FINAL REVIEW
Honors Biology – Unit 1: Structure & Function
Chemistry of Life, Cells, and Homeostasis
I. Classification of Life
Three Domains of Life
Domain Bacteria: Prokaryotic, unicellular organisms with no nucleus. Includes all true bacteria.
Domain Archaea: Prokaryotic organisms that often live in extreme environments (high heat, salt, or acidity). Genetically distinct from bacteria.
Domain Eukarya: Organisms whose cells contain a nucleus and membrane-bound organelles.
Kingdoms within Domain Eukarya
Kingdom Protista: Mostly unicellular eukaryotes. Very diverse; includes protozoa (animal-like), algae (plant-like), and slime molds (fungus-like). Can be autotrophic or heterotrophic.
Kingdom Plantae: Multicellular autotrophs that perform photosynthesis. Examples include trees, ferns, and mosses.
Kingdom Fungi: Mostly multicellular heterotrophs that absorb nutrients. Includes mushrooms and yeast.
Kingdom Animalia: Multicellular heterotrophs that ingest food. Includes sponges, worms, squids, horses, and humans.
II. Common Properties of Life
Order: Living organisms are highly organized; the basic unit of life is the cell.
Reproduction: Organisms can reproduce to produce new individuals.
Growth and Development: Growth and development are guided by specific instructions coded in DNA.
Energy Processing: All living organisms acquire and use energy to maintain organization and carry out processes.
Response to the Environment: Organisms respond to environmental stimuli.
Regulation: Living systems regulate internal conditions (homeostasis).
Evolutionary Adaptation: Populations evolve over generations as individuals with advantageous traits reproduce more successfully.
III. Levels of Biological Organization
Biosphere: All life on Earth and all environments where life exists.
Ecosystem: A community of organisms interacting with their physical environment.
Community: All populations of different species living in an area.
Population: A group of individuals of the same species in one area.
Organism: An individual living thing.
Organ System: A group of organs working together (e.g., nervous system).
Organ: A structure composed of tissues performing a specific function (e.g., brain).
Tissue: A group of similar cells working together.
Cell: The basic unit of structure and function in living things.
Organelle: Specialized structures within cells (e.g., nucleus).
Molecule: Two or more atoms bonded together (e.g., DNA).
Atom: The smallest unit of matter (e.g., carbon).
IV. Chemistry of Life
Atoms and Subatomic Particles
Atoms are extremely small; millions can fit across a tiny space.
Protons: Positively charged
Neutrons: No charge
Electrons: Negatively charged
Elements and Compounds
Element: A pure substance made of one type of atom (e.g., carbon, oxygen). Represented by chemical symbols.
Compound: A substance formed when two or more elements combine in fixed proportions (e.g., NaCl).
Chemical Bonds
Covalent Bonds: Atoms share electrons.
Example: Water (H₂O)
Chemical reactions break existing bonds and form new bonds, releasing or absorbing energy.
V. Water and Life
Polarity of Water
Water is polar because oxygen is more electronegative than hydrogen.
Polarity allows hydrogen bonding, which gives water its unique properties.
Properties of Water That Support Life
Cohesion: Water molecules stick to each other.
Adhesion: Water sticks to other substances.
High Specific Heat: Water resists temperature changes.
Ice is Less Dense Than Liquid Water: Ice floats, insulating bodies of water.
Acids and Bases
Acidic solutions: High H⁺ concentration, low pH.
Basic solutions: High OH⁻ concentration, high pH.
pH scale ranges from 0–14; pH 7 is neutral.
Changes in pH can denature enzymes and disrupt biological processes.
VI. Carbon Chemistry
Carbon has four valence electrons, allowing it to form four covalent bonds.
Carbon can form chains, rings, and complex structures, making it ideal for biological macromolecules.
Functional Groups
Hydroxyl (–OH)
Carbonyl (–CO)
Carboxyl (–COOH)
Amino (–NH₂)
Phosphate (–PO₄)
Functional groups determine the properties and reactivity of organic molecules.
VII. Biological Macromolecules
Overview
Four major classes of macromolecules:
Carbohydrates
Lipids
Proteins
Nucleic Acids
Monomers and Polymers
Monomer: Small building block molecule.
Polymer: Large molecule made of repeating monomers.
Dehydration Synthesis (Condensation)
Joins monomers to form polymers.
Releases water.
Hydrolysis
Breaks polymers into monomers.
Uses water.
VIII. Carbohydrates
Composed of carbon, hydrogen, and oxygen in a 2:1 ratio.
Primary function: short-term energy and structural support.
Types
Monosaccharides: Glucose, fructose, galactose (C₆H₁₂O₆)
Disaccharides: Two monosaccharides bonded (e.g., sucrose)
Polysaccharides:
Starch: Energy storage in plants
Glycogen: Energy storage in animals
Cellulose: Structural support in plant cell walls
Chitin: Structural support in arthropod exoskeletons
IX. Lipids
Mostly composed of carbon and hydrogen.
Not true polymers (no repeating monomers).
Types
Triglycerides: Long-term energy storage
Phospholipids: Form cell membranes; hydrophilic head and hydrophobic tails
Steroids: Chemical messengers (e.g., hormones)
Fatty Acids
Saturated: No double bonds; solid at room temperature
Unsaturated: One or more double bonds; liquid at room temperature
X. Proteins
Made of amino acids linked by peptide bonds.
Amino acids contain a central carbon, amino group, carboxyl group, hydrogen, and R group.
Levels of Protein Structure
Primary: Amino acid sequence
Secondary: Alpha helices and beta sheets
Tertiary: Overall 3D shape
Quaternary: Multiple polypeptide chains
Functions include enzymes, structure, transport, signaling, and defense.
XI. Nucleic Acids
Store and transmit genetic information.
Composed of nucleotides (phosphate, sugar, nitrogenous base).
Types
DNA: Stores hereditary information
RNA: Involved in protein synthesis
XII. Enzymes and Chemical Reactions
Enzymes are proteins that act as biological catalysts.
Lower activation energy required for reactions.
Bind substrates at the active site using the induced fit model.
Factors Affecting Enzyme Activity
Temperature
pH
Inhibitors (competitive and noncompetitive)
Cofactors and coenzymes
Denaturation occurs when enzymes lose shape and function.
XIII. Cells
Cells are the basic unit of structure and function.
Prokaryotic vs. Eukaryotic Cells
Prokaryotes: No nucleus, no membrane-bound organelles
Eukaryotes: Nucleus and membrane-bound organelles
XIV. Cell Membrane and Transport
Plasma Membrane
Composed of a phospholipid bilayer.
Described by the fluid mosaic model.
Selectively permeable.
Passive Transport
No energy required.
Includes diffusion, osmosis, and facilitated diffusion.
Active Transport
Requires energy (ATP).
Includes protein pumps, endocytosis, and exocytosis.
XV. Transport Within Cells
Rough ER: Protein synthesis
Smooth ER: Lipid synthesis and detoxification
Golgi Apparatus: Modifies, sorts, and ships proteins
Transport Vesicles: Move materials between organelles
XVI. Homeostasis
Maintenance of stable internal conditions.
Components
Receptor: Detects change
Control Center: Processes information
Effector: Responds
Feedback Mechanisms
Negative Feedback: Reverses change (e.g., body temperature regulation)
Positive Feedback: Amplifies change (e.g., childbirth)
Honors Biology – Unit 2: Matter & Energy in Organisms and Ecosystems
Ecology, Energy Flow, and Cell Energy
I. Ecology and the Biosphere
What Is Ecology?
Ecology is the study of interactions among organisms and between organisms and their physical environment.
Ecological studies include both biotic (living) and abiotic (nonliving) factors.
The Biosphere
The biosphere includes all regions of Earth where life exists.
It extends from about 5 miles above Earth’s surface to 7 miles below the ocean surface.
Components include:
Land
Water
Atmosphere (air)
II. Ecosystems, Biomes, and Environmental Factors
Ecosystems
An ecosystem consists of all living organisms in an area and their nonliving environment.
Ecosystems vary in size and include interactions between organisms and their surroundings.
Biotic and Abiotic Factors
Biotic factors: Living components of an ecosystem (plants, animals, fungi, bacteria).
Abiotic factors: Nonliving components (sunlight, water, air, temperature, rocks).
Biomes
A biome is a large geographic region defined by its climate and characteristic plants and animals.
III. Energy Flow in Ecosystems
Autotrophs (Producers)
Autotrophs produce their own food by capturing energy.
Photosynthetic autotrophs use sunlight to make food.
Chemosynthetic autotrophs use chemical energy from inorganic compounds.
Heterotrophs (Consumers)
Heterotrophs obtain energy by consuming other organisms.
Herbivores eat plants.
Carnivores eat animals.
Omnivores eat both plants and animals.
Decomposers / Detritivores break down organic waste and recycle nutrients.
IV. Food Chains, Food Webs, and Trophic Levels
Food Chains and Food Webs
Energy flows in one direction: from the sun (or inorganic chemicals) → producers → consumers.
A food chain shows a single pathway of energy transfer.
A food web connects multiple food chains within an ecosystem.
Trophic Levels
Each step in a food chain is a trophic level:
Producers
Primary consumers
Secondary consumers
Tertiary consumers
Ecological Pyramids
Energy Pyramid: Only about 10% of energy is transferred to the next trophic level; the rest is lost as heat.
Biomass Pyramid: Shows the total mass of living tissue at each trophic level.
Pyramid of Numbers: Shows the number of organisms at each trophic level.
Biomagnification
Biomagnification occurs when toxic substances increase in concentration at higher trophic levels.
Example: DDT accumulating in top predators.
V. Cycling of Matter
Biogeochemical Cycles
Matter is recycled within and between ecosystems.
Biogeochemical cycles involve biological, geological, and chemical processes.
Water Cycle
Evaporation: Liquid water → water vapor
Condensation: Water vapor → liquid
Precipitation: Rain, snow, sleet, hail
Transpiration: Water released by plants
Infiltration: Water soaks into soil
Runoff: Water flows over land into bodies of water
Carbon Cycle
Carbon moves through ecosystems via:
Photosynthesis
Cellular respiration
Decomposition
Fossil fuel combustion
Nitrogen Cycle
Nitrogen fixation: Bacteria convert atmospheric N₂ into ammonia or nitrates usable by plants.
Nitrification: Ammonium → nitrites → nitrates
Denitrification: Nitrates converted back into N₂ gas
Nitrogen-fixing bacteria are essential to this cycle.
Phosphorus Cycle
Phosphorus cycles through rocks, soil, water, and organisms.
Does not have a gaseous phase.
Weathering releases phosphates into soil and water.
VI. Community Interactions and Ecosystem Dynamics
Habitat and Niche
Habitat: The physical place an organism lives (its address).
Niche: The role an organism plays in its ecosystem (its occupation).
Community Interactions
Competition: Organisms compete for limited resources.
Predation: One organism (predator) captures and eats another (prey).
Symbiosis:
Mutualism: Both species benefit.
Commensalism: One benefits, the other is unaffected.
Parasitism: One benefits while harming the host.
Ecological Succession
Succession is the gradual change in species composition over time.
Primary succession: Occurs where no soil exists (e.g., volcanic rock).
Secondary succession: Occurs where soil remains after a disturbance (e.g., wildfire).
VII. Population Ecology
Factors Affecting Population Size
Birth rate
Death rate
Immigration
Emigration
Population Growth Patterns
Exponential growth: Rapid growth under ideal conditions (J-shaped curve).
Logistic growth: Growth slows as resources become limited (S-shaped curve).
Carrying Capacity
Carrying capacity (K) is the maximum population size an environment can sustain.
Limits to Growth
Density-dependent factors: Competition, disease, predation.
Density-independent factors: Weather, natural disasters, human activities.
VIII. ATP and Chemical Energy
ATP Structure and Function
ATP (adenosine triphosphate) is the primary energy carrier of cells.
Composed of adenine, ribose, and three phosphate groups.
ATP Cycle
Energy is released when ATP is converted to ADP through hydrolysis.
ATP is regenerated using energy from food.
ATP vs. Glucose
Both store energy.
Glucose stores long-term energy.
ATP provides immediate energy for cellular processes.
IX. Photosynthesis
Overall Equation
6CO₂ + 6H₂O + light energy → C₆H₁₂O₆ + 6O₂
Chloroplast Structure
Thylakoid: Site of light-dependent reactions
Stroma: Site of the Calvin cycle
Light-Dependent Reactions
Require light
Occur in thylakoid membranes
Produce ATP, NADPH, and oxygen
Calvin Cycle
Occurs in the stroma
Uses CO₂, ATP, and NADPH
Produces glucose
Limiting Factors of Photosynthesis
Light intensity
Carbon dioxide concentration
Temperature
X. Cellular Respiration
Aerobic Cellular Respiration
Overall equation:
C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O + ATP
Stages of Cellular Respiration
Glycolysis: Occurs in cytoplasm; breaks glucose into pyruvate; produces small amount of ATP.
Krebs Cycle: Occurs in mitochondrial matrix; releases CO₂ and transfers energy to carriers.
Electron Transport Chain: Occurs in inner mitochondrial membrane; produces most ATP.
Fermentation
Occurs in absence of oxygen
Allows glycolysis to continue
Types:
Lactic acid fermentation
Alcoholic fermentation
Efficiency
Aerobic respiration produces much more ATP than glycolysis alone.
XI. Relationship Between Photosynthesis and Cellular Respiration
Photosynthesis stores energy by making glucose.
Cellular respiration releases energy by breaking down glucose.
The products of one process are the reactants of the other.
XII. Human Impact and Environmental Issues
Biodiversity: Variety of life in an ecosystem
Conservation: Protection and wise use of natural resources
Deforestation: Removal of forests
Invasive species: Non-native species that cause harm
Eutrophication: Nutrient runoff causing excessive plant growth and oxygen loss
Pollution: Harmful substances added to the environment
DNA, RNA, and Protein Synthesis (Honors Biology)
Why DNA Is the Blueprint of Life
DNA is called the blueprint of life because it stores the instructions for building proteins, which determine the structure, function, growth, and behavior of cells and organisms. The sequence of nucleotides in DNA encodes genetic information that can be copied, transmitted, and expressed.
Lesson Topic 1: Structure of DNA
Nucleic Acids
Nucleic acids are macromolecules made of nucleotides. DNA (deoxyribonucleic acid) stores hereditary information, while RNA (ribonucleic acid) helps express that information.
Structure of DNA
DNA is a double helix made of two strands twisted around each other.
The strands are antiparallel (one runs 5′→3′, the other 3′→5′).
Each nucleotide contains:
Deoxyribose sugar
Phosphate group
Nitrogenous base (A, T, C, or G)
Purines: adenine and guanine
Pyrimidines: cytosine and thymine
Bases are held together by hydrogen bonds:
A–T (2 hydrogen bonds)
C–G (3 hydrogen bonds)
Complementary base pairing allows accurate DNA replication.
Scientists Who Discovered DNA’s Structure
Griffith: discovered transformation in bacteria
Avery–MacLeod–McCarty: proved DNA is the transforming factor
Hershey–Chase: confirmed DNA is genetic material using bacteriophages
Chargaff: discovered base-pairing rules
Franklin: produced X-ray diffraction images showing DNA’s helical structure
Watson and Crick: built the DNA model using these discoveries
Lesson Topic 2: DNA Replication
DNA Replication
DNA replication is the process by which DNA is copied before cell division.
Replication is semiconservative: each new DNA molecule contains one original strand and one new strand.
Steps of Replication
Helicase unwinds and separates the DNA strands.
Each original strand acts as a template.
DNA polymerase adds complementary nucleotides in the 5′→3′ direction.
Leading strand: synthesized continuously.
Lagging strand: synthesized in fragments called Okazaki fragments.
DNA ligase joins the fragments together.
Lesson Topic 3: RNA and the Genetic Code
RNA vs DNA
RNA is single-stranded; DNA is double-stranded
RNA contains ribose; DNA contains deoxyribose
RNA uses uracil (U) instead of thymine (T)
Types of RNA
mRNA: carries instructions from DNA to ribosomes
tRNA: brings amino acids to ribosomes
rRNA: makes up ribosomes
Genetic Code
DNA is read in triplets
mRNA contains codons (three-base sequences)
tRNA has anticodons that match codons
Lesson Topic 4: Protein Synthesis
Transcription
Occurs in the nucleus
RNA polymerase uses DNA as a template to build mRNA
Translation
Occurs at ribosomes in the cytoplasm
mRNA codons are read
tRNA delivers amino acids
Amino acids are joined to form a polypeptide chain
Mutations and Protein Synthesis
Mutations are changes in DNA
Substitution: may be silent or cause altered protein
Frameshift: insertion or deletion causing major protein changes
Lesson Topic 5: DNA Technology
DNA Manipulation
Restriction enzymes: cut DNA at specific sequences
Gel electrophoresis: separates DNA fragments by size
PCR: amplifies DNA
DNA fingerprinting: identifies individuals
Impact on Society
DNA technologies are used in medicine, forensics, agriculture, and biotechnology, raising ethical and social concerns.
Inheritance and Variation of Traits
Mendelian Genetics
Gregor Mendel studied inheritance using pea plants
Genes have different forms called alleles
Mendel’s Principles
Dominance
Segregation
Independent Assortment
Genotype vs Phenotype
Genotype: genetic makeup
Phenotype: physical expression
Punnett Squares
Used to predict inheritance
Monohybrid and dihybrid crosses
Patterns of Inheritance
Complete dominance
Incomplete dominance
Codominance
Multiple alleles (ABO blood types)
Polygenic traits (height, skin color)
Sex-linked traits (X-linked)
Mutations and Genetic Disorders
Types of Mutations
Gene mutations: substitution, insertion, deletion
Chromosomal mutations: nondisjunction, deletion, duplication, inversion, translocation
Genetic Disorders
Caused by inherited or spontaneous mutations
Detected using karyotypes, pedigrees, and genetic testing
Applications of Genetics
Selective breeding
Genetic engineering
Recombinant DNA
Gene therapy
Cloning (SCNT)
Cell Growth and Division
Limits to Cell Growth
Surface area-to-volume ratio
DNA overload
The Cell Cycle
Interphase: G1, S, G2
Mitosis: prophase, metaphase, anaphase, telophase
Cytokinesis
Regulation of the Cell Cycle
Checkpoints
Growth factors
Cancer results from loss of control
Meiosis
Produces haploid gametes
Crossing over and independent assortment increase variation
Mitosis vs Meiosis
Mitosis: growth and repair
Meiosis: sexual reproduction
Diversity of Life & Evolution (Honors Biology Notes)
I. Evolution
Evolution is the change in the genetic makeup (gene pool) of a population over time.
Population: All organisms of the same species living in the same area.
Gene pool: All genes, including all alleles, present in a population.
Individuals do not evolve; populations evolve.
II. Evidence for Evolution
A. Fossil Evidence
Fossils are preserved remains or traces of organisms that lived in the past.
Found mainly in sedimentary rock.
Fossil records show that organisms have changed over time and that many species have gone extinct.
B. Structural Evidence
1. Homologous Structures
Structures with similar anatomy due to common ancestry, but with different functions.
Example: Forelimb bones of humans, bats, whales, and cats (humerus, radius, ulna, carpals).
Support divergent evolution.
2. Vestigial Structures
Reduced or unused structures inherited from ancestors.
Example: Pelvic bones in whales, legs of skinks.
3. Analogous Structures (important contrast)
Structures with similar function but different evolutionary origins.
Result of convergent evolution.
C. Evidence from Early Development
Early embryos of different species show similar patterns of development, indicating shared ancestry.
D. Molecular / Biochemical Evidence
Comparison of DNA and amino acid sequences shows degrees of relatedness.
More similarities = closer evolutionary relationship.
III. Artificial Selection
Artificial selection is the selective breeding of organisms by humans to produce desired traits.
Darwin studied artificial selection (ex: pigeons, dogs) to understand how selection changes populations.
IV. Natural Selection
Natural selection is the process by which individuals with traits better suited to their environment survive and reproduce more successfully.
Conditions Required for Natural Selection:
Variation exists within a population.
More offspring are produced than can survive.
Individuals compete for limited resources.
Individuals with advantageous traits (adaptations) have higher fitness.
Fitness: An organism’s ability to survive and reproduce.
Adaptation: An inherited trait that increases fitness.
V. Development of Evolutionary Theory
A. Lamarck’s Hypothesis (Incorrect)
Use and disuse of structures.
Inheritance of acquired characteristics.
Important historically, but unsupported by evidence.
B. Charles Darwin
Sailed aboard the HMS Beagle in 1831.
Observed variation among organisms, especially in the Galápagos Islands.
Proposed evolution by natural selection.
C. Darwin’s Conclusions
Individuals vary naturally.
More organisms are produced than can survive.
Individuals best suited to the environment survive and reproduce.
Over time, populations change and new species can arise.
VI. Evolution and Genetic Change
A. Gene Pool and Allele Frequency
A gene pool contains all alleles in a population.
Relative frequency: How common an allele is compared to others.
B. Sources of Genetic Variation
Mutations: Random changes in DNA.
Gene shuffling: Occurs during meiosis (crossing over, independent assortment).
C. Natural Selection on Traits
Single-gene traits: Can cause shifts in allele frequency.
Polygenic traits: Affect distribution of phenotypes.
D. Types of Natural Selection
Directional selection: Favors one extreme phenotype.
Stabilizing selection: Favors average traits.
Disruptive selection: Favors both extremes.
E. Genetic Drift
Random change in allele frequency in small populations.
1. Founder Effect
Occurs when a small group colonizes a new area.
2. Bottleneck Effect
Occurs after a dramatic reduction in population size.
VII. Speciation
Speciation occurs when populations become reproductively isolated and can no longer interbreed.
Types of Reproductive Isolation:
Geographic isolation: Physical barriers separate populations.
Behavioral isolation: Different mating behaviors.
Temporal isolation: Different mating times.
Example: Kaibab squirrel vs. Abert’s squirrel separated by the Grand Canyon.
VIII. Macroevolution
Macroevolution refers to large-scale evolutionary change over long periods.
Key Patterns:
Adaptive radiation (divergent evolution): One species evolves into many.
Convergent evolution: Unrelated species evolve similar traits.
Coevolution: Two species evolve in response to each other.
Mass extinction: Loss of many species in a short time.
Gradualism: Slow, steady change.
Punctuated equilibrium: Long stability interrupted by rapid change.
IX. Distribution of Species
Species distribution changes due to migration, environmental change, and evolution.
Example: Nine-banded armadillo expanding its range northward in North America.
X. Summary
Evolution explains both the diversity and unity of life.
Natural selection acts on genetic variation within populations.
Over time, evolutionary processes lead to new species and large-scale biological change.