Comprehensive Study Guide: Foundations of College Biology

A. Scientific Process and General Chemistry

1. Scientific Process

The scientific process is a systematic approach to understanding the natural world through observation, hypothesis formation, experimentation, and analysis.

• Observation: Gathering data about phenomena.

• Hypothesis: A testable explanation for an observation.

• Experimentation: Testing hypotheses under controlled conditions.

• Analysis and Conclusion: Interpreting results to support or refute the hypothesis.

• Peer Review and Publication: Sharing findings for validation by the scientific community.

2. Types of Chemical Bonds

Chemical bonds are forces that hold atoms together in molecules and compounds.

• Ionic Bonds: Formed when electrons are transferred from one atom to another, creating charged ions (e.g., NaCl).

• Covalent Bonds: Atoms share pairs of electrons (e.g., H2O, O2).

• Hydrogen Bonds: Weak attractions between a hydrogen atom and an electronegative atom (e.g., between water molecules).

• Van der Waals Interactions: Weak, transient attractions between molecules or parts of molecules.

3. Properties of Water; pH

Water's unique properties are essential for life, and pH measures the concentration of hydrogen ions in a solution.

• Cohesion and Adhesion: Water molecules stick to each other and to other substances.

• High Specific Heat: Water resists temperature changes.

• Solvent Properties: Water dissolves many substances, facilitating biochemical reactions.

• pH Scale: Ranges from 0 (acidic) to 14 (basic); pH 7 is neutral.

• Formula: $\mathrm{pH} = -\log_{10}[\mathrm{H}^+]$

B. Organic Chemistry

1. Major Functional Groups

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

• Hydroxyl (-OH): Found in alcohols; polar.

• Carbonyl (C=O): Found in aldehydes and ketones.

• Carboxyl (-COOH): Found in acids; acts as an acid.

• Amino (-NH2): Found in amino acids; acts as a base.

• Sulfhydryl (-SH): Found in thiols; forms disulfide bonds.

• Phosphate (-PO4): Found in nucleic acids; involved in energy transfer.

• Methyl (-CH3): Nonpolar; affects gene expression.

2. Structure, Functions, and Examples of Four Macromolecules

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

Macromolecule	Monomer	Function	Example
Carbohydrates	Monosaccharides	Energy storage, structure	Glucose, starch, cellulose
Lipids	Glycerol & fatty acids	Energy storage, membranes	Fats, oils, phospholipids
Proteins	Amino acids	Catalysis, structure, transport	Enzymes, hemoglobin
Nucleic Acids	Nucleotides	Genetic information	DNA, RNA

C. Cell Parts

1. Prokaryote vs. Eukaryote

Cells are classified based on the presence or absence of a nucleus and membrane-bound organelles.

• Prokaryotes: No nucleus, no membrane-bound organelles (e.g., Bacteria, Archaea).

• Eukaryotes: Have a nucleus and membrane-bound organelles (e.g., plants, animals, fungi, protists).

2. Organelles; Functions; Plants vs. Animal Cells

Organelles are specialized structures within eukaryotic cells that perform distinct functions.

Organelle	Function	Plant	Animal
Nucleus	Stores genetic material	Yes	Yes
Mitochondria	ATP production	Yes	Yes
Chloroplast	Photosynthesis	Yes	No
Cell Wall	Structure/support	Yes	No
Vacuole	Storage	Large	Small
Lysosome	Digestion	No	Yes

D. Transport

1. Types of Transport In and Out of the Cell

Cells regulate the movement of substances across their membranes through various transport mechanisms.

• Passive Transport: No energy required; includes diffusion, osmosis, and facilitated diffusion.

• Active Transport: Requires energy (ATP); moves substances against their concentration gradient.

• Bulk Transport: Endocytosis (into cell) and exocytosis (out of cell).

2. Hypotonic, Isotonic, and Hypertonic

• Hypotonic: Lower solute concentration outside the cell; water enters cell, may cause lysis.

• Isotonic: Equal solute concentration; no net water movement.

• Hypertonic: Higher solute concentration outside; water leaves cell, causing shrinkage.

E. Enzymes & Metabolism

1. How an Enzyme Works

Enzymes are biological catalysts that speed up chemical reactions by lowering activation energy.

• Active Site: Region where substrate binds.

• Induced Fit: Enzyme changes shape to fit substrate.

• Specificity: Each enzyme acts on a specific substrate.

2. Structure and Importance of ATP

ATP (adenosine triphosphate) is the primary energy carrier in cells.

• Structure: Adenine, ribose, and three phosphate groups.

• Energy Release: Hydrolysis of ATP releases energy: $\mathrm{ATP} + \mathrm{H}_2\mathrm{O} \rightarrow \mathrm{ADP} + \mathrm{P}_i + \text{energy}$

F. Cellular Respiration

1. ATP Production in Presence and Absence of Oxygen

Cells generate ATP through aerobic (with oxygen) and anaerobic (without oxygen) pathways.

• Aerobic Respiration: Glycolysis, Krebs cycle, and electron transport chain; produces up to 38 ATP per glucose.

• Anaerobic Respiration/Fermentation: Glycolysis followed by lactic acid or alcoholic fermentation; yields 2 ATP per glucose.

2. ATP Production via ETC and Chemiosmosis

• Electron Transport Chain (ETC): Series of proteins in the mitochondrial membrane transfer electrons, pumping protons to create a gradient.

• Chemiosmosis: Protons flow back through ATP synthase, driving ATP production.

• Equation: $\mathrm{C}_6\mathrm{H}_{12}\mathrm{O}_6 + 6\mathrm{O}_2 \rightarrow 6\mathrm{CO}_2 + 6\mathrm{H}_2\mathrm{O} + \text{energy (ATP)}$

G. Photosynthesis

1. Light Reactions vs. Calvin Cycle

Photosynthesis occurs in two stages: the light reactions and the Calvin cycle.

• Light Reactions: Occur in thylakoid membranes; convert light energy to chemical energy (ATP, NADPH); release O2.

• Calvin Cycle: Occurs in stroma; uses ATP and NADPH to fix CO2 into glucose.

2. Main Products of Photosynthesis

• Glucose (C6H12O6): Main energy storage molecule.

• Oxygen (O2): Byproduct released into the atmosphere.

• Equation: $6\mathrm{CO}_2 + 6\mathrm{H}_2\mathrm{O} + \text{light energy} \rightarrow \mathrm{C}_6\mathrm{H}_{12}\mathrm{O}_6 + 6\mathrm{O}_2$

H. Mitosis

1. Stages and Control of the Cell Cycle

Mitosis is the process of nuclear division in eukaryotic cells, ensuring genetic continuity.

• Stages: Prophase, Metaphase, Anaphase, Telophase, Cytokinesis.

• Control: Checkpoints (G1, G2, M) regulate progression; cyclins and CDKs are key regulators.

2. Animal vs. Plant Mitosis

• Animal Cells: Cleavage furrow forms during cytokinesis.

• Plant Cells: Cell plate forms to divide the cell.

I. Meiosis

1. Importance of Crossing-Over

Crossing-over during prophase I increases genetic diversity by exchanging DNA between homologous chromosomes.

2. Stages of Meiosis

• Meiosis I: Homologous chromosomes separate.

• Meiosis II: Sister chromatids separate.

3. Gametogenesis in Humans

Process	Location	End Products
Spermatogenesis	Testes	4 sperm cells
Oogenesis	Ovaries	1 ovum + 3 polar bodies

J. Genetics

1. Mendel's Laws

• Law of Segregation: Each individual has two alleles for each gene, which separate during gamete formation.

• Law of Independent Assortment: Genes for different traits assort independently during gamete formation.

2. Exceptions to Mendelian Inheritance

• Incomplete Dominance: Heterozygote shows intermediate phenotype.

• Codominance: Both alleles are fully expressed.

• Pleiotropy: One gene affects multiple traits.

• Polygenic Inheritance: Multiple genes affect a single trait.

3. Solving Genetic Problems

• Punnett Squares: Used to predict genotype and phenotype ratios.

• Probability Calculations: Used for more complex crosses.

K. Molecular Biology

1. DNA Replication

• Semiconservative: Each new DNA molecule has one old and one new strand.

• Key Enzymes: Helicase, DNA polymerase, ligase.

2. Transcription and Translation

• Transcription: DNA is copied into mRNA in the nucleus.

• Translation: mRNA is decoded to build a protein at the ribosome.

3. Regulation of Eukaryotic Genes

• Transcription Factors: Proteins that control gene expression.

• Epigenetic Modifications: DNA methylation, histone modification.

4. Modern Molecular Biology Techniques and Biotechnology

• PCR (Polymerase Chain Reaction): Amplifies DNA sequences.

• Gel Electrophoresis: Separates DNA fragments by size.

• Gene Cloning: Inserting genes into plasmids for replication.

• CRISPR: Genome editing technology.

L. Evolution

1. Theories of Descent with Modification and Common Ancestry

• Descent with Modification: Species change over time, giving rise to new species.

• Common Ancestry: All life shares a common ancestor.

2. Theory of Natural Selection

• Variation: Individuals in a population vary in traits.

• Heritability: Traits are passed to offspring.

• Differential Survival: Individuals with advantageous traits survive and reproduce more.

3. Genetic Basis/Mechanism for Evolution

• Mutation: Source of new genetic variation.

• Gene Flow, Genetic Drift, Selection: Mechanisms that change allele frequencies.

4. Observed Patterns of Change Driven by Natural Selection

• Adaptation: Traits that increase fitness become more common.

• Speciation: Formation of new species due to reproductive isolation.