APBiology

1: Chemistry of Life

Water - Polar molecule: Unequal sharing of electrons creates partial positive (H) and negative (O) charges. - Hydrogen bonds: Weak attractions between H of one molecule and O of another. - Crucial for water's properties. - Properties of water: - Cohesion: Water molecules stick together (due to H-bonds). - Adhesion: Water molecules stick to other polar substances. - High specific heat: Resists temperature change. - High heat of vaporization: Requires a lot of energy to evaporate. - Less dense as solid (ice floats): H-bonds form a crystal lattice. - Excellent solvent: Dissolves polar and ionic substances.

pH - pH scale: Measures H+ concentration (0-14). - Acids: pH < 7 (high H+ concentration). - Bases: pH > 7 (low H+ concentration). - Neutral: pH = 7 (equal H+ and OH-). - Buffers: Resist pH changes by accepting or releasing H+.

Macromolecules - Polymers: Large molecules made of repeating subunits (monomers). - Four main types: - Carbohydrates - Lipids - Proteins - Nucleic acids

Proteins - Monomers: Amino acids (amino group, carboxyl group, R group). - Polymer: Polypeptide. - Functions: Enzymes, structure, transport, defense, etc. - Structure levels: - Primary: Amino acid sequence. - Secondary: Local folding (alpha helix, beta sheet). - Tertiary: Overall 3D shape (interactions between R groups). - Quaternary: Multiple polypeptide chains together. - Denaturation: Loss of protein shape and function (caused by heat, pH, etc.).

Nucleic Acids - Monomers: Nucleotides (sugar, phosphate group, nitrogenous base). - Types: DNA and RNA. - DNA: Stores genetic information, double-stranded helix, bases: A, T, C, G. - RNA: Involved in protein synthesis, single-stranded, bases: A, U, C, G.

Others: - Functional groups: Groups of atoms with specific properties (e.g., hydroxyl, carboxyl, amino). - Importance of carbon: Versatile element, forms covalent bonds, backbone of organic molecules. - Lipids: Diverse group, includes fats, phospholipids, steroids. - Functions: energy storage, insulation, cell membranes. - Carbohydrates: Energy source, structural molecules (e.g., glucose, starch, cellulose).

2. Cell Structure and Function

Cell Organelles - Nucleus: Contains DNA, control center of the cell.
- Ribosomes: Site of protein synthesis.
- Endoplasmic Reticulum (ER): - Rough ER: Studded with ribosomes, protein synthesis and modification.
- Smooth ER: Lipid synthesis, detoxification.
- Golgi Apparatus: Packages and modifies proteins for transport.
- Lysosomes: Breakdown cellular waste and debris. - Mitochondria: Powerhouse of the cell, ATP production.
- Chloroplasts: (Plant cells) Site of photosynthesis.
- Cell Wall: (Plant cells) Provides support and protection.
- Vacuole: Storage of water, nutrients, waste. - Cytoskeleton: Maintains cell shape, aids in cell movement.
Membranes - Fluid mosaic model: Phospholipid bilayer with embedded proteins. - Phospholipids: Hydrophilic heads, hydrophobic tails.
- Proteins: Various functions (transport, signaling, enzymes). - Selectively permeable: Controls what enters and leaves the cell.
Transport - Passive transport: No energy required. - Simple diffusion: Movement of molecules from high to low concentration.
- Facilitated diffusion: Transport proteins aid in movement.
- Active transport: Requires energy (ATP). - Pumps molecules against concentration gradient. - Endocytosis: Bringing substances into the cell.
- Exocytosis: Releasing substances from the cell.
Endosymbiosis Hypothesis - Mitochondria and chloroplasts originated as free-living prokaryotes.
- Were engulfed by larger cells and formed symbiotic relationships.
- Evidence: Double membranes, own DNA, ribosomes.
Compartmentalization - Division of cell into organelles. - Increases efficiency by separating processes.
- Protects cellular components. Surface Area to Volume Ratio - As cell size increases, volume increases faster than surface area.
- Limits cell size. - Important for nutrient uptake and waste removal. Plasma Membrane - Phospholipid bilayer with embedded proteins.
- Can cross: Small, nonpolar molecules (O2, CO2), lipid-soluble molecules.
- Cannot cross: Large molecules, polar molecules, ions.
Water Potential - Measure of free water molecules. - Affected by solute concentration and pressure. - Water moves from high to low water potential.
Osmolarity - Concentration of solute particles in a solution. - Affects water movement. - Tonicity: Describes the relative concentration of solutes in two solutions. - Hypertonic: Higher solute concentration.
- Hypotonic: Lower solute concentration.
- Isotonic: Equal solute concentration.
Osmoregulation - Maintenance of water balance. - Cells use various mechanisms to regulate water intake and loss.

3: Cellular Energetics

Enzymes - Structure: Proteins with specific 3D shape. - Function: Catalysts that speed up chemical reactions by lowering activation energy.
- Active site: Specific region where substrates bind.
- Induced fit model: Enzyme changes shape slightly to fit substrate.
Environmental Factors Affecting Enzymes - Temperature: Optimal temperature for enzyme activity. - High temperatures can denature enzymes.
- pH: Optimal pH for enzyme activity. - Changes in pH can alter enzyme shape and function.
- Substrate concentration: Increased substrate concentration increases reaction rate up to a point.
- Enzyme concentration: Increased enzyme concentration increases reaction rate.
- Cofactors and coenzymes: Non-protein molecules that assist enzyme function.
Activation Energy - Energy required to start a chemical reaction.
- Enzymes lower activation energy.
Energy and Metabolism - Metabolism: All chemical reactions in an organism.
- Anabolic pathways: Build molecules, require energy (e.g., photosynthesis).
- Catabolic pathways: Break down molecules, release energy (e.g., cellular respiration).
- Coupled reactions: Energy released from one reaction drives another.
Photosynthesis - Conversion of light energy into chemical energy (glucose).
- Occurs in chloroplasts.
- Two stages: - Light-dependent reactions: - Convert light energy into ATP and NADPH.
- Oxygen is released as a byproduct.
- Light-independent reactions (Calvin cycle): - Use ATP and NADPH to build glucose from CO2.
Cellular Respiration - Breakdown of glucose to release energy (ATP).
- Occurs in cytoplasm and mitochondria. - Three main stages: - Glycolysis: Breakdown of glucose into pyruvate.
- Krebs cycle (citric acid cycle): Complete oxidation of pyruvate to CO2. - Oxidative phosphorylation (electron transport chain): Produces ATP through chemiosmosis.
Fermentation - The anaerobic process regenerates NAD+ for glycolysis.
- Produces lactic acid or ethanol as a byproduct.

4: Cell Communication and Cell Cycle

Cell Communication and Signaling - Cell signaling: Cells communicate with each other using chemical signals. - Types of cell signaling: - Autocrine: Cell signals itself. - Paracrine: Cell signals nearby cells. - Endocrine: Cell signals distant cells through the bloodstream. - Juxtacrine: Cells communicate through direct contact. Signal Transduction - Reception: Signal molecule binds to a specific receptor on the cell surface. - Transduction: Signal is converted into a cellular response. - Often involves a cascade of events involving second messengers. - Response: Cellular activity is altered (e.g., gene expression, enzyme activation). Disruptions in Signal Transduction Pathways - Can lead to diseases (e.g., cancer, diabetes). - Often involve mutations in receptor proteins or signaling molecules. Feedback Mechanisms - Positive feedback: Amplifies a signal (e.g., childbirth). - Negative feedback: Returns a system to its set point (e.g., blood sugar regulation). The Cell Cycle - Ordered series of events leading to cell division. - Phases: - Interphase: - G1 phase: Cell growth and preparation for DNA replication. - S phase: DNA replication. - G2 phase: Cell growth and preparation for mitosis.
- Mitosis: Division of the nucleus. - Prophase: Chromosomes condense, nuclear envelope breaks down. - Metaphase: Chromosomes align at the metaphase plate. - Anaphase: Sister chromatids separate. - Telophase: Nuclear envelope reforms, chromosomes decondense. - Cytokinesis: Division of the cytoplasm. Regulation of the Cell Cycle - Checkpoints: Control points in the cell cycle to ensure proper progression. - Cyclins and cyclin-dependent kinases (CDKs): Proteins that regulate the cell cycle. - Growth factors: Proteins that stimulate cell division. Cancer - Uncontrolled cell growth and division. - It is caused by mutations in genes that regulate cell cycle. - Can invade surrounding tissues and spread to other parts of the body (metastasis). Apoptosis - Programmed cell death. - Important for development and maintaining tissue homeostasis.

5: Heredity

Meiosis and Genetic Diversity - Meiosis: Cell division that produces gametes (sperm and egg).
- Reduces chromosome number: Diploid (2n) to haploid (n).
- Two divisions: Meiosis I and Meiosis II.
- How meiosis generates genetic diversity: - Crossing over: Exchange of genetic material between homologous chromosomes.
- Independent assortment: Random alignment of homologous chromosomes during metaphase I.
- Random fertilization: Any sperm can fertilize any egg.
Mendelian Genetics and Probability - Mendelian genetics: Study of inheritance patterns discovered by Gregor Mendel.
- Law of segregation: Alleles for a trait separate during gamete formation.
- Law of independent assortment: Alleles for different traits segregate independently.
- Probability: Used to predict the outcome of genetic crosses. - Punnett squares: Visual representation of possible offspring genotypes.
Non-Mendelian Genetics - Exceptions to Mendelian inheritance patterns. - Incomplete dominance: Neither allele is completely dominant (e.g., pink flowers).
- Codominance: Both alleles are expressed equally (e.g., AB blood type).
- Multiple alleles: More than two alleles for a trait (e.g., blood type).
- Polygenic inheritance: Multiple genes influence a trait (e.g., height, skin color).
- Epistasis: One gene affects the expression of another (e.g., coat color in Labrador retrievers).
Linked Genes - Genes located on the same chromosome tend to be inherited together.
- Crossing over can separate linked genes.
- Gene mapping: Determining the relative positions of genes on a chromosome.
Non-nuclear Inheritance - Inheritance of traits outside the nucleus. - Mitochondrial DNA: Inherited maternally.
- Chloroplast DNA: Inherited maternally in plants.
Phenotype = Genotype + Environment - Phenotype: Observable physical traits.
- Genotype: Genetic makeup of an individual.
- Environment: Can influence the expression of genes (e.g., height, skin color).

6: Gene Expression and Regulation

DNA and RNA - Nucleic acids: Polymers of nucleotides. - DNA (Deoxyribonucleic acid): Stores genetic information. - Double-stranded helix. - Nucleotides: deoxyribose sugar, phosphate group, nitrogenous base (A, T, C, G). - RNA (Ribonucleic acid): Involved in protein synthesis. - Single-stranded. - Nucleotides: ribose sugar, phosphate group, nitrogenous base (A, U, C, G). DNA Replication - Process of copying DNA before cell division. - Semi-conservative: Each new DNA molecule contains one old and one new strand. - Enzymes involved: helicase, DNA polymerase, ligase. Transcription and Translation - Transcription: DNA is copied into mRNA. - Occurs in the nucleus. - Enzyme: RNA polymerase. - Translation: mRNA is used to build a protein. - Occurs in the cytoplasm at ribosomes. - Involves tRNA and amino acids. Transcription in Prokaryotes vs. Eukaryotes - Prokaryotes: Simpler, occurs in the cytoplasm. - Eukaryotes: More complex, occurs in the nucleus, and involves RNA processing (introns, exons). Flow of Information from the Nucleus to the Cell Membrane DNA -> mRNA -> protein -> cell function. Regulation of Gene Expression - Control of gene activity. - Prokaryotes: Operons (e.g., lac operon). - Eukaryotes: Transcription factors, epigenetic modifications, RNA processing, protein degradation. Mutations - Changes in the DNA sequence. - Can be beneficial, harmful, or neutral. - Types: substitution, insertion, deletion, frameshift. Biotechnology Use of technology to manipulate genetic material. Techniques - Bacterial transformation: Introducing foreign DNA into bacteria. - Gel electrophoresis: Separating DNA fragments by size. - Polymerase chain reaction (PCR): Amplifying DNA. - CRISPR-Cas9: Genome editing tool.

7: Natural Selection

Evidence of Evolution - Fossil Record: Preserved remains of organisms show changes over time. - Comparative Anatomy: Similarities in structures (homologous, analogous, vestigial) indicate common ancestry or adaptation. - Embryology: Similarities in embryonic development suggest shared evolutionary history. - Molecular Biology: Comparison of DNA and protein sequences reveals genetic relationships. - Biogeography: Distribution of organisms on Earth reflects their evolutionary history and adaptation to different environments. Natural Selection - Definition: The process by which organisms better adapted to their environment tend to survive and produce more offspring. - Key components: - Variation: Differences in traits among individuals. - Overproduction: More offspring are produced than can survive. - Competition: Individuals compete for resources. - Survival of the fittest: Those with advantageous traits are more likely to survive and reproduce. - Adaptation: Traits that increase fitness become more common in the population over time. Artificial Selection - Definition: Selective breeding by humans to develop organisms with desired traits. - Examples: Domesticated animals, crop plants. Sexual Selection - Definition: A type of natural selection where individuals with certain traits are more likely to mate and reproduce. - Examples: Peacock feathers, deer antlers. Population Genetics - Definition: The study of genetic variation within populations. - Key concepts: - Gene pool: The total collection of genes in a population. - Allele frequency: The relative abundance of different alleles. - Genotype frequency: The proportion of individuals with different genotypes. Population Genetics and Genetic Drift - Genetic drift: Random changes in allele frequencies due to chance, especially in small populations. - Founder effect: Loss of genetic variation when a new population is established by a small group of individuals. - Bottleneck effect: Drastic reduction in population size leading to loss of genetic diversity. Hardy-Weinberg Equilibrium - Definition: Describes a population that is not evolving, with allele and genotype frequencies remaining constant. - Conditions for equilibrium: - No mutation - No migration - Large population size - Random mating - No natural selection Phylogeny - Definition: The evolutionary history of a group of organisms. - Phylogenetic trees: Diagrams that represent evolutionary relationships. Speciation - Definition: The process by which new species arise. - Types of speciation: - Allopatric speciation: Geographic isolation leads to reproductive isolation. - Sympatric speciation: New species arise within the same geographic area. Extinction - Definition: The disappearance of a species. - Factors contributing to extinction: - Habitat loss - Climate change - Overexploitation - Invasive species - Disease Phylogeny and Common Ancestry - Common ancestor: An ancestral organism from which different species evolved. - Phylogenetic trees show: - Shared derived characters (synapomorphies) - Branching patterns representing speciation events Modern-Day Examples of Continuing Evolution - Antibiotic resistance: Bacteria evolving resistance to antibiotics. - Pesticide resistance: Insects developing resistance to pesticides. - Human evolution: Ongoing changes in human populations due to factors like diet, climate, and disease. - Climate change adaptation: Species adapting to changing environmental conditions.