AP Biology Review Notes

Chemistry of Life

Unit 1 covers water, carbon chemistry, and macromolecules.

Water

Water is essential for life, composing 80-90% of cells, and biological reactions occur in water.
Water structure: One oxygen and two hydrogen atoms in a bent shape, making it polar.
Electronegativity: Oxygen attracts electrons more than hydrogen, creating partial negative charge on oxygen and partial positive charges on hydrogens.
Hydrogen Bonds: Intermolecular forces due to water's polarity.
Four major properties of water:
- Cohesion and Adhesion: Water sticks to itself and other substances.
- Temperature moderation: High energy needed to break hydrogen bonds.
- Density reduction upon freezing: Ice floats and insulates.
- Universal solvent: Dissolves polar and charged substances, crucial for hydrophilic and hydrophobic interactions.

Carbon

Carbon forms the backbone of biological molecules due to its structure.
Bohr model shows four valence electrons, allowing carbon to form up to four covalent bonds.
Carbon forms chains, branches, single, double, triple bonds, and cyclical rings.
Structure-function relationship: Isomers and enantiomers have the same formula but different structures.
Enantiomers: Right-handed and left-handed versions, only one is usually biologically relevant.

Macromolecules

Four major categories: carbohydrates, lipids, proteins, and nucleic acids (except lipids, all are polymers).
Polymers are made of monomers.
Dehydration synthesis: Monomers combine, releasing water and forming covalent bonds.
Hydrolysis: Reverse reaction, breaking polymers by adding water.

Carbohydrates

Elemental composition: C, H, and O in a 1:2:1 ratio in monosaccharides.
Glucose: Most important monosaccharide, formula $\text{C}6\text{H}{12}\text{O}_6$ .
Polysaccharides:
- Starch: Glucose polymer for storage in plants.
- Glycogen: Glucose polymer for storage in animals.
- Cellulose: Structural polysaccharide in plant cell walls; indigestible by animals (except via symbiosis).
- Symbiosis: Herbivores have bacteria/protists that digest cellulose.

Lipids

Nonpolar and hydrophobic.
Three major classes:
- Fats and oils: Glycerol with fatty acid chains.
  - Saturated fats: Straight chains, solid at room temperature.
  - Unsaturated fats: Kinks in chains, liquid at room temperature.
  - Function: Long-term storage in animals and plants.
- Phospholipids: Glycerol with two fatty acid chains and a phosphate group (charged).
  - Hydrophilic head and hydrophobic tail form bilayers in water, which are the basis of plasma membranes.
- Steroids: Carbon rings.
  - Hormones (testosterone, estrogen): Pass through membranes for signal transduction.
  - Cholesterol: Regulates cell membrane fluidity in animal cells.

Proteins

Most important macromolecule due to diverse functions and structures.
Monomers: 20 amino acids.
Polypeptides: Amino acids linked by peptide bonds.
Amino acid structure: Common template with a unique R group.
- R groups: Polar, nonpolar, and charged groups.
Polypeptide chains: R groups interact, causing twisting and folding into 3D shapes, determining function.
- Interactions include hydrophobic interactions, ionic bonding, and covalent bonding.
Levels of protein structure:
- Primary: Sequence of amino acids.
- Secondary: Alpha helices and beta-pleated sheets.
- Tertiary: Unique shape due to R group interactions.
- Quaternary: Multiple polypeptides combine.

Cell Biology

Unit 2 focuses on cells and their structures.

Cell Theory and Cell Structure

All living things are made of cells.
Last Universal Common Ancestor (LUCA) passed cellular structure to all descendants.
Prokaryotic cells: Simpler structure.
Eukaryotic cells: More complex with additional features.

Features of All Cells

Plasma membrane.
Cytoplasm.
DNA (genetic material).
Ribosomes.
Small size: Limited by surface area to volume ratio.

Endomembrane System

Collection of membrane-bound organelles: Nucleus, endoplasmic reticulum (smooth and rough), Golgi apparatus, plasma membrane, vesicles, and lysosomes.
Proteins for excretion utilize the endomembrane system.
Proteins are produced on the ER surface, put into the lumen, and packaged into vesicles.

Endosymbiosis

Mitochondria and chloroplasts originated as free-living prokaryotes that moved into eukaryotic cells.
Evidence:
- Double membrane.
- Circular DNA.
- Own ribosomes.

Cytoskeleton

Microtubules are spindle fibers during mitotic and meiotic divisions.
Disruptions to microtubules (e.g., Taxol) can limit cell division, useful for cancer treatment.
Plant and animal cell differences primarily covered in general biology.

Plasma Membrane

Fluid Mosaic Model: Phospholipids form foundation, proteins embedded or associated.
Fluidity: Lateral movement, regulated by saturated/unsaturated fatty acids and cholesterol.
- Saturated fatty acids: Decrease fluidity.
- Unsaturated fatty acids: Increase fluidity.
- Cholesterol: Moderates fluidity.
Transport across membranes is a major focus.

Diffusion and Osmosis

Diffusion: Movement from high to low concentration.
Osmosis: Movement of water across a semipermeable membrane from low to high solute concentration.

Transport Mechanisms

Simple diffusion: Nonpolar gases ( $\text{CO}2$ and $\text{O}2$ ) move across the membrane.
Facilitated diffusion: Charged ions and polar substances move with the concentration gradient via channels.
- Channels can be regulated (open/close).
Active transport: Moves substances against the concentration gradient using ATP (e.g., proton pump).
Chemiosmotic potential: Energy stored in concentration differences across the membrane.

Osmosis and Water Movement

Aquaporins: Specialized channels for water movement.
Isotonic solution: Cytoplasmic solute concentration equals environment; no net water movement.
Hypertonic solution: Higher external solute concentration; water leaves the cell, causing shriveling or plasmolysis.
Hypotonic solution: Lower external solute concentration; water rushes into the cell.
- Animal cells: Lysis (bursting).
- Plant cells: Turgid (normal due to cell wall).
Endocytosis and Exocytosis: Bulk transport via membrane vesicles.

Energy, Photosynthesis, and Cell Respiration

Unit 3 focuses on energy flow in biological systems.

Energy

Energy is the capacity to do work.
Three types of work:
- Transport work: Active transport using ATP.
- Mechanical work: Movement requiring force (Newton's laws).
- Chemical work: Reactions requiring energy, particularly creating complex structures.
Entropy: Universe favors breakdown of complex to simple; releases energy (exergonic reaction).
Building complex from simple requires energy (endergonic reaction).
ATP (adenosine triphosphate): Energy currency for chemical reactions.
- ATP breakdown releases energy; ADP and phosphate can be recharged.

Photosynthesis and Cell Respiration

Sunlight converts $\text{CO}_2$ and water into glucose (photosynthesis).
Glucose breakdown releases energy to recharge ADP into ATP (cell respiration).
Plants (autotrophs): Photosynthesis and cell respiration.
Heterotrophs (like humans): Consume sugars produced by plants to charge ATP.

Photosynthesis

Two major parts: Light reaction and Calvin Cycle.
Occurs in chloroplasts: Stroma (inner region) and thylakoids (membrane stacks).

Light Reaction

Electron transport chain along thylakoids.
Photosystems with pigments (chlorophyll) absorb red and blue light.
Excited electrons pass through ETC, pumping $H^+$ ions from stroma to thylakoid space.
ATP synthase: $H^+$ ions flow out, combining ADP and phosphate into ATP (chemiosmotic gradient).
Water is split in Photosystem II to supply electrons, producing oxygen.
Electrons are recharged at Photosystem I and placed into NADPH (electron carrier).

Calvin Cycle

Occurs in stroma.
$RuBP$ (5-carbon) combines with $CO_2$ by Rubisco, forming 3PG.
ATP and NADPH are used to make glyceraldehyde-3-phosphate (G3P).
G3P is partially removed to create sugar; remaining substrates regenerate $RuBP$ .
Alternative carbon fixation methods: C4 and CAM pathways (for gas availability in hot conditions).

Cell Respiration (Aerobic)

Three stages: Glycolysis, Pyruvate oxidation + Krebs cycle, Oxidative phosphorylation.

Glycolysis

Occurs in cytoplasm.
Glucose breaks down into two pyruvate molecules, producing 2 ATP and 2 NADH (electron carriers).

Pyruvate Oxidation and Krebs Cycle

Pyruvates are imported into mitochondria & lose $CO_2$ , gaining coenzyme A (producing NADH).
Pyruvate converts to acetyl CoA, which enters the Krebs Cycle.
Krebs Cycle (in mitochondrial matrix): Acetyl CoA reacts with oxaloacetate (4-carbon), forming citrate.
Releases remaining $CO2$ , producing NADH, $FADH2$ , and ATP.
ATP production: Substrate-level phosphorylation each requiring oxygen.

Oxidative Phosphorylation

Along the inner mitochondrial membrane: ETC.
Electrons from NADH and $FADH_2$ pump protons from matrix to intermembrane space, creating a concentration gradient to leverage ATP synthase.
Oxygen acts as final electron acceptor, combining with electrons and protons to form water.

Anaerobic Respiration & Fermentation

Absence of oxygen means glycolysis is the only energy harvesting process.
NADH cannot be regenerated, so fermentation occurs.
Electrons are dumped back into pyruvate, regenerating $NAD^+$ .

Enzymes

Proteins that catalyze chemical reactions by lowering activation energy.
Enzymes orient substrates, bind temporarily, or create microenvironments.
Enzymes are reusable.
Inhibitors:
- Competitive inhibitors: Bind to the active site.
- Non-competitive inhibitors: Bind to a different site, altering active site shape.
Regulation: Similar to non-competitive inhibition, by regulating active site.

Cell Communication and Cell Division

Cell Communication

Cells relay information, important for multicellular organisms.
Earl W. Sutherland's three phases: Reception, transduction, response.

Reception

Membrane-bound receptors with a signal/ligand binding site.
Ligand binding alters receptor shape, relaying message.
$G$ protein-coupled receptors (common): Ligand binding activates a $G$ protein, activating other things.

Transduction

Receptors activate second messengers (e.g., cyclic AMP).
Cyclic AMP activates protein kinases, which activate more kinases (phosphorylation cascade).
Amplifies message and adds regulation points.

Response

Cytoplasmic responses: Activating enzymes.
Transcription initiation: Producing proteins from genes.
Nonpolar signaling molecules: Pass through membranes and bind to intracellular receptors.

Cell Division

Cell division leads to growth, development, and repair (multicellular organisms).
Passing on genetic information is key.

Diploid Species

Diploidy: Two copies of each chromosome (one from each parent).
Human karyotype: 23 pairs of chromosomes.
Chromosomes: Compacted DNA with histones; contain genes (encode for proteins).

Cell Cycle

Important to know when DNA replication occurs and how it is handled.

Phases

$G_1$ (GAP1): Growth and normal cell life.
$S$ phase: DNA synthesis (replication); chromosomes duplicate.
$G_2$ phase: Checks ensure everything is ready for division.
Mitotic phase: Cell division.
-Prophase: Chromosomes condense; sister chromatids held at centromere; spindle fibers form.
-Prometaphase: Nuclear envelope dissolves; spindle fibers attach to chromosomes.
-Metaphase: Chromosomes align at the metaphase plate.
-Anaphase: Sister chromatids separate into daughter chromosomes.
-Telophase: Chromosomes relax; nucleus reforms.
-Cytokinesis: Physical separation of daughter cells.

Regulation of Cell Division

Uncontrolled division can lead to cancer.
Internal signals: Cyclins and kinases regulate division.
External factors: Growth factors and hormones accelerate division.
Inhibition: Requiring a substrate or density-dependent inhibition.
Errors in cell cycle regulation can cause cancer.

Heredity

Chromosomes and Genes

Genes: Regions on chromosomes that encode for proteins.
Diploid organisms have two copies of each gene.
Alleles: Varied versions of genes that can act as the basis for variations within a population.

Meiosis

Production of haploid cells (gametes).
Gametes: Sperm (males) and eggs (females).
Meiosis occurs in germline cells and has two division events.
Variation in haploid cells produced.
- Prophase I: Recombination event allowing for paternal and maternal chromosomes to exchange alleles creating new combinations not seen before.
- Metaphase I: random assortment of paternal and maternal chromosomes along that central line.
  Crossing creates randomly shuffled versions of chromosomes in every permutation
Ultimately allows for a great degree of variation

Mendel's Study

Challenged the commonly held belief that offspring simply were blends of their parents.
Discrete and heritable particulates that we now call alleles and genes.
3 Major Laws
- Law of segregation: only one of the two alleles are passed on to the next generation from each of the parents. Using Punnett square is also a plus and can be used for meiotic segregation.
- Law of Dominance: Certain dominant alleles can show up 100% even in the presence of recessive counterparts.
- Law of Independent Assortment: see how random assortment of chromosomes and crossing over would create randomly shuffled versions of chromosomes such that multiple genes and their alleles recombine in every permutation.
Atypical Inheritance
- Epistasis: A gene can affect the expression of a different gene.
- Polygenic inheritance: Many genes all contribute to a single character.
- Environmental effects on gene expression: the environment plays a large role.

Chromosomes and Mendelian Genetics

Linkage
- Situation in which two genes are closely located on a single chromosome. With linked loci we do not see independent assortment.
- Genes closer along a chromosome have a lower probability of being split up. As such, allelic combinations of the original parental chromosomes tend to travel together during meiosis.

Gene Expression

Gene expression, DNA replication

DNA structure

Monomer nucleotide composed of four nitrogenous bases, five carbon deoxyribonucleic sugar, and a phosphate group.
DNA is an anti parallel double helix meaning that we have one DNA strand that runs one way and another paired with it that runs the other way.
A five' end of DNA is where that phosphate is exposed, attached to of course the fifth carbon. Down below we see a three' end where the three' carbon is left dangling with its hydroxide.
The anti parallel aspect of the DNA molecule means that the other strand running parallel is actually going in the opposite direction simultaneously following the Chargaff's rule of complementary base pairing.

DNA replication

Each strand has the complete set of data to recreate the opposite strands, As against Ts and Gs against Cs. Just keep in mind that all synthesis of DNA must occur in a five to three prime direction.
During DNA replication, a replication bubble forms, allowing the two strands of DNA molecule to become slightly separated. On one side of the replication bubble, the helicase enzyme sits at the fork unwinding that DNA during replication. The initial enzyme called primase sees the original strand of DNA on one side and creates a short RNA primer from that five to three prime direction. Next the DNA polymerase binds and continues that primer heading towards that replication fork. Newly unbound regions would continue to be copied against this leading strand.
Issue is the opposite strand. the new synthesis of DNA proceeding in the opposite direction to that of the replication fork's movement, primates and DNA polymerase creating disconnected fragments that we call Okazaki fragments.

Gene Expression

Coding and template strand
coding region that contains the real data needed to make proteins but it also has a region called the promoter that is responsible for initiating this entire gene expression pathway.
Coding strand and template strand show that since double stranded, we have two different sets of codes.
Transcription and translation
- Transcription is the process of copying DNA onto an mRNA template and that's where we are going to start
- Three Major Phases
  - Initiation: transcription factors that bind to the promoter to ready it for expression. RNA polymerase then begins the process of making a copy of that DNA as RNA.
  - Elongation: The template strand of DNA is used to create complementary matches with the incoming RNA monomers, thereby temporarily using that complementary base pairing to ensure that the information on the coding strand is copied onto an RNA strand.
  - Terminals
- mRNA processing
  - 5' end capped
  - Poly A tail added to 3'
  - Introns cut out and Exons linked together
- Translation
  - Ribosomes and tRNA play major role in creating polypeptide from messenger DNA.

Gene Expression Regulation

Regulated to allow organisms to respond properly to their environment.
- Bacterial cells - inducible operons like the lac operon are seen
  Regulation sometimes comes out on this exam.

Evolution

Single common ancestor, species gradually changed over billions of years

Darwin and Natural Selection

Traits with advantageous traits would pass on more of their traits over time.
Evolutions as strong a theory as evolution, there is a lot of evidence to back it
- Real-time, homologous structures, vestigal structures

Evolution (Micro and Macro)

Micro- evolution is a change in allele frequency over generations.
Other mechanisms to allele frequencies
- Mutations, gene flow, genetic drift
- Both bottleneck effect (reduction in a population size) and founder effect(moving to a new area to begin anew)

Speciation

Capacity to interbreed and produce fertile offspring.
Reproductive isolation:
- Allopatric and sympatric
- Prezygotic and post zygotic
  Reproductive isolation is key!
Cladograms
- Evolutionary relations on the exam are important

Ecology

How organisms interact with abiotic factors
- Carbon, nitrogen, phosphorus, hydrologic cycles are important
- Energy is revisited, plants create chemical energy through light and create glucose molecules.
  Tracking energy through primary, secondary and tertiary consumers.
Population and ecological interactions matter
- Density dependence and density independence both dictate population size.
Community Ecology - Ways in which different species can interact with one another
- Competition
- Predator and Prey relationships
- Symbiosis
Species Diversity helps communities avoid collapse
- Know Species/Food webs
- Ecological Succession