sharing of electrons between oxygen and hydrogen, leading to partial charges and hydrogen bonding.

• H2O is polar: δ- on O, δ+ on H.

• Leads to hydrogen bonding between molecules.

Four Emergent Properties of Water

1. Moderates Temperature: High specific heat stabilizes climate and body temperature.

2. Cohesion & Adhesion: Cohesion is attraction between water molecules (surface tension); adhesion is attraction to other surfaces (capillary action).

3. Ice Floats: Solid water is less dense than liquid water; life survives under ice.

4. Versatile Solvent: Dissolves ions and polar compounds; surrounds solutes with "hydration shells."

Hydrophilic vs. Hydrophobic

• Hydrophilic: Water-loving (polar, dissolves in water).

• Hydrophobic: Water-repelling (nonpolar, repels water, e.g., oil).

Acids, Bases & pH

Acids, Bases & pH

The pH scale measures the concentration of hydrogen ions in a solution, indicating its acidity or basicity.

• pH Scale: 0–14.

• Acidic: pH < 7.

• Neutral: pH = 7.

• Basic: pH > 7.

• Formula:

• Example: [H+] = 10-3 M → pH = 3.

• Biological fluids: typically between pH 6–8.

• Ocean acidification: CO2 + H2O → carbonic acid → lowers ocean pH.

Carbon Chemistry

Carbon Chemistry

Carbon is the backbone of organic molecules due to its ability to form four covalent bonds, allowing for a diversity of stable structures.

• Can form chains, rings, double/triple bonds.

• Basis of organic chemistry.

Isomers

• Structural isomers: Different arrangement of atoms.

• Cis-trans isomers: Same covalent bonds, different spatial orientation.

• Enantiomers: Mirror images (important in drugs, biology).

Functional Groups

Functional groups are specific groups of atoms within molecules that determine the chemical properties and reactions of those molecules.

1. Hydroxyl (–OH)

2. Carbonyl (C=O)

3. Carboxyl (–COOH)

4. Amino (–NH2)

6. Phosphate (–PO4)

7. Methyl (–CH3)

Biological Macromolecules

Biological Macromolecules

Biological macromolecules are large, complex molecules essential for life, built from smaller subunits called monomers.

• Carbohydrates: Sugars, energy storage.

• Proteins: Amino acids, structure, enzymes.

• Nucleic acids: DNA/RNA, genetic info.

• Lipids: Fats, membranes, hormones (not polymers).