General Biology I: Comprehensive Study Notes

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Chapter 2: The Chemical Context of Life

Atomic Number vs. Atomic Mass

Atomic Number: Number of protons in an atom.
Atomic Mass: Total number of protons and neutrons in an atom.

Ionic vs. Covalent Bonds

Ionic Bonds: Electrons are transferred from one atom to another, resulting in oppositely charged ions that attract each other.
Covalent Bonds: Electrons are shared between atoms.

Polar vs. Nonpolar Covalent Bonds

Polar Covalent: Electrons are shared unequally, creating partial charges (e.g., H2O).
Nonpolar Covalent: Electrons are shared equally between atoms.

Electronegativity

The tendency of an atom to attract electrons in a covalent bond.

Hydrogen Bonds

Weak bonds formed when a hydrogen atom covalently bonded to an electronegative atom is attracted to another electronegative atom.
Example: Bonds between water molecules.

Chapter 3: Water and Life

Emergent Properties of Water

Cohesion: Water molecules stick to each other due to hydrogen bonding.
Adhesion: Water molecules stick to other polar substances (e.g., capillary action in plants).
High Specific Heat: Water resists temperature changes, helping to stabilize environments.
High Heat of Vaporization: Large amount of energy required to convert water from liquid to gas.
Expansion Upon Freezing: Ice is less dense than liquid water, allowing it to float and insulate aquatic life.
Solvent Properties: Water's polarity makes it an excellent solvent for ionic and polar substances.

Hydrophobic vs. Hydrophilic Substances

Hydrophobic: Nonpolar, cannot dissolve in water (e.g., oils).
Hydrophilic: Polar, dissolves in water (e.g., salts, sugars).

Molarity and pH

Molarity (M): Measure of solution concentration, defined as moles of solute per liter of solution.
pH: Measure of acidity; pH < 7 is acidic, pH = 7 is neutral, pH > 7 is basic.

Chapter 4: Carbon and the Molecular Diversity of Life

Organic vs. Inorganic Compounds

Organic Compounds: Contain carbon and hydrogen, often complex (e.g., carbohydrates, proteins).
Inorganic Compounds: May contain carbon, but lack hydrogen or are simpler (e.g., CO2).

Carbon's Bonding Properties

Carbon has 4 valence electrons, allowing it to form up to 4 covalent bonds (single, double, or triple bonds).

Functional Groups

Hydroxyl (-OH): Alcohols; makes molecules polar.
Carboxyl (-COOH): Acids; acts as an acid.
Carbonyl (C=O): Found in sugars; makes molecules reactive.
Amino (-NH2): Amino acids; acts as a base.
Sulfhydryl (-SH): Some amino acids; forms disulfide bonds for protein stability.
Phosphate (-PO4): Nucleotides; helps energy transfer (e.g., ATP).
Methyl (-CH3): Nonpolar; affects DNA expression.

Chapter 5: The Structure and Function of Large Biological Molecules

Dehydration vs. Hydrolysis

Dehydration Reaction: Builds molecules by removing an -OH and H to form water and a new bond.
Hydrolysis: Breaks down polymers by adding water, splitting bonds.

Biological Molecules and Their Monomers

Macromolecule	Monomer	Function
Carbohydrates	Monosaccharides	Energy source, structure (e.g., starch, cellulose)
Proteins	Amino acids	Structure, enzymes, transport, signaling
Lipids	Fatty acids, glycerol	Long-term energy storage, hormones, membranes
Nucleic Acids	Nucleotides	Genetic information (DNA, RNA)

Peptide Bonds and Protein Structure

Peptide Bond: Covalent bond between amino acids in proteins.
Amino Acid Structure: Central carbon, amino group (-NH2), carboxyl group (-COOH), hydrogen, and R group (side chain).

DNA vs. RNA

DNA	RNA
Stable, long-term storage	Temporary, messenger
Deoxyribose sugar	Ribose sugar
Double-stranded	Single-stranded

Central Dogma: DNA → RNA → Protein

Chapter 6: A Tour of the Cell

Prokaryotes vs. Eukaryotes

Prokaryotes: Single-celled, no nucleus or membrane-bound organelles (e.g., Bacteria, Archaea).
Eukaryotes: Multicellular or unicellular, have nucleus and organelles (e.g., Plants, Animals, Fungi, Protists).

Endosymbiotic Theory

Mitochondria and chloroplasts originated from free-living bacteria engulfed by ancestral eukaryotes.

Basic Cell Features

Cytoskeleton: Supports cell structure.
Cilia/Flagella: Movement.
Nucleus: Contains DNA.
Ribosomes: Protein synthesis.
Endoplasmic Reticulum (ER): Rough ER (with ribosomes) synthesizes proteins; Smooth ER synthesizes lipids.
Golgi Apparatus: Modifies, sorts, and packages proteins and lipids.
Lysosomes: Break down waste.
Mitochondria: Site of cellular respiration, ATP production.
Peroxisomes: Detoxify harmful substances.

Plant Cell Exclusive Features

Cell Wall, Vacuoles, Chloroplasts, Plasmodesmata

Chapter 7: Membrane Structure and Function

Molecules That Can Penetrate the Membrane

Small, nonpolar molecules (e.g., O2, CO2) can diffuse freely.
Small, uncharged polar molecules (e.g., H2O) can pass to some extent.
Large, charged, or generally polar molecules require transport proteins.

Passive Transport

No energy required; molecules move down their concentration gradient.
Diffusion: Movement of molecules from high to low concentration.
Osmosis: Diffusion of water across a selectively permeable membrane.

Solution Type	Effect on Cell
Hypertonic	Cell loses water, shrinks
Hypotonic	Cell gains water, swells
Isotonic	No net water movement

Facilitated Transport

Transport proteins help molecules cross the membrane; no energy required.

Active Transport

Requires energy (ATP); moves molecules against their concentration gradient.
Example: Sodium-potassium pump (Na+/K+ pump).

Bulk Transport

Endocytosis: Cell takes in material via vesicles (phagocytosis for solids, pinocytosis for liquids, receptor-mediated for specific molecules).
Exocytosis: Vesicles fuse with membrane to release contents outside the cell.

Chapter 12: The Cell Cycle

Diploid vs. Haploid

Diploid (2n): Two sets of chromosomes (somatic cells).
Haploid (n): One set of chromosomes (gametes).

Homologous Chromosomes vs. Sister Chromatids

Homologous Chromosomes: Pair of chromosomes, one from each parent, separated in meiosis I.
Sister Chromatids: Identical copies of a single chromosome, separated in mitosis and meiosis II.

Stages of Mitosis (PPMAT)

Prophase: Chromosomes condense, spindle forms.
Prometaphase: Nuclear envelope dissolves, spindle attaches to kinetochores.
Metaphase: Chromosomes align at cell equator.
Anaphase: Sister chromatids pulled apart to opposite poles.
Telophase: Nuclear envelope reforms, chromosomes decondense.
Cytokinesis: Cytoplasm divides, forming two cells.

Chapter 13: Meiosis and Sexual Life Cycles

Meiosis

Reduces chromosome number by half, producing haploid gametes.
Two divisions: Meiosis I (homologous chromosomes separate), Meiosis II (sister chromatids separate).

Crossing Over

Occurs during prophase I; homologous chromosomes exchange genetic material, increasing genetic diversity.

Mendel's Laws

Law of Segregation: Each gamete receives only one allele from each gene.
Law of Independent Assortment: Genes for different traits segregate independently during gamete formation.

Chapter 16: The Molecular Basis of Inheritance

DNA Structure

Double helix with sugar-phosphate backbone and nitrogenous bases (A, T, C, G).
Antiparallel strands (5' to 3' and 3' to 5').

Bacterial DNA Replication

Enzyme/Protein	Function
Helicase	Unwinds double helix
SSB	Stabilizes single strands
Primase	Creates RNA primers
DNA Pol I	Removes primers, replaces with DNA
DNA Pol III	Main DNA synthesis
Ligase	Joins Okazaki fragments
Topoisomerase	Relieves tension ahead of fork

Leading Strand: Synthesized continuously.
Lagging Strand: Synthesized in Okazaki fragments.

Chapter 17: Gene Expression: From Gene to Protein

Transcription (DNA → RNA)

Occurs in nucleus; RNA polymerase creates mRNA.
Steps: Initiation (binds promoter), Elongation (builds mRNA), Termination (releases mRNA).

Translation (RNA → Protein)

Occurs in ribosome (cytoplasm).
Steps: Initiation (ribosome binds mRNA), Elongation (tRNA brings amino acids), Termination (stop codon reached).

Genetic Code

Chargaff's Rule: %A = %T, %C = %G in DNA.
Redundancy: Multiple codons can code for the same amino acid, protecting against mutations.

RNA Polymerases

RNA Pol I: Makes rRNA
RNA Pol II: Makes mRNA, snRNA
RNA Pol III: Makes tRNA, other small RNAs

Chapter 18: Regulation of Gene Expression

Gene Regulation in Prokaryotes

Inducible Operon (lac): Presence of lactose removes repressor, allowing transcription.
Repressible Operon (trp): Presence of tryptophan activates repressor, blocking transcription.

Gene Regulation in Eukaryotes

Chromatin Modification: Acetylation loosens, methylation tightens DNA, affecting transcription.
Transcription Factors: Proteins that turn genes on/off.
Alternative Splicing: Multiple proteins from one gene based on splicing.
Epigenetics: Changes in gene activity without altering DNA sequence.

Chapter 20: DNA Tools and Biotechnology

Transgenic/Recombinant DNA

Genetically modified DNA, used to create GMOs.

CRISPR

Gene editing tool that cuts and replaces DNA segments.

PCR (Polymerase Chain Reaction)

Amplifies DNA for analysis.
Steps: Denaturation (heating to separate strands), Annealing (cooling to allow primers to bind), Extension (DNA polymerase adds nucleotides).

Chapter 8: An Introduction to Metabolism

Exergonic vs. Endergonic Reactions

Exergonic	Endergonic
Releases energy	Requires energy input
Spontaneous	Non-spontaneous
Example: Cellular respiration	Example: Photosynthesis

Enzyme Function

Catalysts that speed up chemical reactions by lowering activation energy.
Substrate binds to enzyme's active site; enzyme changes shape (induced fit).

Feedback Inhibition

End product of a pathway inhibits an earlier enzyme, regulating the pathway.

Factors Affecting Enzyme Speed

Substrate concentration
Temperature
pH
Competitive inhibition

Chapter 9: Cellular Respiration and Fermentation

Autotroph vs. Heterotroph

Autotroph: Makes its own food (e.g., plants).
Heterotroph: Consumes other organisms for food (e.g., animals).

Cellular Respiration vs. Photosynthesis

Cellular respiration: Breaks down glucose to produce ATP.
Photosynthesis: Builds glucose using light energy.
Essentially opposite processes.

Cellular Respiration Steps

Glycolysis: Glucose → 2 pyruvate, 2 ATP, 2 NADH (cytoplasm).
Pyruvate Oxidation: Pyruvate → Acetyl-CoA, CO2, NADH.
Krebs Cycle (Citric Acid Cycle): Acetyl-CoA → CO2, NADH, FADH2, ATP.
Oxidative Phosphorylation: Electron transport chain and chemiosmosis produce most ATP (30–32 ATP per glucose).

Chapter 10: Photosynthesis

Photosynthesis Equation

Photosynthesis Steps

Light Reactions: Sunlight absorbed, splits H2O, produces O2, ATP, NADPH.
Calvin Cycle: Uses ATP and NADPH to build glucose from CO2.

Chapter 11: Cell Communication

Cell Signaling Steps

Reception: Cell detects a ligand (signal molecule).
Transduction: Signal relayed by secondary messengers.
Response: Cell responds (e.g., gene expression, enzyme activation).

Ligands and Receptors

Hydrophobic ligands: Bind to intracellular receptors (e.g., steroid hormones).
Hydrophilic ligands: Bind to receptors on the cell membrane.

Secondary Messengers

Molecules that relay signals (e.g., cAMP, Ca2+).

Apoptosis (Programmed Cell Death)

Cell is signaled to die, activates caspases, fragments into small vesicles (apoptotic bodies), which are digested by phagocytes.