Biology: Systems, Structure, and Change

This is where all the vocabulary for the rest of the year gets built: water, the four big molecule families (carbs, fats, proteins, DNA), and how enzymes work. The through-line question is always: how does a molecule's shape decide what it can and can't do?

1. Water polarity and hydrogen bonds+

   Given a diagram of a water molecule's electron distribution, the student explains why water forms hydrogen bonds and predicts which of two unfamiliar small molecules would also be polar.

2. Identifying the four macromolecule types+

   The student classifies an unfamiliar biological molecule as a carbohydrate, lipid, protein, or nucleic acid by identifying its monomer and characteristic functional groups from a structural diagram.

3. Building and breaking polymers with water+

   The student explains how dehydration synthesis builds a polymer from monomers and how hydrolysis reverses it, using water molecules as the shared mechanism, for a polymer type not covered in the worked examples (e.g. a nucleic acid strand when only carbohydrates and proteins were worked).

4. Protein structure and final shape+

   The student compares the four levels of protein structure (primary through quaternary) and explains how a change at the primary level can propagate to change the protein's final 3-D shape.

5. Names and jobs of macromolecules+

   The student recalls the standard names and one-sentence functional role of the four macromolecule classes and their monomers (carbohydrate/monosaccharide, lipid/fatty acid+glycerol, protein/amino acid, nucleic acid/nucleotide).

6. Enzymes and activation energy+

   The student explains why enzymes lower activation energy without being consumed in the reaction, using the enzyme-substrate specificity model for a specific worked enzyme-substrate pair.

7. Temperature, pH, and enzyme activity+

   Given an activity-vs-temperature (or activity-vs-pH) graph for an enzyme the student has never seen, the student predicts the shape of the curve's declining region and justifies the prediction in terms of denaturation changing the active site's shape.

8. Why one amino acid matters+

   The student critiques a claim that 'a small change in one amino acid can't matter much because the protein is still made of the same building blocks,' using evidence from sickle-cell hemoglobin or an equivalent case not previously discussed in class.

9. Science words versus everyday meanings+

   The student interprets a text passage describing an unfamiliar macromolecule's function by identifying which domain-specific terms (e.g. 'denaturation,' 'hydrophobic,' 'substrate') carry technical meaning distinct from their everyday meaning.

The cell as a chemical factory with rooms — each organelle's shape explains what it does, and the membrane's structure explains what can and can't get in or out. This is also where 'homeostasis' first shows up, just not by that name yet.

1. Organelle structure and function+

   Given a labeled diagram of an organelle (nucleus, mitochondrion, rough/smooth ER, Golgi, chloroplast), state the specific structural feature responsible for its named function.

2. Organelles and cell specialization+

   Given a cell's primary job (e.g., secretes hormones, contracts, absorbs nutrients), predict which two organelles should be most abundant and justify the prediction from organelle function.

3. Why the cell membrane is selective+

   Construct a two-part explanation (phospholipid bilayer orientation + embedded protein function) for why the plasma membrane is selectively permeable rather than a simple wall.

4. Diffusion, osmosis, and active transport+

   Classify a given transport scenario (dissolved gas crossing a membrane, glucose moving against its gradient via a pump, water moving toward a solute-dense compartment) as diffusion, osmosis, or active transport, citing the energy requirement as the deciding feature.

5. Calculating osmosis and tonicity+

   Calculate and predict the direction of net water movement for a cell placed in an unfamiliar solute concentration, using tonicity and units of concentration consistently.

6. Surface area and cell size+

   Explain why a cell's surface-area-to-volume ratio decreases as it grows, and connect that ratio to a limit on the rate of material exchange the cell can sustain.

7. How cells show homeostasis+

   Given data or a scenario showing a cell maintaining an internal condition (e.g., ion concentration, water balance) different from its external environment, construct an argument for why this is evidence the cell is actively regulating rather than passively equilibrating.

8. Applying organelles and transport to new cells+

   Given a novel cell type with an unfamiliar micrograph-style image and a described job the cell performs, justify which organelles should be abundant, integrating structure-function reasoning with membrane transport demands the job implies.

What actually happens inside the mitochondria and chloroplasts named in Unit 2 — where a plant's sugar comes from, and how every cell burns that sugar for usable energy, always losing some as heat along the way.

1. Photosynthesis inputs, outputs, and location+

   Given a labeled diagram of a chloroplast, state the location and general inputs/outputs (light, CO2, water -> glucose, O2) of photosynthesis.

2. Respiration inputs, outputs, and locations+

   Given a labeled diagram of a mitochondrion and the three respiration stages, state the general inputs/outputs and location of glycolysis, the Krebs cycle, and the electron transport chain.

3. Why plant cells also respire+

   Explain why a plant cell performs both photosynthesis and cellular respiration rather than photosynthesis alone, using gas-exchange data from light and dark conditions.

4. Energy carriers in photosynthesis and respiration+

   Compare the energy transformations in photosynthesis and respiration, identifying which molecule carries energy INTO each pathway and which carries it OUT.

5. Following energy from sunlight to muscle+

   Trace a labeled carbon atom or joule of energy through a complete diagram from sunlight capture to ATP use in a muscle cell, naming every transformation step and identifying where energy is lost as heat.

6. Tracing energy in a new organism+

   Apply the same energy-tracing logic to an organism and pathway not used during instruction (e.g., a fish or fermenting yeast), with no diagram scaffold provided.

7. Energy transformation and ATP turnover+

   Critique a diagram or verbal claim that states 'the cell makes energy' or 'ATP is stored in bulk,' identifying the specific inaccuracy and restating it using correct transformation language.

8. Heat loss from cells to ecosystems+

   Given a novel ecosystem energy-loss scenario (e.g., why only ~10% of energy transfers between trophic levels), infer that the same heat-loss principle taught for cellular respiration applies at the ecosystem scale.

9. Labeling the energy flow diagram+

   Execute the labeling of a blank respiration/photosynthesis energy-flow diagram by placing all ten unit vocabulary terms in their correct location and sequence.

How a cell copies itself reliably, and what happens when the checkpoint system that makes copying reliable breaks — which is what cancer actually is.

1. Stages of the cell cycle+

   State the three main stages of the cell cycle (interphase, mitosis, cytokinesis) and name the three sub-stages of interphase (G1, S, G2) in correct order.

2. What each mitosis phase looks like+

   Given the four named mitotic phases (prophase, metaphase, anaphase, telophase) and their defining chromosome/spindle behaviors as directly presented in the Day 4-5 worked examples, label a NEW image of each of the four phases with its correct name using the same defining features shown in instruction.

3. Chromosome number at each cell stage+

   Given a labeled diagram of a cell at an unspecified point in the cell cycle, identify the number of chromosomes and whether they are replicated (sister chromatids present) or unreplicated.

4. Why DNA copies before mitosis+

   Explain why DNA must be fully replicated before mitosis begins, using the requirement that each daughter cell receive a complete, identical chromosome set.

5. Putting mitosis images in order+

   Sequence a set of unlabeled microscope images or diagrams of dividing cells into the correct order of mitotic phases (prophase, metaphase, anaphase, telophase) based on chromosome position and spindle behavior.

6. Why cells need checkpoints+

   Explain why a cell cycle checkpoint is functionally necessary in addition to a size- or resource-based trigger, using the DNA-damage example as evidence against a growth-only trigger model.

7. Reading mitotic index data+

   Given a novel mitotic-index table for an unfamiliar tissue sample, determine which stage of the cell cycle is most affected by a described abnormality and predict the downstream consequence for that cell population.

8. How checkpoint drugs treat cancer+

   Evaluate a claim about a specific cancer-treatment mechanism (e.g., a checkpoint-targeting drug) by constructing a short written argument that cites unit evidence about proto-oncogenes, tumor suppressor genes, or checkpoint proteins to support or refute the claim.

9. Same DNA, different genes used+

   Compare mitosis's role in producing genetically identical daughter cells to the AAAS-documented misconception that different body cells contain different DNA, distinguishing 'same DNA' from 'different genes expressed.'

The whole unit is built around one tension: genotype constrains phenotype, it doesn't fully determine it. It opens with identical twins looking different, then moves through meiosis, Punnett squares, incomplete dominance/codominance, and pedigree analysis.

1. What meiosis produces+

   Given a diagram or description of a cell entering meiosis, the student correctly identifies the number of daughter cells produced, their chromosome number relative to the parent cell, and whether they are genetically identical to each other.

2. Why gametes need half the chromosomes+

   The student explains why meiosis, not mitosis, is the process that must occur to produce gametes, citing chromosome number maintenance across generations as the mechanism.

3. Independent assortment versus crossing over+

   The student compares independent assortment and crossing over as two distinct mechanisms of genetic variation during meiosis, identifying what each mechanism does that the other does not.

4. Monohybrid Punnett squares+

   Given a monohybrid cross between two known genotypes for a taught trait (e.g., pea color), the student executes a Punnett square correctly and states the resulting genotype and phenotype ratios.

5. Dihybrid Punnett squares+

   Given a dihybrid cross for two taught traits, the student executes the cross using the branching or grid method to predict genotype and phenotype ratios of offspring.

6. Telling inheritance patterns from ratios+

   Given phenotype ratio data from an unfamiliar cross (not covered in instruction), the student determines whether the data are best explained by simple dominance, incomplete dominance, or codominance, and justifies the choice by citing the specific ratio and phenotype pattern.

7. Genes and environment together+

   The student explains why two organisms with identical genotype for a polygenic or environmentally-influenced trait can display different phenotypes, using a specific mechanism (environmental interaction or gene regulation) rather than restating that 'genes aren't everything.'

8. Reading pedigrees with uncertainty+

   Given a pedigree chart for a trait the student has not seen before, the student states which inheritance pattern(s) are consistent with the evidence shown, identifies what is not yet ruled out, and specifies what additional individual or generation would distinguish between remaining hypotheses.

9. Sorting traits by phenotype pattern+

   The student classifies a given trait description (e.g., human height, ABO blood type, PTC tasting) as monogenic simple-dominant, codominant, incomplete dominant, or polygenic based on the description of its phenotype distribution.

10. Building a model from new ratios+

    Given only a description of offspring phenotype ratios in an organism system never discussed in class or in the unit's resources, the student generates a plausible inheritance model (dominance relationships and number of genes involved) that accounts for the data, and states what additional cross would test that model.

Natural selection taught as a statistical process acting on variation that already exists — directly against the intuitive wrong idea that organisms change themselves on purpose when they need to.

1. Timing of variation and selection+

   Given a case description of a population before and after an environmental change, state whether the heritable variation involved existed before or after the environmental pressure appeared.

2. Changing alleles versus creating alleles+

   Explain, using a specific dataset showing trait-frequency change over generations, why natural selection changing allele frequency is different from natural selection creating a new allele.

3. Homologous and analogous structures+

   Compare a homologous structure pair (e.g., human/bat/whale forelimb) and an analogous structure pair (e.g., bat wing/insect wing), and classify which structural criterion (shared skeletal arrangement vs. shared surface function) sorts them.

4. Building an argument for common ancestry+

   Given fossil-record, comparative-anatomy, and molecular-sequence evidence for a lineage the student has not previously studied, construct a written argument for common ancestry that integrates at least two of the three evidence types.

5. Natural selection versus genetic drift+

   Given population data showing an allele frequency change over several generations, distinguish whether the pattern is more consistent with natural selection or with genetic drift, citing population size and consistency/direction of change as the discriminating features.

6. Judging evidence for a new species+

   Given a description of two geographically separated populations of the same ancestral species with described reproductive behaviors, evaluate whether the evidence given is sufficient to conclude they have become separate species, and identify what additional evidence would be needed.

7. Genetic drift, bottleneck, and founder effects+

   Recall the definition of genetic drift and distinguish it by name from natural selection, bottleneck effect, and founder effect.

8. Arguing for natural selection with data+

   Given the peppered-moth population dataset and a second real dataset (e.g., antibiotic-resistance growth curves) not previously analyzed together, construct a written argument identifying natural selection as the mechanism and explicitly ruling out at least one named alternative (drift, migration, non-heritable variation) using specific features of the data.

Scales Unit 3's energy-loss idea up to whole ecosystems: energy flows one direction and gets lost as heat at every step; matter (carbon, nitrogen, water) cycles and gets reused, it doesn't run out the same way.

1. The 10% rule for energy transfer+

   Given a stated number of kilocalories of biomass at one trophic level, calculate the kilocalories available to the next trophic level using the 10% transfer rule.

2. How respiration explains the 10% rule+

   Explain why cellular respiration's inefficiency (taught in Unit 3) is the mechanistic cause of the 10% energy transfer rule, rather than treating the rule as an independent ecological fact.

3. Food chains and food webs compared+

   Differentiate a food chain model from a food web model in terms of what each does and does not represent about energy flow in a real ecosystem.

4. Tracing one carbon atom around Earth+

   Construct a diagram tracing a carbon atom through at least four reservoirs (atmosphere, living organism, ocean, geosphere/sediment) showing that the atom is neither created nor destroyed, only relocated and chemically transformed.

5. Comparing the carbon and nitrogen cycles+

   Compare the carbon cycle and the nitrogen cycle to identify which structural features (a one-way atmospheric reservoir vs. a cycle requiring biological fixation) are shared and which are unique to each.

6. Using energy math on ecosystem changes+

   Given an unfamiliar ecosystem dataset (species list, biomass at each trophic level, and a proposed change such as introducing a new predator), calculate the energy ceiling at each level and use that math to argue whether the proposed change is sustainable.

7. Energy flow in ecosystems without sunlight+

   Explain, using a specific ecosystem example never discussed in class (e.g., a hydrothermal vent or a cave ecosystem with no sunlight), why energy still flows one direction and is lost at every transfer even when the primary energy source is not sunlight.

8. Predicting effects of removing a species+

   Predict how removing a mid-level consumer from a food web would redistribute energy flow to remaining species, and identify which prediction requires additional evidence beyond the web diagram itself.

Extends the negative-feedback idea from Unit 2 and the resource-ceiling idea from Unit 7 up to whole populations: growth curves, carrying capacity, density-dependent limits, competition, predation, and whether a community bounces back after a disturbance.

1. Exponential and logistic growth curves+

   Given a population-size-over-time graph, the student classifies its growth pattern as exponential, logistic, or neither, and identifies the specific graph feature (constant vs. slowing rate of increase, presence of a plateau) that justifies the classification.

2. Carrying capacity and slowing growth+

   Given a dataset showing a population's growth slowing or reversing, the student determines carrying capacity from the graph and explains why growth rate approaches zero as population size approaches that value.

3. Limiting factors and population density+

   Given two limiting-factor scenarios (one clearly tied to population density, one clearly not), the student classifies each as density-dependent or density-independent and justifies the classification using the mechanism, not just the label of the factor.

4. Negative feedback in cells and populations+

   The student maps population-level density-dependent regulation onto the same three-part feedback structure (deviation, response, return to set point) used to describe body-temperature homeostasis in Unit 2, explicitly stating what plays each role at the population scale.

5. Indirect competition seen in population data+

   Given population data for two species sharing a resource with no observed direct contact between them, the student infers that exploitative competition is occurring and distinguishes this from interference competition using only the pattern of decline in the data.

6. Resilience or lasting change after disturbance+

   Given a predator-prey population dataset with a visible oscillation and a disturbance event embedded partway through, the student evaluates whether the community shows resilience (returns toward its prior dynamic pattern) or a lasting shift, citing specific time points as evidence.

7. Defending a cause for population change+

   Given an unfamiliar multi-year population dataset with an inflection point, the student generates an original argument identifying the best-supported limiting factor and constructs a specific, data-grounded rebuttal to at least one plausible alternative explanation the data do not fully rule out.

8. Population ecology vocabulary+

   The student recalls the definitions of exponential growth, logistic growth, carrying capacity, density-dependent factor, and density-independent factor with correct use in a new sentence.

Applies four ideas from earlier in the year — enzyme specificity, respiration's oxygen need, cell-cycle checkpoints, and selection on existing variation — to real organ systems: digestion, circulation/respiration, and immunity.

1. Digestive organs and what they digest+

   Given a diagram of the digestive tract, identify each organ and state the class of macromolecule it primarily chemically digests.

2. Blood's path and gas exchange+

   Given a red blood cell's starting chamber in the heart, state the correct next stop in the heart-lung-body loop and name whether oxygen or carbon dioxide concentration increases at that stop.

3. Why proteases cannot digest starch+

   Explain why a protease will not break down starch, using the enzyme-substrate specificity model from Unit 1.

4. Breathing, blood, and oxygen at altitude+

   Given a case description of gas exchange at altitude, explain how reduced atmospheric oxygen constrains cellular respiration, linking circulatory/respiratory structure to Unit 3's respiration mechanism.

5. Immune recognition and autoimmune disease+

   Compare the immune system's function to a recognition system versus an attack-only army, and justify which model better explains a described case of autoimmune disease.

6. Antibiotic resistance as natural selection+

   Explain antibiotic resistance in a bacterial population as natural selection acting on pre-existing variation, not as bacteria developing resistance in response to need.

7. Sorting malfunctions by system and level+

   Classify a set of described organ malfunctions (e.g., lactose intolerance, emphysema, untreated strep, cystic fibrosis) by which body system and level of organization (organ, tissue, cell, molecule) is most directly implicated.

8. Diagnosing a brand new case+

   Given an unfamiliar clinical scenario never discussed in class, generate a justified diagnosis of which organ system and mechanism is implicated, using named vocabulary and mechanisms from at least two prior units.

9. What cancer and autoimmune disease share+

   Explain why cancer and autoimmune disease, despite affecting different systems, are both describable as failures of a discrimination mechanism (divide/don't-divide or self/non-self).

10. Comparing two reports of similar disorders+

    Read a technical passage describing a digestive or immune disorder and compare its findings to a second source describing an overlapping but not identical case, noting agreement and contradiction.

Nervous and endocrine systems as two different-looking solutions to the same problem: detect a change, correct it. Reuses Unit 2's ion-channel/membrane vocabulary for neuron signaling and Unit 8's sensor/control-center/effector loop for physiological regulation.

1. Parts of a neuron+

   Given a labeled cross-section diagram of a neuron, identify and name the dendrite, axon, cell body, myelin sheath, and axon terminal.

2. Action potential steps in order+

   Given the step names of the action-potential sequence in scrambled order (resting state, depolarization, sodium channels open, repolarization, potassium channels open), place them in the correct order and state, for each step, whether sodium or potassium is the ion moving and which direction it moves relative to the cell.

3. How ions create an action potential+

   Explain how the movement of sodium and potassium ions across the neuron's membrane, through the same type of channel proteins studied in Unit 2's membrane transport, produces an action potential.

4. Electrical to chemical at the synapse+

   Given a diagram of a synapse mid-transmission, distinguish the segment of the signal that is electrical from the segment that is chemical and identify the point of conversion.

5. Reading a feedback loop diagram+

   Given a completed, fully-labeled example feedback loop diagram (e.g., the temperature-regulation worked example) and its written scenario side by side, identify which drawn box corresponds to which sentence in the scenario text that describes the sensor, control center, and effector.

6. Nervous versus endocrine signaling+

   Compare the nervous and endocrine systems on speed, duration, and reach of response, and justify which system would handle a given novel physiological demand.

7. Building a negative feedback loop+

   Given a description of a novel physiological scenario (e.g., dehydration, fever), construct a negative feedback loop diagram labeling the sensor, control center, and effector using the same three-part structure introduced in Unit 8 for population regulation.

8. Which part of the loop failed+

   Given an unfamiliar physiological malfunction scenario not used in instruction, diagnose which single component of the feedback loop (sensor, control center, or effector) is malfunctioning and justify the diagnosis by pointing to specific textual evidence.

9. Why nerves and muscles need ATP+

   Explain why nerve and muscle tissue require unusually high, continuous rates of cellular respiration, connecting ATP demand to the electrical and mechanical work these tissues perform.

10. The hidden cost of staying stable+

    Given a completely novel, structurally unfamiliar physiological scenario describing a system that maintains a stable output despite an ongoing stressor (e.g., a scenario invented for the task, not modeled on any taught case), generate an argument for why the stable output does not mean the system is inactive, using evidence from the scenario about component-level effort or cost.

11. Telling nervous from endocrine responses+

    Given two written scenarios (one nervous-system-mediated, one endocrine-mediated) describing responses to the same environmental change, classify which coordination system explains each response and cite the specific structural feature (myelinated axon vs. hormone traveling in blood) that justifies the classification.

No new biology here — this is where your child picks one real, unfamiliar biological case and argues it using the four big frames built all year: structure-function, energy transformation, variation/selection, and feedback/homeostasis. It ends with a written argument and an oral defense where you ask unscripted follow-up questions.

1. Which explanatory frame is used+

   Given a short case description, state which of the four explanatory frames (structure-function, energy transformation, variation/selection, feedback/homeostasis) was used to explain a worked example the student has already seen.

2. Sorting tricky cases into four frames+

   Sort eight novel, unfamiliar case descriptions into the four explanatory frames, including at least two cases each deliberately written to be plausible under two different frames.

3. Why one frame fits better+

   For a case correctly sorted into one frame, explain why a second, named frame does not account for the mechanism as well, citing a specific feature of the case that distinguishes them.

4. Real biology case and background+

   Identify a real, ongoing biological case (disease outbreak, conservation problem, or evolving-resistance case) not covered in the course, and state which prior unit's content most directly supplies background knowledge for it.

5. Writing a biology argument with evidence+

   Construct a written scientific argument for the chosen case that states a claim, cites quantitative evidence (a dataset, graph, or model), names at least one specific alternative explanation, and explains why the evidence favors the claim over that alternative.

6. Defending your argument on the spot+

   During oral defense, respond to an unscripted follow-up question by revising or defending a claim using content drawn from a prior unit not already cited in the written draft.

7. Correlation versus cause in your data+

   Distinguish, in a real dataset or graph tied to the chosen case, a correlational pattern from a stated causal mechanism, and identify what additional evidence would be needed to move from one to the other.

8. Reviewing the four explanatory frames+

   Recall, without notes, the definitions of all four explanatory frames and one worked example case for each, as a cumulative check on year-long retention.