Comprehensive Study Notes for College Biology: Genetics, Evolution, Plant Biology, and Ecology

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Mendelian Genetics and Molecular Genetics

Gene Locus, Homologous Pairs, and Meiosis

The gene locus is the specific location of a gene on a chromosome. In diploid organisms, each gene locus is present in two copies—one on each chromosome of a homologous pair (one maternal, one paternal). During meiosis I, homologous chromosomes (and thus the two copies of each locus) separate into different daughter cells. After meiosis II, each gamete contains just one copy of each locus.

Genotype, Phenotype, and Modes of Inheritance

Genotype: The genetic makeup (alleles) of an organism for a trait (e.g., BB, Bb, or bb).
Phenotype: The observable trait resulting from the genotype and environment (e.g., brown or blue eyes).
Modes of Inheritance: Rules connecting genotype to phenotype, including:
- Mendelian (dominant–recessive): Dominant allele masks recessive (Bb shows dominant trait).
- Incomplete dominance: Heterozygote shows intermediate phenotype (e.g., pink flowers from red and white alleles).
- Codominance: Both alleles fully expressed (e.g., AB blood type).
- Sex-linked inheritance: Genes on sex chromosomes affect males and females differently (e.g., X-linked color blindness).
- Polygenic inheritance: Multiple genes contribute to a single phenotype (e.g., height).

Genetic Linkage, Crossing Over, and Recombination Frequency

Genetic linkage occurs when genes are close together on the same chromosome and tend to be inherited together. Crossing over during prophase I of meiosis can separate linked genes, producing recombinant gametes. The recombination frequency (percentage of recombinant offspring) reflects the genetic distance between genes: the farther apart, the higher the frequency. One map unit (centimorgan) equals 1% recombination frequency.

DNA Structure and Replication

DNA nucleotide: Phosphate group, deoxyribose sugar, and a nitrogenous base (A, T, G, C). The base varies; the sugar and phosphate are uniform.
Double helix: Two strands held together by hydrogen bonds (A–T, G–C), running antiparallel (5'→3' and 3'→5').
Replication: DNA polymerases synthesize new DNA only in the 5'→3' direction. The leading strand is synthesized continuously; the lagging strand is synthesized in Okazaki fragments, each starting with an RNA primer.

Central Dogma and Gene Expression

Central Dogma: DNA → RNA → Protein
Transcription: DNA is transcribed to mRNA in the nucleus by RNA polymerase II, using transcription factors and promoter sequences (e.g., TATA box).
Translation: mRNA is translated into protein at ribosomes in the cytoplasm. tRNAs bring amino acids, matching mRNA codons with anticodons.
Mutations: Point mutations (silent, missense, nonsense) and insertions/deletions (frameshift if not a multiple of three) can alter protein sequences.

Evolution and Speciation

Darwinian Evolution and Evidence

Descent with modification: Species arise from ancestral species, accumulating differences over time.
Natural selection: Individuals with advantageous traits leave more offspring, increasing those traits in the population.
Evidence: Direct observation, homology (shared ancestry), fossil record, biogeography, and molecular biology (shared genetic code).

Speciation and Reproductive Isolation

Allopatric speciation: Geographic isolation leads to divergence and formation of new species.
Prezygotic barriers: Prevent mating or fertilization (habitat, temporal, behavioral, mechanical, gametic isolation).
Postzygotic barriers: Prevent hybrid offspring from developing into viable, fertile adults.

Plant Structure, Growth, and Development

Plant Organs and Tissue Types

Roots: Anchor plant, absorb water/minerals, store carbohydrates.
Shoots (stems, leaves, flowers): Support, photosynthesis, reproduction.
Leaves: Main site of photosynthesis, gas exchange via stomata.

Dermal tissue: Outer protective covering (epidermis, cuticle, root hairs).
Vascular tissue: Transport (xylem for water/minerals, phloem for sugars).
Ground tissue: Storage, photosynthesis, support (cortex, pith, mesophyll).

Meristems and Plant Growth

Apical meristems: At root and shoot tips; responsible for primary (lengthwise) growth.
Axillary meristems: At leaf bases; form branches or flowers.
Vascular cambium: Lateral meristem producing secondary xylem (wood) and phloem (thickening stems/roots).
Cork cambium: Lateral meristem producing cork (protective outer layer).

Diagram of plant showing shoot tip, axillary bud meristem, root apical meristems, vascular cambium, and cork cambium Diagram showing primary and secondary growth in plant stems, with details of cambium activity and tissue layers

Turgor Pressure and Water Movement

Turgid cell: Plant cell full of water, providing structural support (especially in non-woody plants).
Transpiration: Evaporation of water from leaves creates negative pressure, pulling water up through xylem (cohesion and adhesion of water molecules).
Guard cells: Regulate stomatal opening/closing, balancing CO₂ uptake and water loss.

Ecology: Populations, Communities, and Ecosystems

Biodiversity: Species Richness and Relative Abundance

Biodiversity includes species richness (number of species) and relative abundance (proportion of each species). Communities with even abundance are more diverse than those dominated by one species.

Two forest communities showing differences in species richness and relative abundance

Population Dispersion Patterns

Clumped: Individuals aggregate in patches (most common; resource-based).
Uniform: Even spacing, often due to territoriality or competition.
Random: Unpredictable spacing, rare in nature.

Patterns of dispersion: clumped, uniform, random

Survivorship Curves and Life History Strategies

Type I: Low mortality early, high late (e.g., humans).
Type II: Constant mortality (e.g., rodents).
Type III: High early mortality, low later (e.g., oysters).

Survivorship curves: Type I, II, III

Predator-Prey Dynamics (Lotka-Volterra Model)

Predator and prey populations cycle: prey increase first, followed by predators. As predators rise, prey decline, then predator numbers fall, allowing prey to recover.

Graph of hare and lynx population cycles

Top-Down vs. Bottom-Up Regulation

Bottom-up: Resource availability controls higher trophic levels.
Top-down: Predators control abundance of lower trophic levels.

Diagram of top-down and bottom-up control in food webs

Resource Partitioning and Ecological Niches

Resource partitioning allows similar species to coexist by using different resources or habitats, reducing direct competition. The ecological niche is the sum of a species' use of biotic and abiotic resources. The fundamental niche is the full potential range; the realized niche is what is actually occupied due to competition.

Diagram of barnacle species showing fundamental and realized niches

Succession in Communities

Succession is the sequence of species colonization and replacement after disturbance. Primary succession starts on bare substrate; secondary succession occurs where soil remains.

Energy Flow and Nutrient Cycling in Ecosystems

Energy flow: Sun → producers → consumers → decomposers; energy lost as heat at each step.
Chemical cycling: Elements (C, N, P, H₂O) cycle between biotic and abiotic components.

Diagram of energy flow and chemical cycling in an ecosystem

Trophic Levels and Energy Pyramids

Primary producers: Plants, algae (autotrophs).
Primary consumers: Herbivores.
Secondary/tertiary consumers: Carnivores.
Decomposers: Break down dead material, recycle nutrients.
Only ~10% of energy transfers to the next level, limiting food chain length.

Energy pyramid showing energy transfer between trophic levels

Biogeochemical Cycles

Water cycle: Evaporation, condensation, precipitation, transpiration, runoff.
Carbon cycle: Photosynthesis, respiration, decomposition, fossil fuel burning.
Nitrogen cycle: Nitrogen fixation, nitrification, assimilation, denitrification.
Phosphorus cycle: Weathering of rocks, uptake by organisms, decomposition, sedimentation.

Diagram of water and carbon cycles Diagram of nitrogen cycle Diagram of phosphorus cycle

Global Change and Ecosystem Dynamics

Global change (e.g., climate change) alters temperature, precipitation, and disturbance regimes, shifting species distributions, changing community composition, and affecting energy flow and nutrient cycling. Species must adapt, migrate, or face decline if their realized niches disappear.

Diagram showing feedback between ecological and evolutionary change

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