Comprehensive Study Guide: Core Concepts in College Biology (Bio 104)

Mendelian Genetics

Gene Locus and Homologous Pairs

The gene locus refers to the specific physical location of a gene on a chromosome. In diploid organisms, each gene locus is present in two copies—one on each homologous chromosome. These copies separate during meiosis I, specifically during anaphase I, when homologous chromosomes are pulled to opposite poles.

• Homologous pairs: Chromosome pairs (one from each parent) that are similar in length, gene position, and centromere location.

• Separation during meiosis: Homologous chromosomes (and thus gene loci) separate during meiosis I, ensuring gametes receive only one copy of each gene.

Key Genetic Terms

• True-breeding: Organisms that, when self-fertilized, produce offspring identical to themselves for a given trait.

• Heterozygous: Having two different alleles at a gene locus (e.g., Aa).

• Homozygous: Having two identical alleles at a gene locus (e.g., AA or aa).

Laws of Inheritance

• Law of Segregation: Each individual has two alleles for each gene, which segregate during gamete formation so that each gamete carries only one allele.

• Law of Independent Assortment: Genes for different traits assort independently of one another during gamete formation, provided they are on different chromosomes.

Genotype and Phenotype

• Genotype: The genetic makeup of an organism (e.g., AA, Aa, or aa).

• Phenotype: The observable traits of an organism, determined by genotype and environment.

• Modes of inheritance: The relationship between genotype and phenotype depends on dominance, co-dominance, incomplete dominance, and sex-linkage.

Modes of Inheritance

• Simple dominant-recessive: One allele is dominant over the other (e.g., Aa shows dominant trait).

• Incomplete dominance: Heterozygotes show an intermediate phenotype (e.g., red x white flowers = pink).

• Co-dominance: Both alleles are fully expressed in heterozygotes (e.g., AB blood type).

• Sex-linked inheritance: Traits associated with genes on sex chromosomes (e.g., X-linked color blindness).

Genetic Linkage and Recombination

• Genetic linkage: Genes located close together on the same chromosome tend to be inherited together.

• Crossing over: Exchange of genetic material between homologous chromosomes during meiosis increases genetic diversity.

• Recombination frequency: Proportional to the distance between genes; used to map gene loci.

Formula: $\text{Recombination\ Frequency} = \frac{\text{Number\ of\ recombinant\ offspring}}{\text{Total\ offspring}} \times 100\%$

Molecular Genetics

DNA Structure

• Nucleotide components: Deoxyribose sugar, phosphate group, nitrogenous base (A, T, C, G).

• Uniform parts: Sugar and phosphate; variable part: nitrogenous base.

• Double helix: Two strands joined by hydrogen bonds between complementary bases (A-T, C-G).

• Antiparallel arrangement: One strand runs 5’ to 3’, the other 3’ to 5’.

DNA Replication

• Directionality: DNA polymerase adds nucleotides in the 5’ to 3’ direction.

• Okazaki fragments: Short DNA segments synthesized on the lagging strand, later joined by DNA ligase.

• RNA primers: Short RNA sequences synthesized by primase to initiate DNA synthesis.

Key enzymes of the replisome: Helicase, primase, DNA polymerase III, DNA polymerase I, ligase, single-strand binding protein, topoisomerase.

Gene Expression

Central Dogma

The Central Dogma of molecular biology describes the flow of genetic information: DNA → RNA → Protein.

• Transcription: DNA is transcribed to mRNA in the nucleus (eukaryotes).

• Translation: mRNA is translated to protein in the cytoplasm by ribosomes.

• Key molecules: RNA polymerase II, transcription factors, mRNA, tRNA, rRNA, ribosomes.

Transcription and Translation Details

• Template strand: DNA strand used to synthesize mRNA.

• Coding strand: DNA strand with the same sequence as mRNA (except T for U).

• tRNA anticodons: Complementary to mRNA codons; ensure correct amino acid is added.

• Reading frame: The way nucleotides are grouped into codons; shifting the frame changes the protein sequence.

Mutations

• Point mutations: Change a single nucleotide (silent, missense, nonsense).

• Insertion/deletion: Add or remove nucleotides; may cause frameshift mutations.

RNA Structure and Differences from DNA

• RNA nucleotide: Ribose sugar, phosphate, nitrogenous base (A, U, C, G).

• Differences: RNA has ribose (not deoxyribose), uracil (not thymine), usually single-stranded.

Transcription Steps

• Promoters: DNA sequences where RNA polymerase binds to initiate transcription.

• Consensus sequences: Common promoter elements recognized by transcription factors.

• Directionality: mRNA synthesized 5’ to 3’.

RNA Processing

• Introns: Non-coding regions removed from pre-mRNA.

• Exons: Coding regions spliced together to form mature mRNA.

• 5’ UTR and 3’ UTR: Untranslated regions flanking the coding sequence; regulate translation and mRNA stability.

Translation Steps

• Initiator tRNA: Binds to start codon at the P site of the ribosome.

• Ribosomal subunits: Small and large subunits assemble on mRNA.

• E, P, A sites: Sites on the ribosome for tRNA binding (Exit, Peptidyl, Aminoacyl).

• Release factor: Protein that recognizes stop codon and terminates translation.

Development and Germ Layers

Genetic Diversity and Sexual Reproduction

• Sexual reproduction increases genetic diversity via independent assortment, crossing over, and random fertilization, enhancing evolutionary adaptation.

Germ Layers

• Diploblasts: Two germ layers (ectoderm, endoderm); e.g., cnidarians.

• Triploblasts: Three germ layers (ectoderm, mesoderm, endoderm); e.g., vertebrates.

Extraembryonic Membranes

• Amnion, chorion, yolk sac, allantois—provide protection, nutrition, waste removal, and gas exchange in amniotes (reptiles, birds, mammals).

Descent with Modification

Darwinian Evolution

• Major concepts: Descent with modification and natural selection.

• Evidence: Fossil record, homology, biogeography, direct observation, molecular biology.

• Homology: Similarity due to shared ancestry (e.g., genetic code, limb structure).

• Fossils: Preserved remains in sedimentary rock strata; provide evidence for geologic time and evolutionary change.

• Origination/extinction: Appearance/disappearance of species in the fossil record.

• Vestigial structures: Remnants of features that served a function in ancestors.

Natural Selection and Speciation

Fitness and Adaptation

• Fitness: Reproductive success; how well an organism’s traits enable survival and reproduction.

• Adaptation: Heritable trait that increases fitness in a given environment.

• Three conditions for natural selection: Variation, heritability, differential reproductive success.

• Mutation: Source of new genetic variation.

Species and Speciation

• Biological species concept: Groups of interbreeding populations reproductively isolated from others.

• Allopatric speciation: Speciation due to geographic isolation.

• Prezygotic vs. postzygotic isolation: Barriers before or after fertilization.

• Sexual selection: Selection for traits that increase mating success.

Phylogeny and Tree Thinking

Phylogenetic Trees

• Represent hypotheses about evolutionary relationships.

• Nodes indicate most recent common ancestors; branching points correspond to speciation events.

• Monophyletic groups (clades): All descendants of a common ancestor.

• Paraphyletic: Includes ancestor and some, but not all, descendants.

• Polyphyletic: Does not include the most recent common ancestor.

• Homology vs. analogy: Homology = shared ancestry; analogy = convergent evolution.

• Principle of parsimony: Simplest explanation (fewest evolutionary changes) is preferred.

Diversity of Life

Major Groups

• Domains: Bacteria, Archaea, Eukarya. Archaea and Eukarya are more closely related; Bacteria is the outgroup.

• Prokaryotes: Use diverse energy and carbon sources; reproduce via conjugation, transformation, transduction.

• Protists: Eukaryotic organisms, diverse in form and function.

• Endosymbiosis: Origin of mitochondria and chloroplasts in eukaryotes.

• Fungi: Heterotrophic, more closely related to animals; important decomposers; form lichens (with algae/cyanobacteria) and mycorrhizae (with plants).

• Animals: Metazoa, Eumetazoa, Bilaterians, Deuterostomes, Chordates, Vertebrates, Amniotes, Mammals (Monotremes, Marsupials, Eutherians), Primates.

• Key innovations: Notochord, vertebrae, jaws, lobed fins, limbs with digits, amniotic egg.

• Chordate characteristics: Notochord, dorsal nerve cord, pharyngeal slits, post-anal tail.

• Amniotes: Adapted for terrestrial life via amniotic egg.

Photosynthesis

Light Reactions and Calvin Cycle

• Inputs/outputs: Light reactions use water and light, produce O2, ATP, NADPH; Calvin cycle uses CO2, ATP, NADPH, produces sugars.

• Location: Light reactions in thylakoid membranes; Calvin cycle in stroma.

• Thylakoid membrane: Site of electron transport and ATP synthesis.

• Photosynthesis vs. respiration: Complementary processes; photosynthesis fixes carbon, respiration releases it.

• Carbon fixation: Incorporation of CO2 into organic molecules during the Calvin cycle.

Plant Anatomy and Physiology

Plant Structure

• Roots: Anchor plant, absorb water/nutrients.

• Shoots: Stems and leaves; support and photosynthesis.

• Leaves: Main site of photosynthesis.

• Tissue types: Dermal (protection), vascular (transport), ground (photosynthesis, storage, support).

• Turgid cell: Cell full of water; maintains structure, especially in non-woody plants; guard cells regulate stomata via turgidity changes.

• Transpiration: Water loss from leaves creates negative pressure, pulling water upward.

• Water movement: Cohesion and adhesion of water molecules facilitate upward movement.

• Symplastic pathway: Water moves through cytoplasm via plasmodesmata.

• Apoplastic pathway: Water moves through cell walls and intercellular spaces.

• Casparian strip: Forces water into symplast before entering vascular cylinder (stele).

• Xylem: Transports water/minerals; dead at maturity.

• Phloem: Transports sugars; living tissue.

• Guard cells: Regulate opening/closing of stomata.

• Meristems: Apical (length), axillary (branches), vascular cambium (secondary growth), cork cambium (bark).

• Secondary growth: Increase in girth; occurs in woody plants.

Plant Reproduction and Diversity

Plant Groups and Innovations

• Major groups: Nonvascular plants, seedless vascular plants, seed plants.

• Phylogeny: Some groups are paraphyletic (e.g., nonvascular plants), others monophyletic (e.g., seed plants).

• Key innovations: E.g., wood, seeds, flowers; each innovation allowed plants to exploit new environments and affected global cycles (carbon, water, atmosphere).

Ecology 1: Introduction to Ecology

Scales and Limits of Ecology

• Scales: Organismal, population, community, ecosystem, landscape, global.

• Distribution/abundance limits: Dispersal (movement), biotic (living), abiotic (non-living) factors.

• Fundamental vs. realized niche: Fundamental = potential range; realized = actual range due to competition, predation, etc.

• Biomes: Distribution determined by latitude, precipitation, temperature; latitude also affects species diversity.

• Biodiversity: Species richness (number of species) and relative abundance (evenness).

• Convergent evolution: Similar adaptations in unrelated species due to similar environments.

Ecology 2: Populations

Population Dynamics

• Vital rates: Birth, death, immigration, emigration.

• Dispersal vs. dispersion: Dispersal = movement of individuals; dispersion = spatial pattern (clumped, uniform, random).

• Survivorship curves: Graphs showing the number of survivors at each age; relate to life history strategies.

• Semelparous: Single reproductive event; iteroparous: Multiple events.

• Age structure graphs: Show population growth trends (expanding, stable, shrinking).

• Exponential growth: $N_t = N_0 e^{rt}$

• Logistic growth: $\frac{dN}{dt} = rN \left(\frac{K-N}{K}\right)$

• Carrying capacity (K): Maximum population size environment can support.

Ecology 3: Communities

Community Interactions

• Predator-prey dynamics: Modeled by Lotka-Volterra equations; predator and prey populations cycle.

• Numerical response: Change in predator numbers due to prey density.

• Functional response: Change in predator feeding rate due to prey density.

• Top-down regulation: Predators control prey populations.

• Bottom-up regulation: Resource availability controls population size.

• Resource partitioning: Species use different resources to reduce competition.

• Ecological niche: Role and position of a species in its environment.

• Succession: Sequence of community changes after disturbance.

Ecology 4: Ecosystems and Global Change

Energy and Nutrient Dynamics

• Energy flow: One-way through ecosystem; matter cycles.

• GPP (Gross Primary Production): Total energy captured by producers.

• NPP (Net Primary Production): GPP minus energy used by producers for respiration ($NPP = GPP - R_a$).

• Ra: Autotrophic respiration.

• Trophic levels: Producers, primary consumers, secondary consumers, etc.

• Food chains/webs: Show energy transfer among trophic levels.

Biogeochemical Cycles

• Water cycle: Evaporation, condensation, precipitation, runoff.

• Phosphorus cycle: Weathering of rocks, uptake by organisms, return via decomposition.

• Carbon cycle: Photosynthesis, respiration, combustion, decomposition.

• Nitrogen cycle: Nitrogen fixation, nitrification, assimilation, ammonification, denitrification.

Global Change

• Human activities alter population, community, and ecosystem dynamics; affect niches and biomes.

Term	Definition
Genotype	Genetic makeup of an organism
Phenotype	Observable traits
Homozygous	Two identical alleles at a locus
Heterozygous	Two different alleles at a locus
Monophyletic	Group containing ancestor and all descendants
Paraphyletic	Group containing ancestor and some descendants
Polyphyletic	Group lacking most recent common ancestor
GPP	Gross Primary Production
NPP	Net Primary Production
Ra	Autotrophic respiration

Additional info: This guide synthesizes the main topics and subtopics from the provided study guide, expanding on each with academic context, definitions, and examples. Equations are provided in LaTeX format as required. For more detailed examples and practice problems, refer to your course worksheets and activities.