Review of Chemistry (Chapter 2)

Atomic Structure and Electron Configuration

Atoms are the fundamental units of matter, composed of protons, neutrons, and electrons. Understanding atomic structure is essential for predicting chemical behavior.

• Atom Structure: Consists of a nucleus (protons and neutrons) surrounded by electrons in orbitals.

• Electron Configuration: Electrons fill orbitals in specific energy levels (shells). The arrangement determines chemical reactivity.

• Valence Electrons: Electrons in the outermost shell; determine bonding capacity.

• Bonding Capacity: Atoms form bonds to fill their valence shells (octet rule for many elements).

Chemical Bonds

Chemical bonds hold atoms together in molecules. The type of bond affects molecular properties.

• Nonpolar Covalent Bonds: Electrons are shared equally (e.g., H2, O2).

• Polar Covalent Bonds: Electrons are shared unequally due to differences in electronegativity (e.g., H2O).

• Ionic Bonds: Electrons are transferred from one atom to another, creating ions (e.g., NaCl).

• Hydrogen Bonds: Weak attractions between a hydrogen atom and an electronegative atom (e.g., between water molecules).

• Van der Waals Interactions: Weak, transient attractions due to temporary dipoles.

Electronegativity

• Definition: The tendency of an atom to attract electrons in a bond.

• Effect: Determines bond polarity; higher difference leads to more polar bonds.

Isomers

• Isomers: Molecules with the same molecular formula but different structures.

• Types: Structural isomers (different covalent arrangements), geometric isomers (different spatial arrangements), enantiomers (mirror images).

Chemical Groups

• Hydroxyl (-OH): Found in alcohols; polar.

• Ketone (C=O within carbon skeleton): Found in sugars.

• Aldehyde (C=O at end of carbon skeleton): Found in sugars.

• Amine (-NH2): Found in amino acids; acts as a base.

• Carboxyl (-COOH): Found in amino acids and fatty acids; acts as an acid.

Biological Macromolecules (Chapters 3–6)

General Properties

• Macromolecules: Large molecules essential for life, including proteins, nucleic acids, carbohydrates, and lipids.

• Monomer: Small building block molecule (e.g., amino acid, nucleotide, monosaccharide).

• Polymer: Long chain of monomers (e.g., polypeptide, DNA, polysaccharide).

Polymerization Reactions

• Condensation/Dehydration Synthesis: Monomers join by removing water.

• Hydrolysis: Polymers are broken down by adding water.

Macromolecule Overview

Structure-Function Relationship: The specific structure of each macromolecule determines its biological function.

Proteins (Chapter 3)

Amino Acid Structure

• General Structure: Central (alpha) carbon, amino group (-NH2), carboxyl group (-COOH), hydrogen, and R group (side chain).

• Peptide Bond: Covalent bond between amino group of one amino acid and carboxyl group of another.

R Group Properties

• Nonpolar: Hydrophobic side chains.

• Polar: Hydrophilic side chains.

• Charged: Acidic (negative) or basic (positive) side chains.

Peptide Bond Formation

• Reaction: Dehydration synthesis forms peptide bonds.

• Directionality: N-terminus (amino end) to C-terminus (carboxyl end).

• R Group Orientation: Side chains project from backbone, affecting folding.

• Peptide Bond Characteristics: Partial double-bond character, planar, limited rotation.

Levels of Protein Structure

• Primary: Sequence of amino acids (peptide bonds).

• Secondary: Local folding (α-helix, β-sheet) via hydrogen bonds.

• Tertiary: 3D shape from interactions among R groups (hydrophobic, ionic, disulfide bonds, etc.).

• Quaternary: Multiple polypeptide chains assemble.

Protein Folding and Function

• Folding Factors: pH, temperature, salt concentration, chaperones.

• Conformational Changes: Enable proteins to perform diverse functions (e.g., enzymes, receptors).

Nucleic Acids (Chapter 4)

Nucleotide Structure

• Components: Phosphate group, five-carbon sugar (ribose or deoxyribose), nitrogenous base (A, T, C, G, U).

• Examples: dATP, dCTP, dTTP, dGTP (deoxyribonucleotides).

Phosphodiester Linkage

• Formation: Dehydration reaction between 5' phosphate and 3' hydroxyl of adjacent nucleotides.

• Directionality: 5' to 3' end.

DNA Structure

• Double Helix: Two antiparallel strands, right-handed helix.

• Dimensions: ~2 nm diameter, 10 base pairs per turn.

• Major/Minor Groove: Grooves formed by backbone geometry; important for protein binding.

• Complementarity: A-T (2 H-bonds), G-C (3 H-bonds).

DNA vs. RNA

• DNA: Double-stranded, deoxyribose, stable.

• RNA: Single-stranded, ribose, uracil instead of thymine, less stable due to 2' hydroxyl group.

RNA World Hypothesis

• Evidence: RNA can store information and catalyze reactions (ribozymes), suggesting early life may have relied on RNA.

Carbohydrates (Chapter 5)

Monosaccharide Structure

• Basic Formula: (CH2O)n

• Numbering Carbons: Start from the end nearest the carbonyl group.

Linear and Ring Forms

• Interconversion: Monosaccharides can switch between linear and ring forms in solution.

Carbohydrate Nomenclature

• Based on: Number of carbons (triose, pentose, hexose), position of carbonyl (aldose, ketose).

Glycosidic Linkages

• Alpha (α) Linkage: OH on C1 below the ring (e.g., starch).

• Beta (β) Linkage: OH on C1 above the ring (e.g., cellulose).

• Functional Differences: β-linkages are more stable and less digestible by animals.

Examples and Functions

• Monosaccharides: Glucose, fructose.

• Disaccharides: Sucrose, lactose.

• Polysaccharides: Starch (plants), glycogen (animals), cellulose (plants), chitin (fungi, exoskeletons).

• Functions: Energy storage, structural support, cell identity (glycoproteins).

Lipids and Membranes (Chapter 6)

Lipid Structure and Function

• Triglycerides: Glycerol + 3 fatty acids; energy storage.

• Phospholipids: Glycerol + 2 fatty acids + phosphate group; main component of membranes.

• Sterols: Four fused rings; e.g., cholesterol, hormones.

Fatty Acid Properties

• Saturation: Saturated (no double bonds, solid at room temp), unsaturated (one or more double bonds, liquid at room temp).

• Chain Length: Longer chains = higher melting temperature.

Plasma Membrane Composition

• Components: Phospholipid bilayer, proteins, cholesterol (in animals), carbohydrates.

Membrane Models

• Fluid Mosaic Model: Membrane is a dynamic, fluid structure with proteins embedded or associated with the bilayer.

• Sandwich Model: Outdated; proteins coat both sides of the lipid bilayer.

Membrane Proteins

• Integral Proteins: Span the membrane; involved in transport, signaling.

• Peripheral Proteins: Attached to membrane surface; support, signaling.

Membrane Fluidity and Permeability

• Factors: Fatty acid saturation, chain length, cholesterol content, temperature.

Transport Across Membranes

• Passive Transport: No energy required (simple diffusion, facilitated diffusion, osmosis).

• Active Transport: Requires energy (ATP); moves substances against gradient.

• Osmosis: Diffusion of water across a semipermeable membrane.

• Hypotonic: Lower solute concentration outside; water enters cell.

• Hypertonic: Higher solute concentration outside; water leaves cell.

• Isotonic: Equal solute concentration; no net water movement.

Types of Membrane Transport

• Simple Diffusion: Movement of small, nonpolar molecules.

• Facilitated Diffusion: Movement via channel or carrier proteins.

• Active Transport: Primary (direct ATP use), secondary (uses gradient established by primary transport).

• Bulk Transport: Endocytosis (phagocytosis, pinocytosis, receptor-mediated), exocytosis.

Cellular Structure and Function (Chapter 7)

Prokaryotic vs. Eukaryotic Cells

• Prokaryotes: No nucleus, no membrane-bound organelles (e.g., bacteria, archaea).

• Eukaryotes: Nucleus, membrane-bound organelles (e.g., plants, animals, fungi, protists).

Plant vs. Animal Cells

• Plant Cells: Cell wall, chloroplasts, large central vacuole.

• Animal Cells: Lysosomes, centrioles.

Cell Size Limitations

• Surface Area-to-Volume Ratio: Limits cell size; eukaryotes overcome this with organelles.

Organelles and Functions

• Nucleus: Stores genetic material.

• Rough ER: Protein synthesis and modification.

• Smooth ER: Lipid synthesis, detoxification.

• Golgi Apparatus: Protein sorting and shipping.

• Lysosome: Digestion and recycling (animal cells).

• Peroxisome: Breaks down fatty acids, detoxifies.

• Endosome: Sorting of endocytosed material.

• Mitochondria: ATP production.

• Chloroplast: Photosynthesis (plants/algae).

• Vacuole: Storage, structure (plants).

Cytoskeleton Components

• Microfilaments (Actin): Cell shape, movement.

• Intermediate Filaments: Structural support.

• Microtubules: Organelle movement, cell division.

Membraneless Structures

• Ribosomes: Protein synthesis.

• Centrosomes: Microtubule organizing center.

Endomembrane System and Protein Trafficking

• Components: Nuclear envelope, ER, Golgi, lysosomes, vesicles, plasma membrane.

• Secreted Proteins: Synthesized in rough ER, processed in Golgi, transported via vesicles.

• Cytosolic Proteins: Synthesized on free ribosomes, remain in cytosol.

• Signal Sequence, SRP, SRP Receptor: Direct proteins to ER.

• Transport Mechanisms: Gated (nuclear pores), translocation (across membranes), vesicular (via vesicles).

• Protein Localization: Determined by signal sequences.

Cell-Cell Junctions and Communication (Chapter 11)

Extracellular Matrix and Cell Wall

• Fiber Composite Model: Network of fibers (e.g., cellulose, collagen) embedded in a matrix (e.g., pectin, proteoglycans).

• Cell Wall (plants): Cellulose fibers in a polysaccharide matrix.

• Extracellular Matrix (animals): Collagen fibers in a proteoglycan matrix.

Cell Communication

• Physical Contact: Cell junctions (gap junctions, plasmodesmata, desmosomes, tight junctions).

• Chemical Signaling: Autocrine (self), paracrine (nearby), endocrine (distant via bloodstream).

Cell-Cell Junctions

• Gap Junctions: Channels between animal cells for ion/small molecule exchange.

• Plasmodesmata: Channels between plant cells.

• Desmosomes: Anchor cells together.

• Tight Junctions: Seal cells to prevent leakage.

Chemical Signals

• Polar Signals: Cannot cross membrane; bind to surface receptors.

• Non-polar Signals: Cross membrane; bind to intracellular receptors.

Cell Signaling Pathways

• Steps: Ligand binds receptor → signal transduction → cellular response.

• Signal Amplification: One signal molecule triggers many responses (e.g., via second messengers or kinase cascades).

Receptor Types

• G-Protein Coupled Receptors (GPCR): Activate G-proteins, trigger second messengers (e.g., cAMP).

• Receptor Tyrosine Kinases (RTK): Dimerize and autophosphorylate, activating downstream pathways.

• Inactivation: GPCRs: GTP hydrolysis; RTKs: phosphatases remove phosphates.

Second Messengers

• Examples: cAMP, Ca2+, IP3.

Cellular Responses

• Possible Outcomes: Changes in gene expression, metabolism, cell movement, apoptosis.