Comprehensive Study Guide: Foundations of College Biology

A. Scientific Process and General Chemistry

1. The 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.

• Scientific Theory: A well-substantiated explanation based on repeated testing and evidence.

2. Types of Chemical Bonds

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

• Covalent Bonds: Atoms share electrons; can be polar (unequal sharing, e.g., H2O) or nonpolar (equal sharing, e.g., O2).

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

3. Properties of Water; pH

• 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 due to its polarity.

• pH Scale: Measures hydrogen ion concentration; $pH = -\log_{10}[H^+]$

• Acids: Increase [H+]; Bases: Decrease [H+].

B. Organic Chemistry

1. Major Functional Groups

• Hydroxyl (-OH): Alcohols; polar.

• Carbonyl (C=O): Aldehydes and ketones.

• Carboxyl (-COOH): Acids; donate H+.

• Amino (-NH2): Bases; accept H+.

• Sulfhydryl (-SH): Thiols; form disulfide bonds.

• Phosphate (-PO4): Energy transfer (e.g., ATP).

• Methyl (-CH3): Affects gene expression.

2. Structure, Functions, and Examples of Macromolecules

• Carbohydrates: Monomers are monosaccharides (e.g., glucose). Function: energy storage, structure (e.g., starch, cellulose).

• Lipids: Not true polymers; include fats, phospholipids, steroids. Function: energy storage, membranes, hormones.

• Proteins: Monomers are amino acids. Function: enzymes, structure, transport, signaling (e.g., hemoglobin, enzymes).

• Nucleic Acids: Monomers are nucleotides. Function: genetic information (DNA, RNA).

C. Cell Parts

1. Prokaryote vs. Eukaryote

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

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

2. Organelles; Functions; Plants vs. Animal Cells

• Nucleus: Contains DNA.

• Mitochondria: ATP production via cellular respiration.

• Chloroplasts: Photosynthesis (plants only).

• Endoplasmic Reticulum (ER): Protein and lipid synthesis.

• Golgi Apparatus: Modifies, sorts, and packages proteins.

• Lysosomes: Digestion (mainly in animal cells).

• Cell Wall: Structure (plants, fungi, some protists).

• Vacuole: Storage (large central vacuole in plants).

D. Transport

1. Types of Transport

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

• Active Transport: Requires energy (ATP); moves substances against concentration gradient (e.g., sodium-potassium pump).

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

2. Tonicity Terms

• Hypotonic: Lower solute concentration outside; water enters cell.

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

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

E. Enzymes & Metabolism

1. How Enzymes Work

• Enzymes: Biological catalysts that speed up reactions by lowering activation energy.

• Active Site: Region where substrate binds.

• Induced Fit: Enzyme changes shape to fit substrate.

2. Structure and Importance of ATP

• ATP (Adenosine Triphosphate): Main energy currency of the cell.

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

• Energy released by hydrolysis of terminal phosphate: $ATP + H_2O \rightarrow ADP + P_i + \text{energy}$

F. Cellular Respiration

1. ATP Production in Presence and Absence of Oxygen

• Aerobic Respiration: Uses oxygen; includes glycolysis, Krebs cycle, and electron transport chain (ETC).

• Anaerobic Respiration/Fermentation: No oxygen; less ATP produced (e.g., lactic acid fermentation).

2. ATP Production via ETC and Chemiosmosis

• ETC creates a proton gradient across the inner mitochondrial membrane.

• ATP synthase uses this gradient to produce ATP (chemiosmosis).

• Overall equation: $C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O + \text{energy (ATP)}$

G. Photosynthesis

1. Light Reactions vs. Calvin Cycle

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

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

2. Main Products of Photosynthesis

• Glucose (C6H12O6), O2

• Overall equation: $6CO_2 + 6H_2O + \text{light energy} \rightarrow C_6H_{12}O_6 + 6O_2$

H. Mitosis

1. Stages and Control of the Cell Cycle

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

• Control: Checkpoints (G1, G2, M) regulate progression.

2. Animal vs. Plant Mitosis

• Animal Cells: Cleavage furrow forms during cytokinesis.

• Plant Cells: Cell plate forms to divide cells.

I. Meiosis

1. Importance of Crossing-Over

• Occurs 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

• Spermatogenesis: Produces four sperm cells per meiosis.

• Oogenesis: Produces one egg and three polar bodies per meiosis.

J. Genetics

1. Mendel's Laws

• Law of Segregation: Alleles separate during gamete formation.

• Law of Independent Assortment: Genes on different chromosomes assort independently.

2. Exceptions to Mendelian Inheritance

• Incomplete dominance, codominance, multiple alleles, polygenic inheritance, sex-linked traits.

3. Solving Genetic Problems

• Punnett squares, probability calculations, pedigree analysis.

K. Molecular Biology

1. DNA Replication

• Semiconservative process; each new DNA has one old and one new strand.

• Key enzymes: DNA polymerase, helicase, ligase.

2. Transcription and Translation

• Transcription: DNA to mRNA in the nucleus.

• Translation: mRNA to protein at the ribosome.

3. Regulation of Eukaryotic Genes

• Transcription factors, enhancers, silencers, epigenetic modifications.

4. Modern Molecular Biology Techniques and Biotechnology

• PCR (Polymerase Chain Reaction), gel electrophoresis, DNA sequencing, CRISPR, cloning.

L. Evolution

1. Theories of Descent with Modification and Common Ancestry

• All life shares a common ancestor; species change over time through descent with modification.

2. Theory of Natural Selection

• Individuals with advantageous traits survive and reproduce more successfully.

• Key requirements: variation, heritability, differential survival/reproduction.

3. Genetic Basis/Mechanism for Evolution

• Mutation, gene flow, genetic drift, natural selection.

4. Observed Patterns of Change Driven by Natural Selection

• Examples: antibiotic resistance, industrial melanism in moths.

Macromolecule	Monomer	Function	Example
Carbohydrate	Monosaccharide	Energy, structure	Glucose, cellulose
Lipid	Fatty acid, glycerol	Energy storage, membranes	Triglyceride, phospholipid
Protein	Amino acid	Enzymes, structure	Hemoglobin, collagen
Nucleic Acid	Nucleotide	Genetic information	DNA, RNA

Additional info: This guide covers foundational topics in introductory biology, including chemistry, cell biology, genetics, molecular biology, and evolution, as outlined in a typical college-level syllabus.