The Chemistry of Life and Cells
Biology rests on chemistry. These cards cover the macromolecules that form living things, the cells that organize them, and the processes that make those cells work.
Molecules of Life
Water is the foundation of life. Its polar covalent bonds and hydrogen bonding give water high specific heat (moderates temperature), cohesion (surface tension, capillary action), adhesion, and universal solvent properties. Ice is less dense than liquid water, which allows aquatic life to survive cold winters.
Carbohydrates are made of C, H, O in approximately 1:2:1 ratio. Monosaccharides like glucose are the building blocks. Polysaccharides like starch and glycogen store energy. Others like cellulose provide structure. They are the primary short-term energy source for cells.
Lipids are hydrophobic molecules with diverse roles. Triglycerides store long-term energy. Phospholipids form cell membranes with hydrophilic heads and hydrophobic tails. Steroids like cholesterol regulate membrane fluidity and serve as signaling molecules.
Proteins are polymers of amino acids (20 standard types) joined by peptide bonds. Their shape determines their function. Proteins act as enzymes, structural support, transport carriers, antibodies, signaling molecules, and more. Denaturation destroys their shape and function.
Nucleic acids are built from nucleotides (sugar + phosphate + nitrogenous base). DNA is double-stranded and stores genetic information. RNA is single-stranded and plays key roles in protein synthesis (mRNA, tRNA, rRNA).
Enzymes are biological catalysts, usually proteins, that lower the activation energy of reactions. They bind substrates in an induced-fit model and are not consumed by the reaction. Temperature, pH, and inhibitors all affect enzyme activity.
Cell Structure and Function
Cell theory states that all living things are composed of cells. The cell is the basic unit of life, and all cells come from pre-existing cells. This principle, proposed by Schleiden, Schwann, and Virchow in the mid-1800s, is one of biology's unifying ideas.
Prokaryotic cells have no membrane-bound organelles, including no nucleus. Their DNA is circular, located in the nucleoid region. They have cell walls (peptidoglycan in bacteria), 70S ribosomes, and may have flagella or pili. Bacteria and Archaea are prokaryotes.
Eukaryotic cells have membrane-bound organelles including a true nucleus. Their DNA is linear and wrapped around histone proteins. They have 80S ribosomes and are typically 10-100 times larger than prokaryotes. Plants, animals, fungi, and protists are eukaryotes.
Organelles each have specific functions:
- Nucleus: DNA storage
- Mitochondria: ATP production via cellular respiration
- Chloroplasts: photosynthesis (plants only)
- Ribosomes: protein synthesis
- Rough ER: protein processing
- Smooth ER: lipid synthesis
- Golgi: packaging and shipping
- Lysosomes: digestion (animal cells)
- Vacuoles: storage (large in plants)
Cell membrane structure is a phospholipid bilayer with embedded proteins. It is selectively permeable. Small nonpolar molecules (O2, CO2) cross freely. Polar and charged molecules require transport proteins. Cholesterol and proteins modulate fluidity and function.
Transport and Metabolism
Passive transport requires no ATP. This includes diffusion (movement down a concentration gradient), osmosis (water movement across a membrane), and facilitated diffusion (using channel or carrier proteins to move molecules down their gradient).
Active transport requires ATP to pump molecules against their concentration gradient. The sodium-potassium pump maintains ion gradients essential for nerve and muscle function. Bulk transport moves large quantities: endocytosis brings material in, exocytosis expels material out.
Osmosis is the movement of water across a selectively permeable membrane toward high solute concentration. In hypotonic environments, cells swell or lyse. In hypertonic environments, they shrink. In isotonic solutions, there is no net water flow.
Cellular respiration converts glucose into usable energy. The overall equation is C6H12O6 + 6 O2 yields 6 CO2 + 6 H2O + 36-38 ATP. Glycolysis occurs in the cytoplasm and produces 2 ATP. The Krebs cycle occurs in the mitochondrial matrix and produces 2 ATP. The electron transport chain occurs in the inner mitochondrial membrane and produces 32-34 ATP via chemiosmosis.
Photosynthesis is the reverse process: 6 CO2 + 6 H2O + light yields C6H12O6 + 6 O2. It occurs in chloroplasts. Light-dependent reactions in the thylakoids split water, produce oxygen, ATP, and NADPH. The Calvin cycle in the stroma uses ATP and NADPH to fix CO2 into glucose via the enzyme RuBisCO.
| Term | Meaning |
|---|---|
| Characteristics of Life | Living things share: organization, metabolism, homeostasis, growth, reproduction, response to stimuli, and evolutionary adaptation. Viruses have some but not all, making their 'alive' status debated. Biology studies systems that exhibit all of these properties. |
| Water's Role in Life | Polar covalent bonds and hydrogen bonding give water high specific heat (moderates temperature), cohesion (surface tension, capillary action), adhesion, and universal solvent properties. Ice is less dense than liquid water, which allows aquatic life to survive cold winters. |
| Carbohydrates | Made of C, H, O in approximately 1:2:1 ratio. Monosaccharides (glucose, fructose), disaccharides (sucrose, lactose, maltose), polysaccharides (starch, glycogen for storage; cellulose, chitin for structure). Primary short-term energy source. |
| Lipids | Hydrophobic molecules. Triglycerides (fats/oils): long-term energy storage. Phospholipids: form cell membranes with hydrophilic heads and hydrophobic tails. Steroids (cholesterol, testosterone): four-ring structure; signaling and membrane fluidity. |
| Proteins | Polymers of amino acids (20 standard) joined by peptide bonds. Functions: enzymes, structure (collagen, keratin), transport (hemoglobin), defense (antibodies), signaling (insulin), movement (actin, myosin). Shape determines function; denaturation destroys shape. |
| Nucleic Acids | DNA and RNA, built from nucleotides (sugar + phosphate + nitrogenous base). DNA is double-stranded, stores genetic information. RNA is single-stranded, involved in protein synthesis (mRNA, tRNA, rRNA). Bases: A, T (or U in RNA), G, C. |
| Enzymes | Biological catalysts, usually proteins, that lower the activation energy of reactions. Substrate binds the active site in an induced-fit model. Affected by temperature, pH, and inhibitors. Enzymes are not consumed and can be used repeatedly. |
| Cell Theory | All living things are composed of cells; the cell is the basic unit of life; all cells come from pre-existing cells. Proposed by Schleiden, Schwann, and Virchow in the mid-1800s. One of biology's unifying principles. |
| Prokaryotic Cells | No membrane-bound organelles, including no nucleus. DNA is circular, in the nucleoid region. Have cell walls (peptidoglycan in bacteria), ribosomes (70S), and may have flagella, pili, or capsules. Domain Bacteria and Domain Archaea. |
| Eukaryotic Cells | Membrane-bound organelles including a true nucleus. Linear DNA wrapped around histones. 80S ribosomes. Includes plants, animals, fungi, and protists. Typically 10-100 times larger than prokaryotes. |
| Organelles (Key) | Nucleus (DNA), mitochondria (ATP via cellular respiration), chloroplasts (photosynthesis, plants only), ribosomes (protein synthesis), rough ER (protein processing), smooth ER (lipid synthesis), Golgi (packaging), lysosomes (digestion), vacuoles (storage, large in plants). |
| Cell Membrane Structure | Phospholipid bilayer with embedded proteins. Selectively permeable: small nonpolar molecules (O2, CO2) cross freely; polar and charged molecules require transport proteins. Cholesterol and proteins (integral, peripheral) modulate fluidity and function. |
| Passive vs. Active Transport | Passive: no ATP required; includes diffusion, osmosis, and facilitated diffusion (through channels or carriers). Active: requires ATP; pumps molecules against their gradient (Na+/K+ pump). Bulk transport: endocytosis (in) and exocytosis (out). |
| Osmosis | Movement of water across a selectively permeable membrane from low to high solute concentration. In hypotonic environments, cells swell (lyse if no wall); in hypertonic, they shrink (crenation in animals, plasmolysis in plants). Isotonic: no net flow. |
| Cellular Respiration | C6H12O6 + 6 O2 → 6 CO2 + 6 H2O + ~36-38 ATP. Stages: glycolysis (cytoplasm, 2 ATP), Krebs/citric acid cycle (mitochondrial matrix, 2 ATP), electron transport chain (inner mitochondrial membrane, ~32-34 ATP via chemiosmosis). |
| Photosynthesis | 6 CO2 + 6 H2O + light → C6H12O6 + 6 O2. Occurs in chloroplasts. Light-dependent reactions (thylakoids): split water, produce O2, ATP, NADPH. Calvin cycle (stroma): uses ATP and NADPH to fix CO2 into glucose via RuBisCO. |
Genetics and Inheritance
DNA, heredity, and how traits pass from parents to offspring. These topics underpin modern biology from medicine to evolution to biotechnology.
DNA and Gene Expression
DNA structure is a double helix with two antiparallel strands (Watson, Crick, Franklin, Wilkins). Each strand has a deoxyribose-phosphate backbone. Nitrogen bases pair A-T (2 hydrogen bonds) and G-C (3 hydrogen bonds). The sequence of bases stores all genetic information.
DNA replication is semiconservative. Each new DNA molecule has one old strand and one new strand (proven by Meselson-Stahl). Helicase unwinds the double helix. Primase adds RNA primers. DNA polymerase III builds new strands in the 5' to 3' direction. The leading strand is synthesized continuously, while the lagging strand is synthesized via Okazaki fragments. Ligase seals the nicks.
Transcription converts DNA to mRNA in the nucleus (eukaryotes). RNA polymerase binds the promoter and synthesizes mRNA using the template strand. Eukaryotic mRNA undergoes processing: a 5' cap is added, a 3' poly-A tail is added, and splicing removes introns and joins exons.
Translation converts mRNA to protein at the ribosome. Codons (3-nucleotide units) specify amino acids via the genetic code. tRNAs carrying amino acids match codons with anticodons. The start codon is AUG. Stop codons are UAA, UAG, and UGA. Peptide bonds form between amino acids as the ribosome moves along the mRNA.
Genetic code is universal (with minor exceptions) and redundant (most amino acids have multiple codons). It is read in triplets without overlap. 64 codons code for 20 amino acids plus start and stop signals. This near-universality supports common descent.
Mutations are changes in DNA sequence. Point mutations include silent (no effect), missense (different amino acid), and nonsense (premature stop) types. Frameshift mutations from insertions or deletions not divisible by 3 are often severe. Chromosomal mutations include duplications, deletions, inversions, and translocations.
Cell Division and Inheritance
Mitosis produces two genetically identical diploid daughter cells from one diploid cell. Phases are: prophase (chromatin condenses, spindle forms), metaphase (chromosomes align), anaphase (sister chromatids separate), and telophase (nuclei reform). Cytokinesis follows, dividing the cytoplasm.
Meiosis produces four genetically unique haploid gametes from one diploid cell through two divisions. Key events are crossing over (prophase I), which shuffles alleles, and independent assortment (metaphase I), which randomly distributes chromosomes. Random fertilization further increases diversity.
Mendel's Law of Segregation states each gamete receives one of two alleles per gene. Mendel's Law of Independent Assortment states alleles for different genes sort independently (unless linked on the same chromosome). These laws were discovered through pea plant experiments in the 1860s.
Punnett squares predict offspring genotypes. A monohybrid cross (Aa × Aa) yields 1 AA : 2 Aa : 1 aa (genotype) or 3:1 (phenotype if A is dominant). A dihybrid cross (AaBb × AaBb) yields a 9:3:3:1 phenotype ratio. A testcross (cross with homozygous recessive) reveals the unknown genotype.
Non-Mendelian inheritance includes incomplete dominance (blended phenotype), codominance (both alleles expressed), multiple alleles (like ABO blood type), polygenic traits (like height), epistasis (one gene masks another), and pleiotropy (one gene affects many traits).
Sex-linked inheritance involves genes on the X chromosome. X-linked recessive traits are more common in males (who have only one X). Females can be carriers. If a mother is a carrier and a son is affected, he inherited the allele from her.
Modern Genetics
Chromosome disorders result from abnormal chromosome number. Down syndrome (trisomy 21), Turner syndrome (XO), and Klinefelter syndrome (XXY) result from nondisjunction during meiosis. They are usually severe and often lethal before birth.
Biotechnology tools enable manipulation and analysis of DNA:
- PCR: amplifies specific sequences using primers and Taq polymerase
- Gel electrophoresis: separates DNA by size
- Restriction enzymes: cut DNA at specific sequences
- CRISPR-Cas9: enables guided genome editing
- DNA sequencing: reads base sequences (Sanger or next-generation methods)
Gene expression regulation controls when and where genes are active. Prokaryotes use operons (lac, trp) with repressor and activator proteins. Eukaryotes use chromatin remodeling, DNA methylation, transcription factors, alternative splicing, and miRNA-mediated degradation. This enables cell differentiation from identical genomes.
Epigenetics involves heritable changes in gene expression without DNA sequence changes. Mechanisms include DNA methylation (usually silencing), histone modification (acetylation typically activates), and non-coding RNAs. Environment, stress, and diet influence these changes, which can persist across generations.
| Term | Meaning |
|---|---|
| DNA Structure | Double helix (Watson, Crick, Franklin, Wilkins). Two antiparallel strands with deoxyribose-phosphate backbones. Nitrogen bases pair A-T (2 hydrogen bonds) and G-C (3 hydrogen bonds). Sequence of bases stores genetic information. |
| DNA Replication | Semiconservative: each new DNA molecule has one old and one new strand (Meselson-Stahl). Helicase unwinds; primase adds RNA primers; DNA polymerase III builds new strands 5' to 3'. Leading strand continuous; lagging strand via Okazaki fragments; ligase seals. |
| Transcription | DNA to RNA in the nucleus (eukaryotes). RNA polymerase binds the promoter and synthesizes mRNA using the template strand. Eukaryotic mRNA is processed: 5' cap, 3' poly-A tail, and splicing (introns removed, exons joined). |
| Translation | mRNA to protein at the ribosome. Codons (3 nucleotides) specify amino acids via the genetic code. tRNAs carrying amino acids match codons with anticodons. Start codon: AUG. Stop codons: UAA, UAG, UGA. Peptide bonds form between amino acids. |
| Genetic Code | Universal (with minor exceptions), redundant (most amino acids specified by multiple codons), and read in triplets without overlap. 64 codons code for 20 amino acids plus start and stop signals. The near-universality supports common descent of all life. |
| Mutations | Changes in DNA sequence. Point mutations: silent (no effect), missense (different amino acid), nonsense (premature stop). Frameshift (insertions/deletions not divisible by 3) often more severe. Chromosomal: duplications, deletions, inversions, translocations. |
| Mitosis | Somatic cell division producing two genetically identical diploid daughter cells. Phases: prophase (chromatin condenses, spindle forms), metaphase (chromosomes align), anaphase (sister chromatids separate), telophase (nuclei reform). Followed by cytokinesis. |
| Meiosis | Produces four genetically unique haploid gametes from one diploid cell through two divisions. Key events: crossing over (prophase I), independent assortment (metaphase I), random fertilization. These produce the genetic diversity natural selection acts on. |
| Mendel's Laws | Law of Segregation: each gamete gets one of two alleles per gene. Law of Independent Assortment: alleles for different genes sort independently into gametes (unless linked on the same chromosome). Based on pea plant experiments (1860s). |
| Punnett Squares | Monohybrid Aa × Aa: 1 AA : 2 Aa : 1 aa genotype (3:1 phenotype if A dominant). Dihybrid AaBb × AaBb: 9:3:3:1 phenotype. Testcross: cross unknown with homozygous recessive (aa) to determine genotype based on offspring ratios. |
| Non-Mendelian Inheritance | Incomplete dominance (blended phenotype, e.g., pink snapdragons), codominance (both alleles expressed, e.g., AB blood type), multiple alleles (ABO blood), polygenic (height, skin color), epistasis (one gene masks another), pleiotropy (one gene affects many traits). |
| Sex-Linked Inheritance | X-linked recessive traits (red-green colorblindness, hemophilia) more common in males because they have only one X. Females can be carriers. Mother is obligate carrier if son is affected; affected father passes X to all daughters (as carriers), never to sons. |
| Chromosome Disorders | Aneuploidy: abnormal chromosome number (Down syndrome = trisomy 21; Turner = XO; Klinefelter = XXY). Result from nondisjunction during meiosis. Usually severe, often lethal before birth. Detected via karyotype analysis. |
| Biotechnology Tools | PCR: amplifies specific DNA sequences using primers and Taq polymerase. Gel electrophoresis: separates DNA by size. Restriction enzymes: cut DNA at specific sequences. CRISPR-Cas9: guided genome editing. DNA sequencing (Sanger, next-gen): reads base sequences. |
| Gene Expression Regulation | Prokaryotes: operons (lac, trp) with operator and repressor/activator proteins. Eukaryotes: chromatin remodeling, DNA methylation, transcription factors at enhancers/promoters, alternative splicing, miRNA-mediated degradation. Enables cell differentiation from identical genomes. |
| Epigenetics | Heritable changes in gene expression without DNA sequence changes. Mechanisms: DNA methylation (usually silencing), histone modification (acetylation typically activates), non-coding RNAs. Influenced by environment, stress, diet; can persist across generations. |
Evolution and Diversity of Life
The theory of evolution and the diversity it explains. These cards cover natural selection, speciation, classification, and the major domains and kingdoms.
Mechanisms of Evolution
Natural selection (Darwin) works through four observations. Individuals vary in heritable traits. More offspring are produced than survive. Survival is nonrandom, favoring advantageous traits. Over generations, these advantageous alleles increase in frequency, shifting the population's genetic makeup.
Evidence for evolution includes the fossil record (transitional forms like Tiktaalik and Archaeopteryx), comparative anatomy (homologous structures and vestigial organs), embryology, molecular biology (shared genes and proteins), biogeography (unique species in isolated regions like the Galápagos), and direct observation (antibiotic resistance, Darwin's finches).
Hardy-Weinberg principle describes non-evolving populations. The equation p^2 + 2pq + q^2 = 1 predicts stable allele and genotype frequencies. This requires five conditions: no mutation, no gene flow, large population size (no drift), no selection, and random mating. Deviations indicate evolution is occurring.
Mechanisms of evolution include:
- Natural selection: nonrandom, adaptive change
- Genetic drift: random change, strongest in small populations
- Gene flow: migration of alleles into a population
- Mutation: ultimate source of variation
- Non-random mating: preference patterns alter frequencies
Types of selection include directional (one extreme favored, like peppered moths), stabilizing (intermediate favored, like human birth weight), disruptive (both extremes favored), and sexual selection (traits that improve mating success).
Speciation and Classification
Speciation is the formation of new species. Allopatric speciation occurs with geographic isolation (Grand Canyon squirrels, Galápagos finches). Sympatric speciation occurs without geographic separation (polyploidy in plants, habitat differentiation in cichlids). The biological species concept defines species as groups whose members interbreed and produce fertile offspring.
Reproductive isolation prevents interbreeding. Prezygotic isolation prevents fertilization: temporal (breeding at different times), habitat (different environments), behavioral (different courtship displays), mechanical (physical incompatibility), or gametic (sperm and egg incompatibility). Postzygotic isolation reduces hybrid fitness: hybrid inviability (poor survival), hybrid sterility (infertility like mules), or hybrid breakdown (problems in later generations).
Taxonomy (Linnaean system) organizes life hierarchically: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species. Binomial nomenclature uses Genus and species names (italicized). Example: Homo sapiens. Modern classification incorporates evolutionary relationships using shared derived characters.
Three domains divide all life. Bacteria are prokaryotes with peptidoglycan cell walls. Archaea are prokaryotes often found in extreme environments; their genes resemble eukaryotes more than bacteria. Eukarya contains all eukaryotic life (plants, animals, fungi, protists). Classification is based largely on ribosomal RNA comparisons (Carl Woese).
Kingdoms of Eukarya include:
- Animalia: multicellular heterotrophs, no cell walls
- Plantae: multicellular photosynthesizers with cellulose cell walls
- Fungi: mostly multicellular heterotrophs (decomposers) with chitin walls
- Protista: diverse, paraphyletic group (algae, protozoa, slime molds)
Viruses are non-cellular infectious agents with nucleic acid (DNA or RNA) in a protein capsid, sometimes with an envelope. They require host cells to replicate. The lytic cycle causes rapid replication and cell rupture. The lysogenic cycle integrates into the host genome as a prophage.
Diversity of Life
Plant groups evolved from aquatic ancestors. Bryophytes (mosses) lack vascular tissue. Pteridophytes (ferns) have vascular tissue and spores. Gymnosperms (conifers) produce naked seeds in cones. Angiosperms (flowering plants) produce seeds in fruits. Flowering plants dominate modern ecosystems with over 300,000 species.
Major animal phyla include:
- Porifera: sponges
- Cnidaria: jellyfish and corals
- Platyhelminthes: flatworms
- Nematoda: roundworms
- Mollusca: clams and octopi
- Annelida: segmented worms
- Arthropoda: insects and crustaceans (most diverse phylum)
- Echinodermata: starfish
- Chordata: vertebrates and relatives
Vertebrate classes include Agnatha (jawless fish), Chondrichthyes (cartilaginous fish like sharks), Osteichthyes (bony fish), Amphibia (frogs), Reptilia (lizards and snakes), Aves (birds), and Mammalia (mammals). This progression shows increasing complexity and adaptations to different environments.
Human evolution shows that our lineage split from other apes 6 to 8 million years ago. Bipedalism evolved early in Australopithecus (about 4 million years ago). Genus Homo appeared about 2.5 million years ago and showed larger brains and tool use. Homo sapiens emerged about 300,000 years ago in Africa, spread globally, and interbred with Neanderthals and Denisovans.
Origin of life: Early Earth had a reducing atmosphere, water, and energy sources (UV, lightning, volcanism). The Miller-Urey experiment (1953) produced amino acids from abiotic conditions. The RNA world hypothesis proposes self-replicating RNA preceded DNA and proteins. First cells were anaerobic prokaryotes appearing about 3.8 billion years ago.
| Term | Meaning |
|---|---|
| Natural Selection (Darwin) | Four observations: individuals vary, variation is heritable, more offspring produced than survive, survival is nonrandom. Conclusion: individuals with advantageous heritable traits reproduce more, shifting allele frequencies over generations. The mechanism of evolution. |
| Evidence for Evolution | Fossil record (transitional forms like Tiktaalik, Archaeopteryx), comparative anatomy (homologous structures, vestigial organs), embryology, molecular biology (shared genes and proteins), biogeography (Galápagos, Australia), and direct observation (antibiotic resistance, Darwin's finches). |
| Hardy-Weinberg Principle | In a non-evolving population, allele and genotype frequencies remain constant. p^2 + 2pq + q^2 = 1. Requires five conditions: no mutation, no gene flow, large population (no drift), no selection, random mating. Deviations indicate evolution is occurring. |
| Mechanisms of Evolution | Natural selection (nonrandom, adaptive), genetic drift (random, strongest in small populations; includes founder effect and bottleneck), gene flow (migration), mutation (ultimate source of variation), and non-random mating. |
| Types of Selection | Directional (one extreme favored, e.g., peppered moths), stabilizing (intermediate favored, e.g., human birth weight), disruptive (both extremes favored), and sexual selection (traits that improve mating success, often via intrasexual competition or female choice). |
| Speciation | Formation of new species. Allopatric: geographic isolation (Grand Canyon squirrels, Galápagos finches). Sympatric: reproductive isolation without geographic separation (polyploidy in plants, habitat differentiation in cichlids). Biological species concept: interbreeding produces fertile offspring. |
| Reproductive Isolation | Prezygotic: prevent fertilization (temporal, habitat, behavioral, mechanical, gametic isolation). Postzygotic: reduce hybrid fitness (hybrid inviability, hybrid sterility like mules, hybrid breakdown in later generations). Maintain species boundaries. |
| Taxonomy (Linnaean System) | Hierarchical: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species. Binomial nomenclature: Genus species (italicized). Example: Homo sapiens. Modern classification incorporates evolutionary relationships (phylogenetics) using shared derived characters. |
| Three Domains | Bacteria: prokaryotes with peptidoglycan cell walls. Archaea: prokaryotes often in extreme environments; genes closer to eukaryotes. Eukarya: all eukaryotic life (plants, animals, fungi, protists). Based largely on ribosomal RNA comparisons (Carl Woese). |
| Kingdoms of Eukarya | Animalia: multicellular heterotrophs, no cell walls. Plantae: multicellular photosynthesizers with cellulose cell walls. Fungi: mostly multicellular heterotrophs (decomposers) with chitin walls. Protista: diverse paraphyletic group (algae, protozoa, slime molds). |
| Viruses | Non-cellular infectious agents consisting of nucleic acid (DNA or RNA) in a protein capsid (sometimes with an envelope). Require host cells to replicate. Lytic cycle: rapid replication, cell lysis. Lysogenic: integration into host genome (prophage). Not in the tree of life. |
| Plant Groups | Bryophytes (mosses, nonvascular), pteridophytes (ferns, vascular, spore-producing), gymnosperms (conifers, naked seeds in cones), angiosperms (flowering plants, seeds in fruits, the dominant modern group with ~300,000 species). |
| Animal Phyla (Major) | Porifera (sponges), Cnidaria (jellyfish, corals), Platyhelminthes (flatworms), Nematoda (roundworms), Mollusca (clams, octopi), Annelida (segmented worms), Arthropoda (insects, crustaceans, most species of any phylum), Echinodermata (starfish), Chordata (vertebrates and relatives). |
| Vertebrate Classes | Agnatha (jawless fish: hagfish, lamprey), Chondrichthyes (cartilaginous: sharks, rays), Osteichthyes (bony fish), Amphibia (frogs, salamanders), Reptilia (lizards, snakes, turtles), Aves (birds), Mammalia (egg-laying monotremes, pouched marsupials, placental mammals). |
| Human Evolution | Lineage split from other apes ~6-8 MYA. Bipedalism evolved early (Australopithecus, ~4 MYA). Genus Homo (~2.5 MYA) showed larger brain sizes and tool use. H. sapiens emerged ~300,000 years ago in Africa, spread globally, interbred with Neanderthals and Denisovans. |
| Origin of Life | Early Earth: reducing atmosphere, water, energy sources (UV, lightning, volcanism). Miller-Urey experiment (1953) produced amino acids from abiotic conditions. RNA world hypothesis: self-replicating RNA preceded DNA and proteins. First cells: anaerobic prokaryotes, ~3.8 BYA. |
Ecology and Human Biology
How organisms interact with each other and their environments, plus a tour of human physiology. These cards round out general biology's scope.
Ecology and Ecosystems
Levels of ecology organize life from small to large scales:
- Organism: an individual
- Population: members of one species in one location
- Community: all species in one location
- Ecosystem: community plus abiotic environment
- Biome: large-scale regional ecosystem
- Biosphere: all life on Earth
Each level has emergent properties not present at lower levels.
Population growth follows two main models. Exponential growth (J-curve) assumes unlimited resources and produces dN/dt = rN. Logistic growth (S-curve) includes carrying capacity (K) and produces dN/dt = rN((K-N)/K). Real populations slow as they approach carrying capacity.
Community interactions shape ecosystems:
- Competition: two species compete for resources (both harmed)
- Predation: predator eats prey (predator gains, prey loses)
- Parasitism: parasite lives on host (parasite gains, host loses)
- Herbivory: herbivore eats plant (herbivore gains, plant loses)
- Mutualism: both species benefit (clownfish and anemones, bees and flowers)
- Commensalism: one species benefits, one unharmed (cattle egrets and cattle)
Competitive exclusion states that two species cannot indefinitely share the same niche.
Energy flow through ecosystems starts with producers (autotrophs). Primary consumers (herbivores) eat plants. Secondary consumers eat herbivores. Tertiary consumers eat secondary consumers. Decomposers recycle nutrients. Only about 10% of energy transfers to each level, which limits food chain length.
Biogeochemical cycles recycle matter:
- Carbon: photosynthesis captures it, respiration and combustion release it, decomposition recycles it
- Nitrogen: bacteria fix N2 from air, nitrification converts it to nitrate, assimilation incorporates it into organisms, denitrification returns it to atmosphere
- Water: evaporation from oceans and land, precipitation returns it
- Phosphorus: weathering releases it, sedimentation buries it; no atmospheric component
Human activity disrupts all cycles.
Ecological succession describes how communities change over time. Primary succession begins on bare rock (glacial retreat, lava flows) where pioneers like lichens establish themselves. Secondary succession occurs after disturbance where soil remains (fire, farm abandonment). Succession tends toward a climax community, though disturbance often resets it.
Biodiversity has three levels: genetic (variation within species), species (number and evenness), and ecosystem (habitat variety). High biodiversity supports stability and resilience. Major threats are summarized as HIPPO: habitat loss, invasive species, pollution, population growth, overharvesting, and climate change.
Climate change results from rising atmospheric CO2 (over 420 ppm, up from 280 ppm pre-industrial) and other greenhouse gases that trap heat. Consequences include global warming, sea-level rise, ocean acidification, shifted species ranges, increased extreme weather, and ecosystem disruption.
Human Body Systems
Nervous system processes information. The central nervous system (brain and spinal cord) coordinates activity. The peripheral nervous system includes the somatic (voluntary) and autonomic systems. The sympathetic system triggers fight-or-flight responses. The parasympathetic system triggers rest-and-digest responses. Neurons communicate via action potentials and neurotransmitters.
Endocrine system uses hormones for communication. The hypothalamus and pituitary gland control many other glands. Key hormones regulate blood sugar (insulin and glucagon), metabolism (thyroid hormones), stress response (cortisol), and reproduction (sex hormones).
Circulation and respiration: The heart pumps blood. The right side sends blood to the lungs (pulmonary circulation). The left side sends blood to the body (systemic circulation). Red blood cells carry oxygen via hemoglobin. Gas exchange occurs in alveoli and at tissues via diffusion across partial pressure gradients. Most CO2 travels as bicarbonate.
Digestion breaks down food mechanically and chemically. The mouth starts starch digestion with amylase. The stomach uses pepsin to begin protein digestion in acid. The small intestine completes digestion and absorbs nutrients across villi. The large intestine absorbs water. Waste exits via the rectum.
Immune system has innate and adaptive components. Innate immunity is nonspecific and fast: skin, mucus, phagocytes, natural killer cells, complement proteins, and inflammation. Adaptive immunity is specific and has memory: B cells produce antibodies (humoral immunity), and T cells coordinate immunity and kill infected cells (cellular immunity). Vaccines work by triggering adaptive memory.
Reproduction and development: Humans use internal fertilization. Embryos develop in the uterus over about 40 weeks. Gametes are produced via meiosis. The zygote undergoes cleavage, blastulation, gastrulation, and organogenesis. Three germ layers form: ectoderm (skin, nerves), mesoderm (muscle, bone, blood), and endoderm (gut lining).
Homeostasis maintains stable internal conditions despite external changes. Humans regulate:
- Body temperature (about 37°C)
- Blood glucose (70-100 mg/dL fasting)
- Blood pH (7.35-7.45)
- Osmolarity
- Ion concentrations
Negative feedback loops restore normal conditions when deviations occur. Failure causes disease.
Evolution and medicine connects evolutionary thinking to health. Antibiotic resistance shows natural selection favoring resistant bacteria. Vaccine design targets conserved viral features. Cancer involves somatic evolution within a body. Genetic disease results from mutations and inheritance patterns. Evolution is a unifying framework for understanding health.
| Term | Meaning |
|---|---|
| Levels of Ecology | Organism → population (same species, same place) → community (all species, same place) → ecosystem (community + abiotic environment) → biome (large-scale regional ecosystem) → biosphere (all life on Earth). Each level has emergent properties. |
| Population Growth | Exponential (J-curve): dN/dt = rN; unlimited resources. Logistic (S-curve): dN/dt = rN((K-N)/K); carrying capacity K limits growth. r-selected species: many offspring, little care. K-selected: few offspring, much parental investment. |
| Community Interactions | Competition (-/-), predation (+/-), parasitism (+/-), herbivory (+/-), mutualism (+/+, e.g., clownfish and anemones, bees and flowers), commensalism (+/0, e.g., cattle egrets and cattle). Competitive exclusion: two species cannot share the same niche indefinitely. |
| Energy Flow | Producers (autotrophs) capture energy (usually via photosynthesis). Consumers: primary (herbivores) → secondary → tertiary → quaternary. Decomposers recycle nutrients. Only ~10% of energy transfers up each level (10% rule); limits food chain length. |
| Biogeochemical Cycles | Carbon: photosynthesis, respiration, combustion, decomposition. Nitrogen: N2 fixation by bacteria, nitrification, assimilation, denitrification. Water: evaporation, precipitation. Phosphorus: no atmospheric component; weathering and sedimentation drive it. Human activity disrupts all. |
| Ecological Succession | Primary: begins on bare rock (e.g., after glacier retreat or lava flow); pioneers are typically lichens. Secondary: after disturbance where soil remains (fire, farm abandonment). Ends in a relatively stable climax community, though disturbance often resets it. |
| Biodiversity | Three levels: genetic (within species), species (number and evenness), ecosystem (variety of habitats). High biodiversity supports stability and resilience. Threats: habitat loss, invasive species, pollution, population, overharvesting, climate change (HIPPO). |
| Climate Change | Rising atmospheric CO2 (over 420 ppm, up from ~280 ppm pre-industrial), methane, and other greenhouse gases trap heat. Consequences: global warming, sea-level rise, ocean acidification, shifted ranges, increased extreme weather, ecosystem disruption. |
| Human Nervous System | Central: brain and spinal cord. Peripheral: nerves outside CNS, subdivided into somatic (voluntary) and autonomic (involuntary, sympathetic fight-or-flight, parasympathetic rest-and-digest). Neurons communicate via action potentials and neurotransmitters. |
| Human Endocrine System | Glands secrete hormones into the blood to affect distant target cells. Hypothalamus and pituitary control many glands. Key hormones: insulin and glucagon (blood sugar), thyroid hormones (metabolism), cortisol (stress), sex hormones (reproduction). |
| Circulation and Respiration | Heart pumps blood: right side to lungs (pulmonary), left side to body (systemic). Red blood cells carry O2 via hemoglobin. Gas exchange occurs in alveoli and at tissues via diffusion across partial pressure gradients. CO2 travels mostly as bicarbonate. |
| Digestion | Mechanical and chemical breakdown of food. Mouth (amylase starts starch digestion) → stomach (pepsin begins protein digestion in acid) → small intestine (enzymes complete digestion, villi absorb nutrients) → large intestine (water absorption) → rectum/anus. |
| Immune System | Innate (nonspecific, fast): skin, mucus, phagocytes, NK cells, complement, inflammation. Adaptive (specific, with memory): B cells produce antibodies (humoral); T cells coordinate immunity and kill infected cells (cellular). Vaccines work via adaptive memory. |
| Reproduction and Development | Humans use internal fertilization; embryos develop in the uterus (~40 weeks). Gametes produced via meiosis. Zygote undergoes cleavage, blastulation, gastrulation, and organogenesis. Three germ layers: ectoderm (skin, nerves), mesoderm (muscle, bone, blood), endoderm (gut lining). |
| Homeostasis in Humans | Tightly regulated internal conditions: body temperature (~37°C), blood glucose (~70-100 mg/dL fasting), blood pH (7.35-7.45), osmolarity, and many ion concentrations. Negative feedback loops maintain these despite environmental changes; failure causes disease. |
| Evolution and Medicine | Evolutionary thinking informs medicine: antibiotic resistance (natural selection favors resistant bacteria), vaccine design (must target conserved viral features), cancer (somatic evolution within a body), and genetic disease (mutations and their inheritance). A unifying framework. |
How to Study biology Effectively
Mastering biology requires the right study approach, not just more hours. Research in cognitive science shows three techniques produce the best outcomes: active recall (testing yourself), spaced repetition (reviewing at optimized intervals), and interleaving (mixing related topics).
FluentFlash builds on all three. The FSRS algorithm schedules every term for review at exactly the moment you are about to forget it. This maximizes retention while minimizing study time.
Why Passive Review Fails
The most common mistake is relying on passive review. Re-reading notes, highlighting textbook passages, or watching lecture videos feels productive but produces only 10-20% of the retention that active recall achieves. Flashcards force your brain to retrieve information, strengthening memory pathways far more than recognition alone.
Pair this with spaced repetition scheduling, and you can learn in 20 minutes daily what would take hours of passive review.
A Practical Study Plan
Start by creating 15-25 flashcards covering the highest-priority concepts. Review them daily for the first week using FSRS scheduling. As cards become easier, intervals automatically expand from minutes to days to weeks. You are always working on material at the edge of your knowledge.
After 2-3 weeks of consistent practice, biology concepts become automatic rather than effortful.
Daily Study Steps
- Generate flashcards using FluentFlash AI or create them manually from your notes
- Study 15-20 new cards per day, plus scheduled reviews
- Use multiple study modes (flip, multiple choice, written) to strengthen recall
- Track your progress and identify weak topics for focused review
- Review consistently; daily practice beats marathon sessions
- 1
Generate flashcards using FluentFlash AI or create them manually from your notes
- 2
Study 15-20 new cards per day, plus scheduled reviews
- 3
Use multiple study modes (flip, multiple choice, written) to strengthen recall
- 4
Track your progress and identify weak topics for focused review
- 5
Review consistently, daily practice beats marathon sessions
Why Flashcards Work Better Than Other Study Methods for biology
Flashcards are one of the most research-backed study tools for any subject. The reason comes down to how memory works. When you read a textbook passage, your brain stores information in short-term memory. Without retrieval practice, it fades within hours.
Flashcards force retrieval, which is the mechanism that transfers information from short-term to long-term memory.
The Testing Effect
The "testing effect" is documented in hundreds of peer-reviewed studies. Students who study with flashcards consistently outperform those who re-read by 30-60% on delayed tests. This is not because flashcards contain more information. It is because retrieval strengthens neural pathways in ways passive exposure cannot.
Every time you successfully recall a biology concept from a flashcard, you make that concept easier to recall next time. This creates durable, retrievable knowledge.
FSRS Amplifies Effectiveness
FluentFlash amplifies this effect with the FSRS algorithm, a modern spaced repetition system. It schedules reviews at mathematically-optimal intervals based on your actual performance. Cards you find easy get pushed further into the future. Cards you struggle with come back sooner.
Over time, this builds remarkable retention with minimal time investment. Students using FSRS-based systems typically retain 85-95% of material after 30 days. Compare this to roughly 20% retention from passive review alone.