General Biology: Foundations, Cell Structure, and Biochemistry Study Notes

Biological Organization and Classification

Levels of Biological Organization

Biology studies life from the molecular to the ecosystem level, organizing living systems into hierarchical levels.

• Biosphere: The global sum of all ecosystems.

• Ecosystem: Community of organisms and their physical environment.

• Community: All populations of different species in an area.

• Population: Group of individuals of the same species.

• Organism: Individual living entity.

• Organ System: Group of organs working together.

• Tissue: Group of similar cells performing a function.

• Cell: Basic unit of life.

• Organelle: Specialized structure within a cell.

• Molecule: Chemical structure consisting of two or more atoms.

• Atom: Smallest unit of matter.

Taxonomy and Classification

Taxonomy organizes living organisms into hierarchical categories based on shared characteristics.

• Species (e.g., Vulpes)

• Genus (e.g., Vulpes)

• Family (e.g., Canidae)

• Order (e.g., Carnivora)

• Class (e.g., Mammalia)

• Phylum (e.g., Chordata)

• Kingdom (e.g., Animalia)

• Domain (e.g., Eukarya)

Three Domains of Life

All living organisms are classified into three domains based on cellular and genetic differences.

• Bacteria: Prokaryotic, unicellular organisms.

• Archaea: Prokaryotic, often extremophiles, unicellular.

• Eukaryota: Eukaryotic, includes animals, plants, fungi, and protists.

Domain	Cell Type	Examples
Bacteria	Prokaryotic	Cyanobacteria, E. coli
Archaea	Prokaryotic	Halophiles, Methanogens
Eukaryota	Eukaryotic	Animals, Plants, Fungi

Scientific Inquiry and Experimental Design

Types of Science

Science uses observation and experimentation to understand the natural world.

• Discovery Science: Based on observation and measurement.

• Hypothesis-Based Science: Uses experiments to test specific predictions.

Experimental Considerations

• Independent Variable: Factor manipulated in an experiment.

• Dependent Variable: Factor measured in response.

• Replication: Repeating experiments to ensure reliability.

• Data Analysis: Interpreting results using statistics.

• Reporting: Communicating findings.

Evolution and Natural Selection

Darwin's Observations and Inferences

Charles Darwin proposed natural selection as the mechanism for evolution.

• Individual Variation: Individuals vary in heritable traits.

• Overproduction: More offspring are produced than can survive.

• Unequal Reproductive Success: Individuals best suited to their environment produce more offspring.

• Accumulation of Favorable Traits: Advantageous traits become more common over generations.

Descent with Modification

• Species change over time, giving rise to new species.

Genetics and Molecular Biology

Genetic Information

Genetic information is stored in DNA and expressed through RNA and proteins.

• DNA: Heritable blueprint for life.

• Genes: Segments of DNA encoding proteins.

• Messenger RNA (mRNA): Intermediate between DNA and protein synthesis.

Gene Expression

• DNA Synthesis: Replication

• RNA Synthesis: Transcription

• Protein Synthesis: Translation

• Proteins are made of amino acids.

Gene Expression in Action

• Pancreas cells monitor blood glucose.

• Insulin is a product of gene expression.

• Glucose storage requires membrane transport proteins and enzymes.

Chemistry of Life

Elements and Atoms

Life is composed of a limited set of elements, with carbon, hydrogen, oxygen, and nitrogen being most abundant.

• Atoms: Protons, neutrons, electrons.

• Atomic Mass: Sum of protons and neutrons.

• Isotopes: Atoms with same number of protons but different neutrons.

Radioactive Isotopes

• Decay spontaneously, emit energy, can be detected and are sometimes dangerous.

Electron Shells

• Electrons exist in shells; 1st and 2nd shells are most important for organisms.

• Stable atom has full valence shell.

Covalent Bonds

• Sharing of electrons between atoms.

• Electronegativity: Measure of attraction for shared electrons.

• Polar covalent: Unequal sharing.

• Non-polar covalent: Equal sharing.

Bond Type	Length (Å)	Strength (kcal/mol)
C-H	1.09	98.8
O-H	0.96	110.6
N-H	1.01	93.0
C=O	1.23	176.0
C-N	1.47	73.0

Properties of Water

Unique Properties

Water is essential for life due to its chemical and physical properties.

• Cohesiveness: Surface tension.

• Thermal Stability: Buffers temperature variation.

• Ice Floats: Due to lower density than liquid water.

• Excellent Solvent: Dissolves salts, electrolytes, proteins, and sugars.

• Lipids: Hydrophobic molecules form barriers in water.

Acidic vs. Basic Conditions

• Water dissociates: $H_2O \rightarrow H^+ + OH^-$

• pH = $-\log[H^+]$

• Pure water: pH 7

• Acidic: pH < 7; Basic: pH > 7

• Buffers absorb free H+ or OH-

Metabolic Acidosis

• Condition where acids build up in the body.

• Causes: Untreated diabetes, loss of bicarbonate, kidney conditions.

• Normal blood pH: 7.35–7.45

• Acidemia: Blood pH below 7.35; severe acidosis below 7.20

Biological Molecules

Carbohydrates

Carbohydrates are energy storage molecules and structural components.

• Monosaccharides: Simple sugars (e.g., glucose).

• Polysaccharides: Starch, glycogen, cellulose, chitin.

• Disaccharides: Sucrose (glucose + fructose).

• Pentoses: Five-carbon sugars.

• Hexoses: Six-carbon sugars.

Lipids

• Hydrophobic molecules, not true polymers.

• Energy storage, insulation, and padding.

• Phospholipids form plasma membranes.

• Hormones: Steroids and prostaglandins.

• Saturated vs. unsaturated fatty acids.

Proteins

• Polymers of amino acids.

• Structure: Amino acid sequence, 3D shape, interactions of subunits.

• Functions: Enzymes, transport, hormones, antibodies, toxins.

• Protein structure: Polypeptide chain linked by covalent peptide bonds.

Nucleic Acids

• Polymers of nucleotides (phosphate group, sugar, nitrogenous base).

• Bases: Adenine (A), Thymine (T, DNA only), Uracil (U, RNA only), Cytosine (C), Guanine (G).

• DNA: Double-stranded, complementary pairing, genetic inheritance.

• RNA: Single-stranded, directs protein synthesis.

Cell Structure and Function

Microscopy

• SEM: Surface structure.

• TEM: Internal structure.

• Most cells are microscopic; smallest unit of life.

• Human eye resolution: 0.1 mm; light microscope: 0.2 μm.

Plasma Membranes

• Phospholipid Bilayer: Double layer of phospholipids.

• Fluid Mosaic Model: Membrane is flexible and contains proteins.

• Selectively Permeable: Controls entry and exit of substances.

Prokaryotic Cells

• Small, lack membrane-bound organelles.

• Unicellular organisms.

• Domains: Bacteria and Archaea.

Additional info:

• Protists are mostly single-celled eukaryotes, but some are multicellular.

• Jane Goodall's research on chimpanzees established standards for behavioral studies and ethics in animal research.

• CRISPR-Cas9 is a modern gene editing technology.