Honors Biology.

How to use this guide

Study a section, then explain its ideas from memory. Practice diagrams and cause-and-effect relationships—not just vocabulary. At the end, answer the review questions without looking at the key.

1. Science skills

• Independent variable: the factor deliberately changed.

• Dependent variable: the measured outcome.

• Controlled variables: factors kept the same.

• Control group: baseline for comparison; it does not receive the tested treatment (when appropriate).

• Hypothesis: a testable, falsifiable explanation or prediction.

• Theory: a broad, well-supported scientific explanation—not a guess.

• Data: observations and measurements; use repeated trials and adequate sample sizes to improve reliability.

• Graphing: put the independent variable on the x-axis and dependent variable on the y-axis; label axes and units.

Think like a scientist: A correlation means two variables change together; it does not by itself prove that one causes the other.

2. Chemistry of life

Atoms, bonds, and water

• Atoms contain protons (+), neutrons (0), and electrons (−). Valence electrons influence bonding.

• Covalent bonds share electrons; ionic bonds form after electron transfer; hydrogen bonds are weak attractions important in water and DNA.

• Water is polar, so it forms hydrogen bonds. Its cohesion, adhesion, temperature moderation, and ability to dissolve many substances support life.

• pH: acids are below 7, neutral is 7, and bases are above 7. Each pH unit represents a tenfold change in hydrogen-ion concentration.

Biological macromolecules

• Enzymes are biological catalysts: they lower activation energy and are not consumed by the reaction.

• Enzyme activity depends on conditions such as temperature and pH. Extreme conditions may change an enzyme's shape (denaturation) and reduce its function.

• ATP is a short-term energy carrier; cells couple ATP breakdown to energy-requiring processes.

3. Cells and transport

Cell structures

• Cell membrane: selectively permeable boundary; phospholipid bilayer with proteins.

• Nucleus: stores most eukaryotic DNA.

• Ribosomes: build proteins.

• Mitochondria: carry out most cellular respiration in eukaryotic cells.

• Chloroplasts: photosynthesis in plants and algae.

• Rough ER: processes proteins for membranes or export; smooth ER: lipid synthesis and other functions.

• Golgi apparatus: modifies, sorts, and packages molecules.

• Lysosomes: digest and recycle materials in many animal cells.

• Vacuoles: storage; plant cells often have a large central vacuole.

• Cell wall: support and protection in plants, fungi, and many prokaryotes.

Prokaryotes lack a nucleus and membrane-bound organelles. Eukaryotes have a nucleus and membrane-bound organelles. Both have DNA, ribosomes, cytoplasm, and a cell membrane.

Moving across membranes

• Diffusion: particles move from higher to lower concentration.

• Osmosis: diffusion of water across a selectively permeable membrane.

• Facilitated diffusion: passive movement through a membrane protein; no cellular energy required.

• Active transport: movement against a concentration gradient; requires energy, often ATP.

• Endocytosis/exocytosis: vesicles move large materials into/out of a cell.

• Hypertonic solution: water tends to leave a cell; hypotonic: water tends to enter; isotonic: no net water movement.

4. Energy in cells

Photosynthesis

Overall equation:

$6CO_2 + 6H_2O + light \rightarrow C_6H_{12}O_6 + 6O_2$

• Occurs in chloroplasts. Light energy is stored as chemical energy in sugars.

• The oxygen released comes from water molecules split during the light-dependent reactions.

• Light-dependent reactions capture light energy; the Calvin cycle uses that energy to build sugar from carbon dioxide.

Cellular respiration

Overall equation:

$C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O + ATP$

• Occurs mainly in mitochondria in eukaryotic cells; glycolysis occurs in the cytoplasm.

• Aerobic respiration uses oxygen and yields much more ATP than fermentation.

• Fermentation allows glycolysis to continue when oxygen is unavailable; it yields little ATP. Examples include lactic-acid fermentation and alcoholic fermentation.

• Photosynthesis and respiration are related in their matter cycling, but they are not simply exact reversals in every step.

5. Cell cycle and inheritance

Cell division

• The cell cycle includes interphase (G1 growth, S DNA replication, G2 preparation) and division.

• Mitosis makes two genetically similar daughter cells for growth, repair, or asexual reproduction.

• Mitosis stages: prophase, metaphase, anaphase, telophase; cytokinesis divides the cytoplasm.

• Meiosis makes haploid sex cells. Two divisions produce four genetically different cells.

• Crossing over and independent assortment increase genetic variation.

• Cancer involves loss of normal cell-cycle regulation.

DNA and protein synthesis

• DNA is a double helix made of nucleotides. Base pairing: A–T, C–G. RNA uses U instead of T.

• DNA replication copies DNA before cell division.

• Transcription: DNA information is copied into mRNA.

• Translation: ribosomes read mRNA codons; tRNA brings amino acids to build a protein.

• A gene's DNA sequence can influence a protein's amino-acid sequence, which can affect a trait.

• A mutation is a DNA sequence change. Its effects may be harmful, beneficial, or neutral; effects depend on context.

Genetics

• Alleles are different forms of a gene. Genotype is allele combination; phenotype is observable trait.

• In a simple dominant/recessive model, a dominant allele masks a recessive allele in a heterozygote. Many traits do not follow this simple pattern.

• Homozygous: two matching alleles; heterozygous: two different alleles.

• For a cross of Aa × Aa, expected genotypes are 1 AA : 2 Aa : 1 aa; if A is completely dominant, expected phenotypes are 3 dominant : 1 recessive. These are probabilities, not guaranteed outcomes for a small family.

• Incomplete dominance: heterozygote has an intermediate phenotype. Codominance: both alleles are expressed. Multiple alleles and polygenic traits add further complexity.

• Sex-linked traits are often associated with genes on sex chromosomes; inheritance patterns can differ by sex.

6. Evolution and classification

• Evolution is change in heritable traits of populations across generations.

• Natural selection acts on existing heritable variation: individuals with traits that improve reproductive success in a particular environment tend to leave more offspring.

• Individuals do not evolve because they "need" to; populations change over generations.

• Other sources of evolutionary change include mutation, genetic drift, and gene flow.

• Evidence includes fossils, comparative anatomy, embryology, biogeography, and molecular similarities.

• Homologous structures reflect shared ancestry, even if functions differ. Analogous structures have similar functions but evolved independently.

• Binomial nomenclature names each species with genus and species (for example, Homo sapiens). Classification groups organisms by shared characteristics and evolutionary relationships.

7. Ecology

• Levels of organization: organism → population → community → ecosystem → biome → biosphere.

• Biotic factors are living or once-living; abiotic factors are nonliving environmental conditions.

• Producer/autotroph: makes organic molecules, often using light. Consumer/heterotroph: obtains energy by eating other organisms. Decomposer: breaks down dead matter and recycles nutrients.

• Food chains/webs show feeding relationships. Arrows point from the food/energy source to the consumer.

• Energy flows through ecosystems; matter cycles. Only a fraction of energy at one trophic level is transferred to the next (often approximated as 10%).

• Carbon cycle: photosynthesis takes in CO₂; respiration, decomposition, and combustion release it.

• Nitrogen cycle: bacteria help convert nitrogen into forms organisms can use; decomposers return nitrogen compounds to the environment.

• Carrying capacity is the population size an environment can sustain over time.

• Interactions: competition (−/−), predation (+/−), mutualism (+/+), commensalism (+/0), parasitism (+/−).

• Biodiversity supports ecosystem resilience. Habitat loss, invasive species, pollution, overharvesting, and climate change can threaten it.

8. Common mix-ups to avoid

• Plants perform both photosynthesis and cellular respiration.

• Matter (such as carbon atoms) is recycled; energy flows and is ultimately dissipated as heat.

• Diffusion and facilitated diffusion do not require ATP; active transport does.

• Mitosis creates two similar cells; meiosis creates four genetically varied haploid cells.

• A dominant allele is not necessarily more common, stronger, or better.

• Natural selection is not intentional: the environment does not give organisms traits because they need them.

• Food-web arrows show energy transfer, not simply "who is bigger" or "who eats whom" in the direction of the arrowhead.

9. Practice questions

1. In an experiment testing how light intensity affects plant growth, identify the independent variable, dependent variable, and two controlled variables.

2. Why can a high fever interfere with enzyme function?

3. A cell is placed in a hypertonic solution. Which direction will water move overall?

4. Write the balanced overall equations for photosynthesis and cellular respiration.

5. How are photosynthesis and respiration connected through matter and energy?

6. What is the difference between transcription and translation?

7. In the cross Aa × Aa, what is the probability of aa offspring? What is the probability of the dominant phenotype under complete dominance?

8. Give two sources of genetic variation in sexually reproducing populations.

9. A population of insects becomes more resistant to a pesticide over many generations. Explain this using natural selection.

10. In a food chain, what does an arrow from grass to a rabbit represent?

11. Why does available energy generally decrease at higher trophic levels?

12. Classify each interaction: a bee gets nectar while pollinating a flower; a tick feeds on a dog; two plants compete for light.

Answer key

1. Independent: light intensity. Dependent: plant growth (define how it is measured). Controls could include plant species, water, soil, temperature, and growth time.

2. High temperatures can change an enzyme's shape, including its active site, reducing its ability to bind substrate and catalyze reactions.

3. Water moves out of the cell overall, toward the higher solute concentration.

4. Photosynthesis: 6CO₂ + 6H₂O + light → C₆H₁₂O₆ + 6O₂. Respiration: C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O + ATP.

5. Photosynthesis stores light energy in sugars and uses CO₂ and water; respiration releases usable energy from sugars and produces CO₂ and water. Atoms cycle; energy changes form and flows.

6. Transcription makes RNA from a DNA template; translation uses mRNA codons to assemble a protein at a ribosome.

7. aa: 1/4 (25%). Dominant phenotype: 3/4 (75%), assuming complete dominance and equal allele segregation.

8. Crossing over and independent assortment during meiosis; random fertilization also contributes.

9. Some insects already had heritable variation in resistance. Pesticide exposure favored resistant insects, which survived and reproduced more; resistance alleles became more common over generations.

10. Energy and matter move from grass (food source) to rabbit (consumer).

11. Organisms use much of the energy for life processes and release it as heat; not all biomass is eaten or digested.

12. Bee and flower: mutualism; tick and dog: parasitism; plants: competition.

Quick self-check

I can explain each process without notes, draw and label a cell, trace matter through photosynthesis and respiration, solve a one-trait Punnett square, and support an evolution claim with variation, inheritance, and differential reproductive success.