Comprehensive Study Guide: Foundations of Biology (Final Exam Review)

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): molecule → organelle → cell → tissue → organ → organ system → organism → population → community → ecosystem → biosphere.

• Communities consist of all populations of different species in an area; tissues are groups of similar cells performing a 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, falsifiable explanation for an observation.

• Theory: A broad, well-supported explanation for a wide range of phenomena.

Characteristics of Science & Scientific Method

• Science is empirical, testable, repeatable, and self-correcting.

• 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 (e.g., H2O).

• Ionic bonds: Electrons are transferred, creating charged ions (e.g., NaCl).

Polar vs. Non-Polar Covalent Bonds

• Polar covalent: Unequal sharing of electrons (e.g., H2O); leads to partial charges and affinity for water.

• Non-polar covalent: Equal sharing (e.g., O2); molecules are hydrophobic.

Module 3: Water and Life

Hydrogen Bonding and Water Properties

• Hydrogen bonds form between the partial positive H of one water molecule and the partial negative O of another.

• Responsible for cohesion, adhesion, high specific heat, and water's 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; water's high specific heat stabilizes temperature.

Module 4: Carbon and Molecular Diversity

Carbon Bonding and Macromolecules

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

Functional Groups

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

• Often involved in chemical reactions and determine molecule function.

Module 5: Structure and Function of Large Biological Molecules

Dehydration Synthesis and Hydrolysis

• Dehydration synthesis: Joins monomers by removing water to form polymers.

• Hydrolysis: Breaks polymers into monomers by adding water.

Carbohydrates

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

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

Lipids

• Unified by hydrophobicity (non-polar hydrocarbon regions).

• Phospholipids have hydrophilic heads and hydrophobic tails, forming bilayers in membranes.

Proteins

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

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

• R-groups (side chains) determine amino acid properties and protein folding.

• Levels of structure:

  • Primary: Amino acid sequence.

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

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

  • Quaternary: Multiple polypeptide chains.

Nucleic Acids

• Nucleotide: sugar, phosphate, nitrogenous base.

• Polynucleotide: sugar-phosphate backbone, nitrogenous bases.

• DNA: double helix; RNA: single-stranded. DNA stores genetic info; RNA involved in protein synthesis.

Module 6: A Tour of the Cell

Surface Area-to-Volume Ratio

• As cells grow, volume increases faster than surface area, limiting size for efficient exchange.

Organelle Functions

• Protein synthesis: ribosomes, rough ER.

• Endomembrane system: ER, Golgi, lysosomes, vesicles, 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

• Phospholipids have hydrophilic heads and hydrophobic tails, forming a selectively permeable bilayer.

Diffusion and Osmosis

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

• Osmosis: Diffusion of water across a membrane.

Passive vs. Active Transport

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

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

• Electrochemical gradient: Combined effect of concentration and charge differences.

Bulk Transport

• Large substances moved via endocytosis (into cell) and exocytosis (out of cell).

Module 8: Introduction to Metabolism

Exergonic vs. Endergonic Reactions

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

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

ATP and Energy Coupling

• ATP stores energy in unstable phosphate bonds; hydrolysis releases energy for cellular work.

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 and chemiosmosis produce most ATP.

Anaerobic Respiration vs. Fermentation

• Anaerobic respiration: Uses electron transport chain with a final electron acceptor other than O2.

• Fermentation: No electron transport chain; regenerates NAD+ by transferring electrons to organic molecules.

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 during the Calvin cycle.

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 in non-dividing cells.

• Sister chromatids: Identical copies of a chromosome, joined at the centromere.

• Homologous chromosomes: Chromosome pairs with the same genes but possibly different alleles.

• Daughter cells: Cells produced by division.

• Mitosis: Division of the nucleus.

• Cytokinesis: Division of the cytoplasm.

• Cell cycle: Ordered sequence of events (G1, S, G2, M, and possibly G0).

Mitosis Overview

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

• Produces two genetically identical diploid daughter cells.

Module 13: Meiosis and Sexual Life Cycles

Role of Meiosis

• Reduces chromosome number by half, producing haploid gametes from diploid cells.

• Homologous chromosomes separate in meiosis I; sister chromatids separate in meiosis II.

Sexual Life Cycle

• Fertilization restores diploid number; mitosis develops multicellular organism from zygote.

Genetic Variation Mechanisms

• Independent assortment: Random orientation of homologs in meiosis I.

• Crossing over: Exchange of genetic material between homologs during prophase I.

• Random fertilization: Any sperm can fertilize any egg.

Module 16: The Molecular Basis of Inheritance

DNA Replication

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

• Replication is semi-conservative and proceeds with leading (continuous) and lagging (discontinuous, Okazaki fragments) strands.

Module 17: Gene Expression: From Gene to Protein

Transcription and Translation

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

• Linear sequence of codons determines amino acid sequence in polypeptides.

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

• Transcription steps: initiation, elongation, termination.

• RNA modification: 5' cap, 3' poly-A tail, splicing (removal of introns, joining of exons).

• tRNA brings amino acids to ribosome; ribosomes catalyze peptide bond formation.

• Translation: initiation (start codon), elongation (polypeptide growth), termination (stop codon).

• Given a DNA template, transcribe to mRNA and translate to amino acids using codon table.

Mutations

• Point mutations: Single nucleotide changes (substitutions or insertions/deletions).

• Missense: Changes one amino acid; nonsense: introduces stop codon.

• Insertions/deletions can cause frameshift mutations, altering downstream amino acids (often more harmful than substitutions).

Modules 14 & 15: Mendelian Genetics and Chromosomal Inheritance

Key Genetic Terms

• Genotype: Genetic makeup; phenotype: observable traits.

• Character: Heritable feature (e.g., flower color); trait: variant of a character (e.g., purple).

• Dominant: Expressed if present; recessive: masked by dominant allele.

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

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

• Complete dominance: Dominant allele masks recessive; 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: behavior of chromosomes during meiosis.

• Punnett squares predict probabilities of offspring genotypes/phenotypes.

Multiple Alleles and Codominance

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

Pedigree Analysis

• Pedigrees trace inheritance patterns and predict probabilities of genotypes/phenotypes in offspring.

Sex Determination and Linked Genes

• XY system determines sex; X-linked genes show unique inheritance patterns (e.g., color blindness).

• Linked genes: Genes close together on a chromosome tend to be inherited together, affecting expected ratios.

Term	Definition	Example
Genotype	Genetic makeup	AA, Aa, aa
Phenotype	Physical trait	Purple flowers
Homozygous	Two identical alleles	AA or aa
Heterozygous	Two different alleles	Aa
Dominant	Expressed if present	A
Recessive	Masked by dominant	a

Additional info: This guide synthesizes and expands upon the provided study guide, adding definitions, examples, and context for clarity and completeness. For diagrams (e.g., cell cycle, mitosis, meiosis), students should refer to textbook figures or lecture slides for visual representation.