Biology Foundations: Chemistry, Macromolecules, Cells, and Scientific Inquiry

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Elements, Atoms, and Atomic Structure

Essential Elements of Life

Essential elements: About 20–25% of the 92 natural elements are required for life.
Major elements: Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter.
Secondary elements: Calcium, phosphorus, potassium, and sulfur comprise most of the remaining 4%.
Trace elements: Required by organisms in only minute quantities (e.g., magnesium, chlorine, sodium).

Atoms and Subatomic Particles

Atom: The smallest unit of matter that retains the properties of an element.
Matter: Anything that takes up space and has mass; all matter is composed of atoms.
Nucleus: Contains protons (positive charge) and neutrons (neutral).
Electrons: Form a "cloud" of negative charge around the nucleus.
Mass units: Neutron and proton mass are nearly identical, measured in daltons (atomic mass units).
Atoms are electrically neutral when the number of protons equals the number of electrons.

Atomic Number, Isotopes, and Atomic Mass

Atomic number: Number of protons in an atom; defines the element.
Isotopes: Atoms of the same element with different numbers of neutrons (e.g., Carbon-12 vs. Carbon-14).
Radioactive isotopes: Unstable; decay spontaneously, emitting energy and/or subatomic particles.
Half-life: Time required for half the atoms of a radioactive sample to decay.
Atomic mass: Sum of protons and neutrons.
Weight: Force exerted on a substance by gravity (differs from mass).

Electron Shells, Orbitals, and Valence Electrons

Electron shells: Energy levels where electrons reside; first shell holds 2 electrons, second and third hold up to 8 each.
Valence electrons: Electrons in the outermost shell; determine chemical reactivity.
Octet rule: Atoms are most stable with a full outer shell (usually 8 electrons).

Ions and Oxidation-Reduction

Ions: Atoms with unequal numbers of protons and electrons.
Cation: More protons than electrons; positive charge.
Anion: More electrons than protons; negative charge.
Oxidation: Loss of electrons.
Reduction: Gain of electrons.

Chemical Bonds and Molecular Structure

Chemical Bonds

Ionic bonds: Formed when electrons are transferred from one atom to another (e.g., NaCl).
Covalent bonds: Atoms share pairs of electrons.
Nonpolar covalent: Equal sharing of electrons (e.g., H2, O2).
Polar covalent: Unequal sharing due to differences in electronegativity (e.g., H2O).
Hydrogen bonds: Weak attractions between a hydrogen atom covalently bonded to one electronegative atom and another electronegative atom (important in water, DNA, proteins).

Molecules, Compounds, and Isomers

Molecule: Group of atoms held together by chemical bonds.
Compound: Molecule composed of two or more different elements.
Isomers: Compounds with the same molecular formula but different structures and properties.
Structural isomers: Different covalent arrangements.
Cis-trans isomers: Same covalent bonds, different spatial arrangements.
Enantiomers: Mirror images; often only one is biologically active.

Water Chemistry and Properties

Emergent Properties of Water

Cohesion: Water molecules stick to each other (surface tension).
Adhesion: Water molecules stick to other substances (meniscus formation).
High specific heat: Water resists temperature changes; moderates climate.
High heat of vaporization: Requires much energy to evaporate; enables evaporative cooling.
Expansion upon freezing: Ice is less dense than liquid water; floats and insulates aquatic life.
Versatility as a solvent: Dissolves many substances due to polarity and hydrogen bonding.

Hydrophilic and Hydrophobic Substances

Hydrophilic: Affinity for water; dissolve easily (e.g., salts, sugars).
Hydrophobic: Repel water; do not dissolve (e.g., oils, fats).

pH, Acids, Bases, and Buffers

pH scale: Measures hydrogen ion concentration; ranges from 0 (acidic) to 14 (basic), with 7 as neutral.
Acids: Increase H+ concentration; pH < 7.
Bases: Decrease H+ concentration (increase OH-); pH > 7.
Buffers: Maintain stable pH by absorbing or releasing H+ ions; essential for biological systems (e.g., blood).

Water Chemistry Equations

Fahrenheit to Celsius:
Celsius to Fahrenheit:

Macromolecules: Structure and Function

Overview of Macromolecules

Four main types: Carbohydrates, lipids, proteins, nucleic acids.
Monomers: Small building blocks (e.g., monosaccharides, amino acids, nucleotides).
Polymers: Long chains of monomers (e.g., polysaccharides, polypeptides, nucleic acids).
Dehydration synthesis: Joins monomers by removing water.
Hydrolysis: Breaks polymers by adding water.

Carbohydrates

Monosaccharides: Simple sugars (e.g., glucose, fructose, galactose).
Disaccharides: Two monosaccharides joined (e.g., sucrose, lactose, maltose).
Polysaccharides: Many monosaccharides (e.g., starch, glycogen, cellulose, chitin).
Functions: Energy storage (starch, glycogen), structure (cellulose, chitin).

Lipids

Fats and oils: Glycerol + fatty acids; energy storage, insulation, cushioning.
Saturated fatty acids: No double bonds; solid at room temperature (e.g., butter).
Unsaturated fatty acids: One or more double bonds; liquid at room temperature (e.g., olive oil).
Trans fats: Artificially hydrogenated; associated with health risks.
Phospholipids: Glycerol + 2 fatty acids + phosphate; form cell membranes (bilayer structure).
Steroids: Four fused rings; include cholesterol, hormones (testosterone, estrogen).

Proteins

Amino acids: 20 types; contain amino group, carboxyl group, and variable R group.
Peptide bonds: Link amino acids into polypeptides.
Levels of structure:
- Primary: Sequence of amino acids.
- Secondary: Alpha-helix (-helix), beta-pleated sheet (-sheet); stabilized by hydrogen bonds.
- Tertiary: 3D folding due to R group interactions.
- Quaternary: Multiple polypeptide chains (e.g., hemoglobin).
Denaturation: Loss of structure and function due to heat, acid, or other factors.
Functions: Enzymes, defense, storage, transport, regulation, motion, structure.

Nucleic Acids

Nucleotides: Monomers; consist of phosphate group, five-carbon sugar, nitrogenous base.
DNA: Double helix; deoxyribose sugar; bases A, T, G, C; stores genetic information.
RNA: Single strand; ribose sugar; bases A, U, G, C; involved in protein synthesis.
Central Dogma: DNA → RNA → Protein.

Organic Chemistry and Functional Groups

Carbon and Organic Molecules

Organic chemistry: Study of carbon compounds.
Carbon: Atomic number 6; 4 valence electrons; forms diverse skeletons and functional groups.
Hydrocarbons: Molecules of only carbon and hydrogen; nonpolar, hydrophobic, energy-rich.

Functional Groups

Group	Structure	Properties	Example
Hydroxyl	—OH	Polar, forms hydrogen bonds	Alcohols (ethanol)
Carbonyl	C=O	Polar; aldehyde (end), ketone (middle)	Acetone, propanal
Carboxyl	—COOH	Acidic, donates H+	Acetic acid
Amino	—NH2	Basic, accepts H+	Glycine
Sulfhydryl	—SH	Stabilizes proteins	Cysteine
Phosphate	—OPO32-	Acidic, energy transfer	ATP, DNA
Methyl	—CH3	Nonpolar, hydrophobic	5-methylcytosine

Biological Organization and Evolution

Levels of Biological Organization

Atoms
Molecules
Organelles
Cells (smallest living unit)
Tissues
Organs and Organ Systems
Organisms
Populations
Communities
Ecosystems
Biosphere

Emergent Properties

New properties arise at each level of organization due to interactions among components.

Cells: Prokaryotic vs. Eukaryotic

Feature	Prokaryotic Cell	Eukaryotic Cell
Nucleus	Absent	Present
Organelles	Absent	Present
Examples	Bacteria, Archaea	Plants, Animals, Fungi, Protists

Cell Theory

All living things are made of cells.
Cells are the basic unit of life.
All cells arise from pre-existing cells.

Genetic Information and Inheritance

Genes: Units of inheritance; segments of DNA.
Chromosomes: Structures containing DNA.
Alleles: Different versions of a gene.

Taxonomy and Classification

Classification hierarchy: Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species.
Three domains: Bacteria, Archaea, Eukarya.
Binomial nomenclature: Genus + species (e.g., Homo sapiens).

Evolution and Natural Selection

Darwin's Theory of Evolution

Species show evidence of "descent with modification" from common ancestors.
Natural selection is the mechanism for evolution.
Individuals with advantageous traits survive and reproduce more successfully.

Key Observations

Variation exists within populations.
Traits are heritable.
More offspring are produced than survive.
Competition for resources is inevitable.
Organisms best suited to their environment are more likely to survive and reproduce.

Scientific Method and Experimental Design

Steps of the Scientific Method

Observation
Question
Hypothesis (testable explanation)
Prediction
Experiment
Results
Conclusion

Variables in Experiments

Independent variable: Manipulated by researcher (x-axis).
Dependent variable: Measured outcome (y-axis).
Controlled variables: Kept constant to ensure valid results.

Controlled Experiments

Compare experimental group to control group.
Change only one variable at a time.
Example: Redi's maggot experiment disproved spontaneous generation.

Theories in Science

Theory: Broader than a hypothesis; supported by extensive evidence.
Examples: Cell theory, theory of evolution.

Laboratory Techniques and Measurement

Metric System and Unit Conversions

Base units: Meter (length), gram (mass), liter (volume).
Prefixes: kilo (103), hecto (102), deca (10), deci (0.1), centi (0.01), milli (0.001).
"Down to the right, up to the left" mnemonic for decimal movement.

Scientific Notation

Standard form:
n = number between 1 and 10; a = integer exponent.
Positive exponent: Large numbers; negative exponent: Small numbers.

Significant Figures

Leading zeros are not significant.
Zeros between non-zero digits are significant.
Trailing zeros may be significant depending on context.
Rounding: If digit to right is 5 or more, round up.

Density, Mass, and Volume

Formulas:
- Density:
- Mass:
- Volume:
Volume by displacement: Measure change in water level when object is submerged.

Lab Equipment

Graduated cylinder: Measures liquid volume; read at bottom of meniscus at eye level.
Digital scale: Measures mass; use tare function to zero before measuring.
Thermometer: Measures temperature in Celsius.
Pipettes/eyedroppers: Transfer small liquid volumes; practice for consistency.

Applications and Environmental Context

Water Chemistry in Nature

Water's properties (cohesion, adhesion, high specific heat, solvent ability) are essential for life.
Ice floats, insulating aquatic life in winter.
Evaporative cooling regulates body temperature in organisms.

Ocean Acidification

Excess CO2 dissolves in oceans, forming carbonic acid and lowering pH.
Threatens coral reefs and marine biodiversity.

Nutrition and Deficiency

Scurvy: Disease caused by vitamin C deficiency; prevented by fresh fruits or supplements.

Defense Mechanisms and Adaptation

Example: Wood ants spray formic acid as a chemical defense, an adaptation shaped by natural selection.

Summary Table: Key Biological Macromolecules

Macromolecule	Monomer	Bond Type	Function	Example
Carbohydrate	Monosaccharide	Glycosidic	Energy, structure	Starch, cellulose
Lipid	Fatty acid, glycerol	Ester	Energy storage, membranes	Triglyceride, phospholipid
Protein	Amino acid	Peptide	Enzymes, structure, transport	Hemoglobin, collagen
Nucleic Acid	Nucleotide	Phosphodiester	Genetic information	DNA, RNA

Additional info:

Some explanations and examples have been expanded for clarity and completeness.
Tables have been constructed to summarize and compare key concepts.
All equations are provided in LaTeX format as required.