AP Bio

“Working hard or hardly working”

Unit 1: Statistics

In statistics, the Null Hypothesis is a foundational concept stating that there is no statistically significant difference between two groups in an experiment. This hypothesis assumes that any differences observed are due to chance, not a real effect.

To test this, scientists often use the Chi-Square Test, a statistical method that compares observed results with expected outcomes. The degrees of freedom (df) in a chi-square test is calculated as n - 1, where "n" is the number of categories.

The null hypothesis is rejected if the chi-square value is greater than the critical value. This means the results are unlikely due to chance and supports the alternative hypothesis—that a real difference exists between the groups.

It's also important to understand basic calculations to analyze data. The mean is the average of a data set and is calculated by adding all the values together and dividing by the number of data points. For example, in Data Set A (1, 2, 3, 4, 5), the mean is (1+2+3+4+5)/5 = 3. The median is the middle value in a sorted data set.

Unit 2: Chemistry of Life

Water Properties

Water is essential for life because of its unique chemical properties. Its polarity allows for hydrogen bonding between molecules. A single water molecule has polar covalent bonds, with oxygen being slightly negative and hydrogens slightly positive. This allows water molecules to stick together through hydrogen bonds.

Cohesion: when water molecules are attracted to each other due to the hydrogen bonds.

Adhesion: when water molecules are attracted to other polar molecules due to hydrogen bonds.

High specific heat: due to water’s hydrogen bonds, more energy is required to separate water molecules during phase changes. When a person sweats, the sweat will evaporate, and this will have a cooling effect on the person.

Moderating climate: since water has a high heat capacity, it can absorb and release large amounts of energy, helping to stabilize temperatures in the environment and providing a more consistent climate for ecosystems.

Expanding upon freezing: since water has the ability to form hydrogen bonds there is more space between water molecules in the solid state than in the liquid state, making ice less denser than liquid water. This unique property allows ice to float on water, creating an insulating layer that protects aquatic life during colder seasons.

Great solvent: due to water’s partially positive and negative ends, it can easily dissolve ionic conpounds and other polar molecules.

The pH scale measures the concentration of H⁺ ions in a solution. It plays a major role in homeostasis as organisms need to maintain stable pH levels for proper cellular function. A high H⁺ concentration means the solution is acidic, while a high OH⁻ concentration indicates a base.

Buffers are crucial in maintaining pH. They can form acids or bases in response to changing pH levels in the cell.

Carbon-Based Molecules

Carbon is the backbone of life because it can form four covalent bonds, allowing for diverse molecular shapes like chains, branches, and rings. It bonds with H, O, N, P, and S to form organic molecules essential to life.

Carbon is central to macromolecules, which are large molecules made of smaller units called monomers. These monomers join to form polymers through dehydration synthesis, where water is removed. Hydrolysis breaks down polymers, adding water to split the bonds.

Types of Macromolecules

Carbohydrates are composed of carbon, hydrogen, and oxygen in a 1:2:1 ratio. They include:

• Monosaccharides (e.g., glucose, fructose)

• Disaccharides (e.g., sucrose, lactose)

• Polysaccharides (e.g., starch, glycogen, cellulose)

Carbohydrates provide immediate energy, energy storage, and structural support in plants.

Lipids are nonpolar and hydrophobic, meaning they don't mix with water. They include:

• Triglycerides: glycerol + 3 fatty acids

• Phospholipids form the cell membrane glycerol 2 fatty acids and a phosphate group

• Steroids: four-ring structures like cholesterol

• Waxes: protective barriers (e.g., earwax)

Proteins are made of amino acids, which link via peptide bonds. Each amino acid has an amino group, a carboxyl group, and R-group. Protein structure has four levels:

1. Primary: amino acid sequence

2. Secondary: alpha helices and beta sheets

3. Tertiary: 3D folding

4. Quaternary: multiple polypeptides together

Proteins function as enzymes, transporters, immune defenders, and regulators.

Nucleic Acids store and transmit genetic information. They are made of nucleotides (sugar, phosphate, nitrogen base). Two main types:

• DNA: double-stranded; uses A-T and C-G

• RNA: single-stranded; uses A-U and C-G

ATP is a nucleotide that provides energy for cellular work.

Introduction to Cells

Cells are the basic unit of life. There are two main types:

• Prokaryotic cells (e.g., bacteria): lack a nucleus and organelles and have a nucleoid region where they store their DNA

• Eukaryotic cells (e.g., animal and plant cells): have a nucleus and membrane-bound organelles

Important organelles include:

• Ribosomes function in protein synthesis, translating messenger RNA into polypeptide chains to create proteins essential for cellular functions.

• Nucleus: contains DNA and controls the cell

• Mitochondria: smooth outer membrane and a folded inner membrane,e which increases the surface area available for energy production during cellular respiration. Also contains the mitochondrial matrix where various enzymes facilitate the metabolic processes necessary for ATP production and the Krebs cycle.

• Endoplasmic Reticulum (ER): The rough ER is used to synthesize proteins, while the smooth ER is used to synthesize lipids.

• Golgi Apparatus: packages, modifies, and transports proteins.

• Lysosomes contain hydrolytic enzymes to digest molecules and break down waste.

• Vacuole: used for food and water storage; also used to provide turgor pressure in plants.

• Chloroplasts contain thylakoids which can be stacked into grana. The liquid inside is called the stroma.

Cell Membrane and Transport

The cell membrane is a phospholipid bilayer with proteins, allowing semi-permeable transport. There are two main types of transport:

• Passive Transport: like diffusion; no energy needed

• Active Transport: like the sodium-potassium pump; requires energy

Cells also use endocytosis and exocytosis:

• Endocytosis: taking substances in

  • Phagocytosis: cell eating

  • Pinocytosis: cell drinking

• Exocytosis: releasing substances out

Electrochemical gradients are important for processes like nerve signaling. Secondary active transport uses these gradients to move substances against their concentration.

Water potential: the potential energy of water in a solution

Water flows from areas of high water potential to areas of low water potential. The higher the water potential, the more water there is in a solution, which means water flows from a hypotonic solution to a hypertonic solution

Unit 3":

Enzymes

Enzymes are biological catalysts that lower the activation energy of reactions. Their activity depends on:

• Temperature: if the temperature exceeds the enzyme’s optimum temperature, the enzyme will denature

• pH: if the enzymes’ pH exceeds the optimum pH, the enzyme will denature.

Competitive inhibitors are similar in shape to substrates and compete with substrates for the enzymes’ active site.

Allosteric inhibitors or non-competitive inhibitors do not bind to the active site of the enzyme but rather bind to the allosteric site, which changes the shape of the enzyme.

Enzymes are reusable and are not consumed in reactions, making them efficient helpers in countless biological processes.

Photosynthesis

Photosynthesis occurs in the chloroplasts of plant cells and is the process that converts light energy into chemical energy stored in glucose. It consists of two main stages: the light reactions and the Calvin cycle.

🔆 Light Reactions (occur in the thylakoid membranes):

• Light is absorbed by Photosystem II, exciting electrons and splitting water molecules (photolysis) to release oxygen.

• Electrons travel through the electron transport chain, which pumps H⁺ ions into the thylakoid space, creating a proton gradient.

• Light hits Photosystem I, re-energizing the electrons, which are used to reduce NADP⁺ into NADPH.

• ATP is produced as H⁺ flows back into the stroma through ATP synthase (a process called chemiosmosis).

• The light reactions produce ATP, NADPH, and O₂ (as a byproduct).

🌱 Calvin Cycle (occurs in the stroma):

• The Calvin cycle uses CO₂, ATP, and NADPH to build G3P, which is used to form glucose.

• The enzyme RuBisCO fixes carbon by attaching CO₂ to RuBP, forming 3-PGA.

• ATP and NADPH are used to convert 3-PGA into G3P (a 3-carbon sugar).

• Some G3P exits to form glucose, while the rest regenerates RuBP to continue the cycle.

Cellular Respiration

Definition:
Cellular respiration is the process by which cells break down glucose (or other food molecules) to produce ATP, the energy currency of the cell.

Formula:

C6H12O6+6O2→6CO2+6H2O+ATP (energy)

📍 The 4 Stages of Cellular Respiration

1. Glycolysis (in the cytoplasm)

• What happens:

  • Glucose (6C) is split into 2 molecules of pyruvate (3C each).

• Key points:

  • Happens in the cytoplasm

  • Anaerobic (does not need oxygen)

  • Products:

    • 2 ATP (net gain)

    • 2 NADH (electron carriers)

    • 2 Pyruvate

2. Pyruvate Oxidation (between glycolysis & Krebs)

• Each pyruvate is converted into acetyl-CoA (2C), releasing CO₂.

• Location: Mitochondrial matrix

• Products (per glucose):

  • 2 Acetyl-CoA

  • 2 CO₂

  • 2 NADH

3. Krebs Cycle (Citric Acid Cycle) (in the mitochondrial matrix)

• Acetyl-CoA enters the cycle. The carbons are gradually broken down.

• What’s produced (per glucose):

  • 6 NADH

  • 2 FADH₂

  • 2 ATP

  • 4 CO₂

4. Electron Transport Chain (ETC) + Chemiosmosis (on the inner mitochondrial membrane)

• NADH & FADH₂ donate electrons to the ETC.

• Electrons move through protein complexes, pumping H⁺ ions into the intermembrane space.

• This creates a proton gradient.

• H⁺ flows back through ATP synthase, driving ATP production.

• The final electron acceptor = Oxygen, which forms H₂O with electrons and H⁺.

• ATP made: 34 ATP

Unit 4: Cell Communication

Types of Signaling

1. Paracrine Signaling

   • Short distance diffuses through the extracellular matrix.

   • Example: Synaptic signaling (neurotransmitters).

2. Endocrine Signaling

   • Long-distance, slower, but long-lasting effects.

   • Example: Hormones.

3. Autocrine Signaling

   • The cell signals itself.

   • Example: Cell death signaling.

4. Direct Signaling via Gap Junctions

   • Small molecules pass directly between cells.

Receptors

• Internal Receptors: Hydrophobic ligands (e.g., steroid hormones) diffuse across the membrane and interact with receptors inside the cell.

• Cell-Surface Receptors:

  1. Ion Channel-Linked Receptors: Open a pore for ions when ligand binds.

  2. G-Protein-Linked Receptors: Activate G-proteins to trigger a response.

  3. Enzyme-Linked Receptors: Example: Receptor Tyrosine Kinase (RTK)—activates phosphorylation cascades.

Signal Transduction

• Ligand binds receptor → Signal is transmitted inside the cell.

• Dimerization: Two receptors bind to form a stable complex.

• Signaling Pathway: Chain reaction activating enzymes and proteins.

• Signal Integration: Multiple signals activate the same response.

Intracellular Signaling

• Phosphorylation: Adds phosphate group (by kinase) to activate/deactivate proteins.

• Second Messengers: Example: cAMP (cyclic AMP), activated by enzymes.

• Cell Response:

  • Gene expression

  • Metabolism changes

  • Cell Death (Apoptosis)

Cell Cycle

Phases of the Cell Cycle

1. Interphase (Cell growth and preparation)

   • G₁ Phase: Cell grows, checks for DNA damage.

   • S Phase: DNA replication (sister chromatids form).

   • G₂ Phase: Cell prepares for division (organelles duplicate).

2. Mitotic (M) Phase (Cell division)

   • Mitosis (Karyokinesis): Nucleus divides.

   • Cytokinesis: Cytoplasm splits into two cells.

Mitosis Stages

1. Prophase: Chromosomes condense, nuclear envelope breaks down.

2. Prometaphase: Spindle fibers attach to centromeres.

3. Metaphase: Chromosomes align in the middle.

4. Anaphase: Sister chromatids separate and move to opposite sides.

5. Telophase: Chromosomes decondense, nuclear envelope reforms.

Cell Cycle Regulation

Checkpoints

1. G₁ Checkpoint: Checks cell size, nutrients, and DNA damage.

2. G₂ Checkpoint: Ensures DNA replication is complete.

3. M Checkpoint: Ensures all chromatids are attached to spindle fibers.

Regulatory Proteins

• Positive Regulators: Promote cell cycle progression.

  • Example: Cyclins and Cyclin-Dependent Kinases (Cdks).

• Negative Regulators: Stop cell cycle if errors are found.

  • Example: p53, p21, Rb (Retinoblastoma protein).

Cancer and the Cell Cycle

• Uncontrolled cell growth due to mutations in regulatory genes.

• Proto-oncogenes → Mutate into oncogenes, causing excessive division.

• Tumor Suppressor Genes (e.g., p53) prevent uncontrolled division.

  • Mutations in these genes can lead to cancer

Unit 5:

🔬 5.1: Meiosis

• Meiosis creates 4 genetically unique haploid gametes from a diploid cell.

• Happens in two rounds: Meiosis I (separates homologous chromosomes) & Meiosis II (separates sister chromatids).

• Crossing over in Prophase I creates new allele combinations.

• Independent assortment of chromosomes in Metaphase I increases variation.

• Leads to genetic diversity in sexually reproducing organisms.

🧬 5.2: Meiosis and Genetic Diversity

• Crossing over = homologous chromosomes exchange DNA → new allele combinations.

• Random assortment = random lineup of maternal/paternal chromosomes.

• Random fertilization = any sperm + any egg = more variation.

• Genetic diversity is crucial for evolution and survival in changing environments.

🧫 5.3: Mendelian Genetics

• Genes: units of inheritance; alleles: different forms of a gene.

• Law of Segregation: alleles separate during gamete formation.

• Law of Independent Assortment: genes on different chromosomes assort independently.

• Use Punnett squares to predict genotype and phenotype ratios.

• Monohybrid cross: one gene (Aa × Aa → 1:2:1 genotype, 3:1 phenotype).

• Dihybrid cross: two genes (AaBb × AaBb → 9:3:3:1 phenotype ratio).

🧪 5.4: Non-Mendelian Genetics

• Incomplete dominance: blended phenotype (Red × White = Pink).

• Codominance: both alleles expressed (Type AB blood).

• Multiple alleles: more than two options (e.g., IA, IB, i for blood type).

• Polygenic traits: multiple genes affect one trait (e.g., height, skin color).

• Pleiotropy: one gene affects multiple traits.

• Epistasis: one gene controls expression of another.

• Sex-linked traits: genes on X chromosome → males affected more often (e.g., colorblindness).

👨‍👩‍👧‍👦 5.5: Environmental Effects on Phenotype

• Genotype ≠ destiny: the environment can affect gene expression.

  • Example: Fur color in Arctic foxes changes with season.

• Nutrition, temperature, light can alter phenotypes.

• Phenotypes = result of genotype + environment.

📊 5.6: Chromosomal Inheritance

• Genes are located on chromosomes.

• Linked genes = genes close together on the same chromosome → inherited together.

• Recombination frequency: used to map gene distance; the farther apart, the more likely crossing over happens.

• Chromosomal mutations: deletion, duplication, inversion, translocation.

• Nondisjunction: failure of chromosomes to separate → aneuploidy (e.g., Down syndrome = trisomy 21).

🧬 5.7: Pedigrees

• Diagrams used to track inheritance of traits across generations.

• Can show dominant, recessive, autosomal, or sex-linked inheritance.

• Autosomal dominant: every generation affected.

• Autosomal recessive: skips generations.

• X-linked recessive: mostly affects males; females can be carriers.

Unit 6

1. Structure of DNA and RNA

• DNA: Double helix, deoxyribose sugar, A-T and C-G (hydrogen bonds).

• RNA: Single strand, ribose sugar, A-U and C-G.

• Nucleotides: Sugar + phosphate + nitrogen base.

🔹 2. Replication (S phase of cell cycle)

• Purpose: Make an exact DNA copy.

• Enzymes:

  • Helicase: Unzips DNA.

  • DNA Polymerase: Adds new nucleotides (5’→3’ direction).

  • Ligase: Seals fragments on the lagging strand (Okazaki fragments).

• Semi-conservative: Each new DNA has one old strand and one new strand.

🔹 3. Transcription (DNA → RNA)

• Happens in the nucleus (eukaryotes).

• Enzyme: RNA Polymerase.

• Uses a DNA template to make mRNA.

• Promoter: Starting point for transcription.

• Introns are cut out, exons stay.

• mRNA processing:

  • 5’ cap

  • Poly-A tail

  • Splicing

🔹 4. Translation (RNA → Protein)

• Happens in the ribosome.

• mRNA codons (3-base units) are read.

• tRNA brings amino acids and matches the anticodon to the mRNA codon.

• Starts at AUG (methionine).

• Ends at stop codon (UAA, UAG, UGA).

🔹 5. Gene Regulation

• Prokaryotes: Operons

  • Lac operon: Inducible (off until lactose present)

  • Trp operon: Repressible (on until too much tryptophan)

• Eukaryotes:

  • Transcription factors

  • Epigenetics (methylation = off, acetylation = on)

  • RNA interference (miRNA can block translation)

🔹 6. Mutations

• Point mutation: One base is changed.

  • Silent: No change in amino acid.

  • Missense: Changes an amino acid.

  • Nonsense: Creates a stop codon.

• Frameshift: Insertion/deletion — shifts the reading frame.

🔹 7. Biotech Applications

• PCR: Amplifies DNA.

• Gel electrophoresis: Separates DNA by size.

• Restriction enzymes: Cut DNA at specific sequences.

• CRISPR: Edit genes.