Comprehensive Study Guide: Foundations of Biology

Module 1: Foundations of Biology

Levels of Biological Organization

• Biological organization refers to the hierarchy of complex biological structures and systems that define life using a reductionistic approach.

• Levels (from smallest to largest): Atoms → Molecules → Organelles → Cells → Tissues → Organs → Organ Systems → Organisms → Populations → Communities → Ecosystems → Biosphere.

• Communities are groups of interacting populations in a given area; tissues are groups of similar cells performing a specific function.

Eukaryotes vs. Prokaryotes

• Eukaryotes have membrane-bound organelles (including a nucleus); prokaryotes lack these structures.

• Reproduction: Prokaryotes reproduce by binary fission; eukaryotes by mitosis/meiosis.

Natural Selection and Evolution

• Natural selection is a mechanism of evolution where individuals with advantageous traits survive and reproduce more successfully.

• Key principles: Variation, inheritance, differential survival, and reproduction.

Hypothesis vs. Theory

• Hypothesis: A testable, specific prediction.

• Theory: A broad, well-supported explanation of natural phenomena.

Characteristics of Science & Scientific Method

• Science is empirical, testable, repeatable, and falsifiable.

• Steps: Observation → Question → Hypothesis → Experiment → Analysis → Conclusion.

• Peer review ensures validity and reliability of scientific findings.

Module 2: Chemical Context of Life

Atomic Structure and Elements

• Atoms consist of protons (positive), neutrons (neutral), and electrons (negative).

• The atomic number defines the element (number of protons).

• Isotopes differ in neutron number; ions differ in electron number, affecting charge.

Covalent vs. Ionic Bonds

• Covalent bonds: Atoms share electrons.

• Ionic bonds: Electrons are transferred, creating charged ions.

Polar vs. Non-Polar Covalent Bonds

• Polar covalent: Unequal sharing of electrons (e.g., H2O).

• Non-polar covalent: Equal sharing (e.g., O2).

• Polarity affects solubility in water.

Module 3: Water and Life

Hydrogen Bonding and Water Properties

• Hydrogen bonds are weak attractions between the hydrogen of one molecule and an electronegative atom of another.

• Responsible for water's cohesion, adhesion, high specific heat, and solvent abilities.

Solutions and Solubility

• Solvent: Substance that dissolves another (e.g., water).

• Solute: Substance dissolved (e.g., salt).

• Solution: Homogeneous mixture of solvent and solute.

• Water dissolves polar and ionic substances due to its polarity.

Temperature, Thermal Energy, and Specific Heat

• Temperature: Average kinetic energy of molecules.

• Thermal energy: Total kinetic energy.

• Specific heat: Energy required to raise 1g of a substance by 1°C.

Module 4: Carbon and Molecular Diversity

Carbon Bonding and Macromolecules

• Carbon forms four covalent bonds, allowing for diverse molecular structures (chains, rings, branches).

Functional Groups

• Groups of atoms that confer specific properties to molecules (e.g., hydroxyl, carboxyl, amino, phosphate).

• Often involved in chemical reactions.

Module 5: Structure and Function of Biological Molecules

Polymer Synthesis and Breakdown

• Dehydration synthesis: Joins monomers by removing water.

• Hydrolysis: Breaks polymers into monomers by adding water.

Carbohydrates

• Monosaccharide formula: $C_nH_{2n}O_n$

• Functions: Energy storage (e.g., starch, glycogen) and structure (e.g., cellulose, chitin).

Lipids

• Unified by hydrophobicity (nonpolar hydrocarbon regions).

• Phospholipids: Form bilayers due to amphipathic nature (hydrophilic head, hydrophobic tails).

Proteins

• Functions: Enzymes, transport, structure, signaling, etc.

• Structure of a dipeptide: Amino group, carboxyl group, central carbon, R-group, peptide bond.

• Levels of structure:

  • Primary: Amino acid sequence.

  • Secondary: Alpha helices, beta sheets (hydrogen bonds).

  • Tertiary: 3D shape (R-group interactions).

  • Quaternary: Multiple polypeptides.

Nucleic Acids

• Nucleotide: Sugar, phosphate, nitrogenous base.

• Polynucleotide: Sugar-phosphate backbone, nitrogenous bases.

• DNA: Double helix; RNA: Single-stranded.

Module 6: A Tour of the Cell

Cell Size and Surface Area-to-Volume Ratio

• As cells grow, volume increases faster than surface area, limiting size due to exchange efficiency.

Organelle Functions

• Protein synthesis: Ribosomes, rough ER.

• Endomembrane system: ER, Golgi, vesicles, lysosomes, plasma membrane.

• Metabolism: Mitochondria (energy), chloroplasts (photosynthesis).

Endosymbiotic Theory

• Mitochondria and chloroplasts originated as free-living prokaryotes engulfed by ancestral eukaryotes.

Cytoskeleton

• Dynamic network of fibers (microtubules, microfilaments, intermediate filaments) for support, movement, and transport.

Module 7: Membrane Structure and Function

Amphipathic Nature of Membranes

• Phospholipid bilayer has hydrophilic heads and hydrophobic tails, affecting permeability.

Diffusion and Osmosis

• Substances move down concentration gradients (high to low concentration).

• Osmosis: Diffusion of water across a selectively permeable membrane.

Passive vs. Active Transport

• Passive: No energy required (diffusion, facilitated diffusion, osmosis).

• Active: Requires energy (ATP) to move substances against gradients.

Bulk Transport

• Endocytosis: Intake of large particles.

• Exocytosis: Export of materials.

Module 8: Introduction to Metabolism

Exergonic vs. Endergonic Reactions

• Exergonic: Release energy, increase entropy ($\Delta G < 0$).

• Endergonic: Require energy, decrease entropy ($\Delta G > 0$).

ATP and Energy Coupling

• ATP stores energy in unstable phosphate bonds.

Enzymes and Activation Energy

• Enzymes lower activation energy, speeding up reactions without being consumed.

Module 9: Cellular Respiration and Fermentation

Major Stages of Cellular Respiration

• Glycolysis: Cytoplasm; glucose → pyruvate, ATP, NADH.

• Citric Acid Cycle: Mitochondrial matrix; acetyl CoA → CO2, ATP, NADH, FADH2.

• Oxidative Phosphorylation: Inner mitochondrial membrane; electron transport chain & chemiosmosis produce ATP.

Anaerobic Respiration vs. Fermentation

• Anaerobic respiration: Uses electron acceptors other than O2.

• Fermentation: Partial breakdown of glucose without electron transport chain.

Module 10: Photosynthesis

Stages of Photosynthesis

• Light reactions: Thylakoid membranes; convert light energy to ATP and NADPH, release O2.

• Calvin cycle: Stroma; uses ATP and NADPH to fix CO2 into sugars.

Carbon Fixation

• Incorporation of CO2 into organic molecules.

Module 12: The Cell Cycle and Mitosis

Key Terms

• Genome: All genetic material in a cell.

• Chromosome: DNA molecule with associated proteins.

• Chromatin: DNA-protein complex.

• Sister chromatids: Identical copies of a chromosome.

• Homologous chromosomes: Chromosome pairs with same genes.

• Daughter cells: Result from cell division.

• Mitosis: Division of nucleus.

• Cytokinesis: Division of cytoplasm.

• Cell cycle: Life cycle of a cell (G1, S, G2, M, G0).

Cell Cycle and Mitosis

• G0: Non-dividing state.

• Mitosis: Prophase, metaphase, anaphase, telophase.

Module 13: Meiosis and Sexual Life Cycles

Meiosis and Gamete Formation

• Meiosis produces haploid gametes from diploid cells by separating homologous chromosomes.

Sexual Life Cycle

• Fertilization: Fusion of haploid gametes to form diploid zygote.

• Mitosis develops multicellular organism from zygote.

Stages of Meiosis

• Meiosis I: Homologous chromosomes separate.

• Meiosis II: Sister chromatids separate.

Genetic Variation Mechanisms

• Independent assortment, crossing over, random fertilization.

Module 16: Molecular Basis of Inheritance

DNA Replication

• Leading strand: Synthesized continuously.

• Lagging strand: Synthesized in Okazaki fragments.

• Occurs during S phase (eukaryotes) or before binary fission (prokaryotes).

Module 17: Gene Expression

Transcription and Translation

• Codon: Three-nucleotide sequence on mRNA coding for an amino acid.

• RNA polymerase binds promoter to initiate transcription; terminator signals end.

• Transcription: Initiation, elongation, termination.

• RNA modification: 5' cap, poly-A tail, splicing (removal of introns, joining exons).

• tRNA: Brings amino acids to ribosome; ribosome catalyzes peptide bond formation.

• Translation: Initiation (start codon), elongation (polypeptide synthesis), termination (stop codon).

Mutations

• Point mutations: Single nucleotide changes.

• Base-pair substitution: One base replaced by another (e.g., sickle cell anemia).

• Insertion/deletion: Addition or loss of bases; may cause frameshift mutation (alters reading frame).

• Missense: Changes amino acid; nonsense: Creates stop codon.

• Frameshift mutations are often more harmful than substitutions.

Modules 14 & 15: Mendelian Genetics and Chromosomal Inheritance

Key Genetic Terms

• Genotype: Genetic makeup; phenotype: Physical expression.

• Character: Heritable feature; trait: Variant of a character.

• Dominant: Expressed allele; recessive: Masked allele.

• Homozygous: Two identical alleles; heterozygous: Two different alleles.

• Monohybrid cross: One gene; dihybrid cross: Two genes.

• Complete dominance: One allele masks another; incomplete dominance: Intermediate phenotype; codominance: Both alleles expressed (e.g., AB blood type).

Mendelian Inheritance

• Genes have alleles for different traits; dominant alleles mask recessive ones.

• Law of segregation: Alleles separate during gamete formation.

• Law of independent assortment: Genes on different chromosomes assort independently.

• Basis: Chromosome behavior in meiosis.

• Punnett squares predict offspring probabilities.

Multiple Alleles and Codominance

• Genes may have more than two alleles (e.g., ABO blood types).

Pedigree Analysis

• Used to determine inheritance patterns and predict probabilities of genotypes/phenotypes.

Sex Determination and Linked Genes

• XY system: Males (XY), females (XX).

• X-linked genes: Inherited on X chromosome (e.g., color blindness).

• Linked genes: Genes close together on a chromosome tend to be inherited together.

Term	Definition	Example
Genotype	Genetic makeup	AA, Aa, aa
Phenotype	Physical trait	Tall, short
Dominant	Expressed allele	A in Aa
Recessive	Masked allele	a in Aa
Homozygous	Identical alleles	AA or aa
Heterozygous	Different alleles	Aa