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

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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 allele per 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: Alleles of different genes assort independently during gamete formation, unless genes are linked.

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 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:

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 is synthesized 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: (1) Helicase, (2) Single-strand binding protein, (3) Topoisomerase, (4) Primase, (5) DNA polymerase III, (6) DNA polymerase I, (7) DNA ligase.

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 vs. 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: Binds to stop codon, terminating translation.

Development and Germ Layers

Genetic Diversity and Sexual Reproduction

Sexual reproduction increases genetic diversity via independent assortment, crossing over, and random fertilization, accelerating 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—protect and nourish the embryo in reptiles and mammals.

Descent with Modification

Darwinian Evolution

Two major concepts: (1) Descent with modification, (2) Natural selection.
Evidence: Fossils, homology, biogeography, direct observation, molecular biology.

Fossils and Strata

Fossil: Preserved remains or traces of organisms, typically found in sedimentary rock strata.
Strata: Layers of rock representing sequential time periods.

Homology and Vestigial Structures

Homology: Similarity due to shared ancestry (e.g., genetic code, limb bones).
Vestigial structures: Remnants of features that served a function in ancestors.

Natural Selection and Speciation

Fitness and Adaptation

Fitness: The ability to survive and reproduce, passing genes to the next generation.
Adaptation: A heritable trait that increases fitness in a given environment.

Conditions for Natural Selection

Variation in traits, heritability, differential survival/reproduction.

Speciation

Biological species concept: Groups of interbreeding populations reproductively isolated from others.
Allopatric speciation: Speciation due to geographic separation.
Prezygotic vs. postzygotic isolation: Barriers before or after fertilization.

Phylogeny and Tree Thinking

Phylogenetic Trees

Represent hypotheses about evolutionary relationships.
Nodes indicate most recent common ancestors; branching points relate to speciation.
Monophyletic (clade), paraphyletic, polyphyletic groups distinguished by inclusion of ancestors and descendants.

Homology vs. Analogy

Homology: Similarity due to shared ancestry.
Analogy (homoplasy): Similarity due to convergent evolution, not common ancestry.
Parsimony: The simplest explanation (fewest evolutionary changes) is preferred.

Diversity of Life

Domains and Major Groups

Domains: Bacteria, Archaea, Eukarya. Archaea is more closely related to Eukarya; Bacteria is the outgroup.
Prokaryotes: Use diverse energy and carbon sources; reproduce via conjugation, transformation, transduction.
Fungi: Heterotrophic, more closely related to animals, important decomposers, form lichens and mycorrhizae.
Animals: Metazoa, Eumetazoa, Bilaterians, Deuterostomes, Chordates, Vertebrates, Amniotes, Mammals (Monotremes, Marsupials, Eutherians), Primates.

Key Innovations in Vertebrates

Notochord, vertebrae, jaws, lobed fins, limbs with digits, amniotic egg—each innovation marks a branching point in vertebrate evolution.

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 glucose.
Location: Light reactions in thylakoid membranes; Calvin cycle in stroma.
Carbon fixation: Incorporation of CO2 into organic molecules during the Calvin cycle.

Photosynthesis vs. Cellular Respiration

Photosynthesis and respiration are complementary; the outputs of one are the inputs of the other, cycling carbon and energy through the biosphere.

Plant Anatomy and Physiology

Plant Structure

Roots: Anchor plant, absorb water/nutrients.
Shoots: Stems and leaves; support and photosynthesis.
Leaves: Main site of photosynthesis.

Plant Tissues

Dermal: Protective outer covering.
Vascular: Xylem (water transport, dead at maturity), phloem (sugar transport, living tissue).
Ground: Photosynthesis, storage, support.

Water Movement and Turgor

Turgid cell: Cell with high water pressure; maintains plant structure, especially in non-woody plants.
Transpiration: Water loss from leaves creates negative pressure, pulling water up through xylem.
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).

Meristems and Growth

Apical meristems: Primary growth (lengthening).
Axillary meristems: Branch formation.
Vascular cambium: Secondary growth (thickening).
Cork cambium: Produces protective outer bark.

Plant Reproduction and Diversity

Major Plant Groups

Nonvascular plants, seedless vascular plants, seed plants; phylogenetic relationships reflect evolutionary innovations.
Monophyletic groups include all descendants of a common ancestor; paraphyletic groups do not.

Key Innovations in Plants

Examples: Wood (secondary xylem), seeds, flowers, vascular tissue—each innovation allowed plants to colonize new environments and impact global cycles.

Ecology 1: Introduction to Ecology

Scales of Ecology

Organismal, population, community, ecosystem, landscape, global.

Distribution and Limiting Factors

Dispersal, biotic (living) factors, abiotic (non-living) factors limit species distributions.
Fundamental niche: Full range of conditions a species can occupy.
Realized niche: Actual conditions occupied due to competition and other factors.

Biomes and Biodiversity

Latitude, precipitation, and temperature determine biome distribution and species diversity.
Biodiversity: Species richness (number of species) and relative abundance (evenness).

Ecology 2: Populations

Population Dynamics

Vital rates: Birth, death, immigration, emigration.
Dispersal (movement between populations) vs. dispersion (pattern within a population: clumped, uniform, random).
Cohort: Group of individuals born at the same time.

Population Growth Models

Exponential growth:
Logistic growth:
K: Carrying capacity; maximum population size environment can support.

Ecology 3: Communities

Predator-Prey Dynamics

Described by Lotka-Volterra model; predator and prey populations cycle in response to each other.
Numerical response: Change in predator numbers due to prey density.
Functional response: Change in predator feeding rate due to prey density.

Community Structure

Top-down regulation: Predators control community structure.
Bottom-up regulation: Resource availability controls community structure.
Resource partitioning reduces competition; competitive exclusion principle states that two species cannot occupy the same niche indefinitely.
Succession: Sequence of community changes after disturbance.

Ecology 4: Ecosystems and Global Change

Energy and Matter Flow

Energy flows one-way through ecosystems; matter cycles.
GPP (Gross Primary Production): Total energy captured by producers.
NPP (Net Primary Production): GPP minus energy used by producers for respiration ().
GPP > NPP > Ra (autotrophic respiration).

Trophic Levels and Food Webs

Producers, primary consumers, secondary consumers, etc.; energy transfer is inefficient (~10% per level).

Biogeochemical Cycles

Water, phosphorus, carbon, and nitrogen cycles move elements through ecosystems.

Global Change

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

Cycle	Main Reservoir	Key Processes
Water	Oceans	Evaporation, precipitation, transpiration
Carbon	Atmosphere, biomass	Photosynthesis, respiration, combustion
Nitrogen	Atmosphere	Nitrogen fixation, nitrification, denitrification
Phosphorus	Rocks, soil	Weathering, uptake by plants

Additional info: This guide synthesizes and expands upon the study guide outline, providing definitions, examples, and context for each major topic in introductory college biology.