biol 1306 unit 1
Chapter 2 Notes: Water and Carbon: The Chemical Basis of Life
1. Basic Atomic Structure & Periodic Trends
Abundant Biological Elements: Carbon (C), Hydrogen (H), Nitrogen (N), and Oxygen (O) make up 96% of matter in living organisms.
Subatomic Particles:
Protons: Positively charged particles in the nucleus.
Neutrons: Uncharged (neutral) particles in the nucleus.
Electrons: Negatively charged particles orbiting the nucleus. Most of an atom's volume consists of empty space.
Atomic Terminology:
Atomic Number: Equal to the number of protons.
Mass Number: Equal to the total number of protons + neutrons.
Dalton (Da): The mass unit for subatomic particles (1 Da = 1x10⁻²⁴ g). Electrons have negligible mass.
Valence & Chemical Reactivity:
Valence Shell: The outermost electron shell.
Valence: The number of unpaired valence electrons. Atoms are most stable when their outer valence shells are completely filled.
2. Types of Chemical Bonds & Properties
Electronegativity: The pull an atom exerts on shared electrons, determined by proton count and distance of the valence shell from the nucleus.
Electronegativity increases moving up and to the right on the periodic table.
Relative biological electronegativities: O > N > S ≈ C ≈ H ≈ P.
3. Chemical Properties of Water
Universal Solvent: Water's polar nature and ability to form hydrogen bonds make it an effective solvent for polar molecules and ionic compounds (hydrophilic). Nonpolar molecules do not dissolve well in water (hydrophobic).
Key Properties of Water:
Cohesion & Surface Tension: Water molecules stick to each other via hydrogen bonding, resisting external forces on liquid surfaces.
Adhesion: Water molecules stick to other polar surfaces (e.g., forming a meniscus against glass).
Density Anomaly: Liquid water is denser than solid ice because freezing forces water molecules into an open crystal lattice. Ice acts as an insulating blanket on aquatic environments.
High Specific Heat & Heat of Vaporization: Absorbs large amounts of thermal energy without drastic temperature changes because hydrogen bonds must first be broken. Evaporative cooling (sweating) relies on high heat of vaporization.
Acid-Base Behavior & pH:
Dissociates dynamically: 2 H₂O ⇌ H₃O⁺ + OH⁻
Acids: Release protons (H⁺) into solution, raising [H₃O⁺] and lowering pH.
Bases: Accept protons, lowering [H₃O⁺] and raising pH.
pH: Measured on a logarithmic scale: pH = -log[H⁺]. Pure water has a neutral pH of 7.
4. Chemical Evolution & The Origin of Life
Theory of Chemical Evolution: Complex carbon-containing molecules developed from simple environmental inputs (volcanic gases, hydrothermal vents). Eventually, a self-replicating molecule developed, initiating biological evolution by natural selection.
Energy Dynamics & Thermodynamics:
First Law of Thermodynamics: Energy cannot be created or destroyed, only transferred or transformed.
Potential Energy: Stored energy in chemical bonds (nonpolar C-H bonds hold high potential energy; polar O-H bonds hold low potential energy).
Spontaneity: Reactions proceed spontaneously if products have lower potential energy than reactants and/or if entropy (disorder) increases.
Explanatory Models
Prebiotic Soup Model: Atmospheric gases were exposed to sunlight/lightning kinetic energy, condensing with rainwater into oceans to form an organic soup of complex compounds.
Surface Metabolism Model: Dissolved reactive gases in deep-sea hydrothermal vents adhered to mineral walls; minerals served as catalysts for spontaneous synthesis.
Experimental Evidence
Stanley Miller Experiment: Simulated early Earth conditions using a glass apparatus with gases (CH₄, NH₃, H₂, H₂O vapor), heat, and electrical sparks (lightning). The experiment synthesized precursors to life, including formaldehyde, hydrogen cyanide, and amino acids (glycine).
Photochemical Synthesis: Modern experiments show high-energy UV photons can split simple molecules into highly reactive free radicals, generating organic precursors.
5. Organic Molecules & Functional Groups
Carbon's Versatility: With 4 valence electrons, carbon forms 4 covalent bonds, permitting chains, rings, single, double, and triple bonds.
Functional Groups:
Chapter 3 Notes: Protein Structure and Function
1. Introduction to Amino Acids & Monomers
Macromolecule Synthesis & Breakdown:
Condensation (Dehydration) Reaction: Joins monomers by removing a water molecule to form a covalent bond
Hydrolysis Reaction: Breaks down polymers into monomers by adding a water molecule.
Amino Acid Core Structure: Consists of a central alpha-carbon (alpha-carbon) bonded to four groups:
A hydrogen atom (-H)
An amino functional group (-NH2)
A carboxyl functional group (-COOH)
A variable side chain / R-group
Ionization in Water: At physiological pH, the amino group acts as a base and gains a proton (-NH3+), while the carboxyl group acts as an acid and loses a proton (-COO-). These charges keep amino acids in solution and influence reactivity.
2. Properties of Amino Acid Side Chains (R-Groups)
Chemical Nature: The 20 unique R-groups determine an amino acid's specific physical and chemical properties.
Hydrophilic vs. Hydrophobic:
Hydrophilic: Polar and charged R-groups interact readily with water via hydrogen bonding or ionic interactions.
Hydrophobic: Nonpolar R-groups lack charged or electronegative atoms and coalesce away from water.
Determining R-Group Categories
Acidic (Negative Charge): Side chain lost a proton (e.g., Aspartate, Glutamate).
Basic (Positive Charge): Side chain gained a proton (e.g., Lysine, Arginine, Histidine).
Uncharged Polar: Contains highly electronegative atoms like oxygen or nitrogen with partial charges (e.g., Serine, Threonine, Tyrosine, Asparagine, Glutamine).
Nonpolar: Consists primarily of carbon and hydrogen atoms (e.g., Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Cysteine, Phenylalanine, Tryptophan, Proline).
3. The Peptide Bond & Polypeptide Backbone
Peptide Bond Formation: A covalent C-N bond formed between the carboxyl group of one amino acid and the amino group of another via a condensation reaction.
Backbone Features:
R-Group Orientation: Side chains extend outward from the backbone to interact with water and other residues.
Directionality: Runs from the N-terminus (free amino group on the left) to the C-terminus (free carboxyl group on the right).
Flexibility: While the peptide bond itself cannot rotate (due to double-bond character), single bonds on either side allow rotation and flexing.
Chain Length Classification:
Oligopeptide (Peptide): Fewer than 50 amino acids.
Polypeptide: More than 50 amino acids.
Protein: A complete, functional folded macromolecule (may consist of one or more polypeptides).
4. The Four Levels of Protein Structure
R-Group Interactions in Tertiary Structure:
Hydrogen Bonds: Form between polar side chains and opposite partial charges.
Hydrophobic Interactions & van der Waals: Water forces nonpolar side chains together, stabilized by weak electrical attractions.
Covalent Disulfide Bonds: Strong linkages between sulfur-containing cysteine residues (-S-S-).
Ionic Bonds: Form between oppositely charged basic and acidic side chains.
Multimeric Types: Dimers (2 subunits), Homodimers (2 identical subunits), Heterodimers (non-identical subunits), and Macromolecular Machines (complexes like the ribosome).
5. Protein Folding, Regulation, and Functions
Thermodynamics of Folding: Folded states are generally spontaneous and energetically more stable than unfolded (denatured) states.
Chaperones: Molecular chaperones (such as Hsp90) facilitate proper folding and prevent improper aggregation.
Prions and Disease: Misfolded proteins that induce normal proteins to adopt infectious, disease-causing configurations rich in beta-sheets (e.g., "Mad Cow" disease).
Biological Functions of Proteins:
Catalysis: Enzymes accelerate specific reactions at their active site by orienting substrates.
Structure: Provides structural support for cells and tissues.
Movement: Motor proteins transport intracellular cargo and drive cellular motion.
Signaling: Intercellular messaging molecules.
Transport: Regulates passage of materials across membranes and throughout the organism.
Defense: Antibodies target pathogens for destruction.Chapter 4 Notes: Nucleic Acids & The RNA World
1. Structure of Nucleotides & Nucleic Acids
Nucleotide Components: Every nucleotide consists of three bonded parts:
A phosphate group bonded to the 5' carbon of the sugar.
A 5-carbon sugar (pentose).
A nitrogenous base bonded to the 1' carbon of the sugar.
Ribose vs. Deoxyribose:
Ribose (in RNA): Has a reactive hydroxyl group (-OH) attached to its 2' carbon.
Deoxyribose (in DNA): Lacks an oxygen atom at the 2' carbon, having a hydrogen atom (-H) instead.
Both sugars feature a hydroxyl group (-OH) on the 3' carbon.
Nitrogenous Bases:
Purines (2-ring structure): Adenine (A) and Guanine (G).
Pyrimidines (1-ring structure): Cytosine (C), Uracil (U - RNA only), and Thymine (T - DNA only).
2. Polymerization & Directionality
Phosphodiester Linkage: Nucleotides polymerize via condensation reactions, forming a phosphodiester bond between the phosphate group on the 5' carbon of one nucleotide and the -OH group on the 3' carbon of another.
Directionality: The sugar-phosphate backbone runs in a 5' to 3' direction. The 5' end has an unlinked phosphate group, while the 3' end has an unlinked hydroxyl group where new nucleotides are added.
Activated Nucleotides: Polymerization requires energy. Adding two extra phosphate groups creates nucleoside triphosphates (e.g., Adenosine Triphosphate / ATP). Hydrolysis of these phosphate groups releases energy to drive polymerization spontaneously.
3. DNA Structure & Function
Secondary Structure: Two antiparallel strands form a double helix with a sugar-phosphate backbone on the exterior and base pairs facing the interior.
Base Pairing: Purines pair with Pyrimidines via hydrogen bonding: Adenine pairs with Thymine (A-T), and Guanine pairs with Cytosine (G-C).
Stabilization: Hydrophobic interactions and van der Waals forces stabilize the twisted structure, creating major and minor grooves.
Tertiary Structure: DNA supercoils or wraps around protein complexes called histones to compact its structure inside cells.
Replication Process:
Hydrogen bonds between base pairs are broken to separate strands.
Free deoxyribonucleotides pair with complementary bases on the template strand.
Phosphodiester linkages form to build the complementary strand.
4. RNA Structure & Versatility
Primary Structure: Contains ribose sugar, a sugar-phosphate backbone, and bases A, U, G, C. The 2' -OH group makes RNA significantly less stable and more reactive than DNA.
Secondary Structure: Most commonly single-stranded; folds back on itself to form "stem-and-loop" hairpin structures via internal hydrogen bonding between complementary bases
Tertiary Structure: Hairpins fold into complex 3D shapes (such as pseudoknots).
Catalytic Activity (Ribozymes): RNA can act as an enzyme. Ribozymes have active sites that catalyze chemical reactions, supporting the RNA World Hypothesis—the idea that early life relied on RNA for both storing genetic information and self-replication.
Chapter 5 Notes: Carbohydrates
1. Monosaccharides (Simple Sugars)
Chemical Formula: General ratio of (CH2O)n, where n represents the number of carbon-hydrate units.
Structural Distinctions:
Carbonyl Group Placement:
Aldose: Carbonyl group (C=O) located at the end of the carbon chain.
Ketose: Carbonyl group (C=O) located within the carbon chain.
Carbon Count: Triose (3 carbons), Pentose (5 carbons), Hexose (6 carbons).
Ring Formation: In aqueous environments, linear sugars fold into ring structures (e.g., alpha-glucose vs. beta-glucose based on hydroxyl orientation at carbon-1).
2. Glycosidic Linkages & Polysaccharides
Monosaccharides join via condensation reactions to form covalent glycosidic linkages between hydroxyl groups.
Energy Storage Polysaccharides:
Starch: Plant storage molecule made of alpha-glucose monomers linked by alpha-1,4 and alpha-1,6 linkages; forms helices.
Glycogen: Animal storage molecule kept in liver and muscle cells; highly branched alpha-glucose polymer with alpha-1,6 linkages every ~10 monomers.
Structural Polysaccharides:
Cellulose: Plant cell wall component made of beta-glucose joined by beta-1,4 linkages. Alternating flipped monomers allow parallel strands to form strong hydrogen bonds.
Chitin: Fungal cell walls and arthropod exoskeletons; made of N-acetylglucosamine (NAG) monomers joined by beta-1,4 linkages.
Peptidoglycan: Bacterial cell wall component; alternating monosaccharides linked by beta-1,4 linkages, cross-linked by short amino acid peptide chains.
3. Biological Roles of Carbohydrates
Structural Support: Fibrous beta-1,4 linkages resist hydrolysis by most organisms and exclude water, providing durability.
Cell Identity:
Monosaccharides attach to proteins (glycoproteins) or lipids (glycolipids) on the outer cell membrane.
Functions as identification badges for cell-cell recognition, signaling, and fertilization events.
Energy Storage & Yield:
Carbohydrates contain many C-H and C-C bonds with high potential energy.
Enzymes like amylase (for starch) and phosphorylase (for glycogen) hydrolyze alpha-linkages to release glucose.
Breakdown of glucose yields energy used to synthesize ATP.Chapter 6 Notes: Lipids, Membranes, and Early Cells
1. Lipid Structure and Properties
General Characteristics: Lipids are carbon-containing compounds that are insoluble in water due to a high proportion of nonpolar hydrocarbon chains (where electrons are shared equally)
Isoprenoids vs. Fatty Acids:
Isoprenoids: Hydrocarbon chains built from isoprene subunits that serve as pigments, scents, vitamins, and sex hormone precursors, as well as building blocks for complex lipids.
Fatty Acids: Unbranched hydrocarbon chains containing 14–20 carbon atoms attached to a polar carboxyl functional group.
Bond Saturation & Physical State:
Saturated Fatty Acids: Contain only single bonds between carbons, holding the maximum number of hydrogen atoms. They form straight tails that pack tightly, making them solid at room temperature (e.g., butter, beeswax).
Unsaturated Fatty Acids: Contain one or more double bonds in the hydrocarbon chain (removing hydrogen atoms) which creates a "kink" in the chain. Kinks prevent tight packing, keeping unsaturated lipids liquid at room temperature (e.g., safflower oil).
Polyunsaturated: Hydrocarbon tails that contain multiple double bonds.
2. Three Major Types of Cellular Lipids
Lipids do not share a single common monomer structure, but are categorized into three main types:
Steroids: Characterized by a bulky, four-ring structure. Functional groups attached to the ring carbons distinguish different steroids (e.g., cholesterol in plasma membranes, estrogen, testosterone).
Fats (Triacylglycerols / Triglycerides): Formed when three fatty acids link to a glycerol molecule via dehydration reactions, creating ester linkages. Their primary function is energy storage because the large number of high-energy C-H and C-C bonds store twice as much chemical energy as carbohydrates.
Phospholipids: Consist of a glycerol linked to two nonpolar hydrophobic fatty acid tails and a charged/polar hydrophilic head (containing a phosphate group and a polar molecule like choline).
3. Membrane Structures and Permeability
Amphipathic Structures: Phospholipids and fatty acids are amphipathic (containing both hydrophobic and hydrophilic regions). In water, they spontaneously aggregate to keep hydrophobic tails away from water:
Micelles: Small spherical aggregates formed by free fatty acids.
Lipid Bilayers: Paired sheets formed by phospholipids, where hydrophilic heads face the outer and inner aqueous environments, while hydrophobic tails face inward toward each other.
Liposomes: Artificial membrane-bound vesicles formed in laboratory settings.
Selective Permeability: Bilayers allow certain substances to cross more easily than others:
High Permeability: Small, nonpolar molecules (such as oxygen, carbon dioxide, nitrogen).
Moderate Permeability: Small, uncharged polar molecules (such as water, glycerol).
Low Permeability: Large, uncharged polar molecules (such as glucose, sucrose).
Very Low / Lowest Permeability: Small ions (such as sodium, potassium, chloride).
Factors Affecting Permeability & Fluidity:
Tail Length & Saturation: Bilayers with short, unsaturated tails have higher permeability and fluidity because kinks create gaps. Bilayers with long, saturated tails pack tightly, resulting in lower permeability.
Cholesterol: Inserting cholesterol into membranes decreases permeability by filling spaces between tails.
Temperature: Membrane fluidity and permeability increase as temperature rises.
Membrane Dynamics:
Phospholipids are in constant lateral motion within their layer, but rarely "flip-flop" spontaneously to the opposite layer.
Fluid-Mosaic Model: Replaced the older "sandwich model" by demonstrating that membranes are dynamic mixtures of lipids and proteins where integral proteins span the bilayer and peripheral proteins attach to the surfaces.
4. Mechanisms of Transport Across Membranes
Passive Transport (Does NOT require energy input):
Diffusion: Net movement of solutes down their concentration gradient until equilibrium is reached.
Osmosis: The diffusion of water across a selectively permeable membrane toward a region of higher solute concentration.
Hypertonic Solution: Outer solution has higher solute concentration than inside; water flows out, causing the cell/vesicle to shrink.
Hypotonic Solution: Outer solution has lower solute concentration than inside; water flows in, causing the cell/vesicle to swell or burst.
Isotonic Solution: Equal concentrations inside and outside; no net water movement.
Facilitated Diffusion: Passive transport aided by membrane proteins:
Channel Proteins: Form selective pores that allow specific ions or water (aquaporins) to pass down electrochemical gradients. Some channels are gated and open/close in response to specific signals.
Carrier Proteins: Undergo conformational (shape) changes when a target solute binds, transporting molecules (like GLUT-1 moving glucose) across the membrane.
Active Transport (Requires energy input, typically ATP):
Primary Active Transport (Pumps): Moves substances against their concentration or electrochemical gradient. Example: The Sodium-Potassium Pump (Na+/K+-ATPase) uses ATP hydrolysis to pump 3 sodium ions out of the cell and 2 potassium ions into the cell.
Secondary Active Transport (Co-transport): ATP-driven pumps establish strong electrochemical gradients that represent potential energy. As an ion moves down its established gradient, it powers the transport of a second molecule against its own concentration gradient (e.g., Na+/glucose symporter).1. Fundamental Cell Concepts & Types
Cell Theory Basics
Core Definition: All organisms consist of cells, and all cells arise from pre-existing cells.
Essential Cellular Components:
Proteins: Perform the majority of cellular functions.
Nucleic Acids: Store, transmit, and process genetic information.
Carbohydrates: Provide chemical energy, carbon building blocks, structural support, and cellular identity.
Plasma Membrane: Functions as a selectively permeable barrier enclosing the cell.
Morphological & Phylogenetic Classification
Morphological Types:
Prokaryotes: Lack a membrane-bound nucleus; typically range from 1 to 10 µm in diameter.
Eukaryotes: Contain a membrane-bound nucleus; typically range from 5 to 100 µm in diameter. Includes unicellular and multicellular organisms such as protists, fungi, plants, and animals.
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Three Domains of Life:
Bacteria (Prokaryotic)
Archaea (Prokaryotic)
Eukarya (Eukaryotic)
Benefits of Cellular Compartmentalization
Organelle Bins: Organelles divide the internal cell volume into specialized compartments.
Key Advantages:
Offsets the low surface-area-to-volume ratio in larger cells.
Separates incompatible chemical reactions.
Increases the efficiency of chemical reactions.
2. Eukaryotic Organelles & Structures
Summary Table of Organelle Features
Endosymbiosis Theory
Origins: Mitochondria and chloroplasts evolved from free-living prokaryotic bacteria that were engulfed by an ancestral eukaryote.
Supporting Evidence:
Both possess their own circular DNA independent of the nuclear genome.
Both manufacture their own ribosomes.
Both grow and divide independently of host cell division via binary fission-like processes.
3. Dynamic Cellular Processes & Transport Systems
System 1: Nuclear Transport
Nuclear Envelope: Perforated by nuclear pore complexes composed of ~30 distinct proteins, controlling inbound and outbound traffic.
Inbound Traffic: Nucleoside triphosphates, DNA replication proteins, RNA transcription proteins, and ribosomal structural proteins.
Outbound Traffic: Synthesized mRNA molecules and assembled ribosome subunits.
Nuclear Localization Signal (NLS): A specific 17-amino-acid sequence that acts as a molecular "zip code," tagging cytosolic proteins for entry through the nuclear pore complex.
System 2: The Endomembrane System & Secretory Pathway
Secretory Pathway Route: Rough ER → Vesicle → Golgi Apparatus (cis to trans) → Secretory Vesicle → Plasma Membrane / Exocytosis.
The Signal Hypothesis:
Ribosome synthesizes an ER signal sequence (20 amino acids long).
Signal Recognition Particle (SRP) binds the signal sequence, pausing translation.
The SRP-ribosome complex binds to an SRP receptor located on the Rough ER membrane.
SRP is released; translation resumes, feeding the polypeptide through a channel called the translocon into the ER lumen.
The ER signal sequence is cleaved off, and protein folding/glycosylation occurs inside the lumen.
Golgi Sorting & Vesicle Delivery:
Proteins receive unique carbohydrate tags in the Golgi cisternae (e.g., mannose-6-phosphate marks lysosomal enzymes).
Trans-Golgi receptors bind specific tags and package proteins into targeted transport vesicles.
System 3: Lysosomal Recycling Pathways
Receptor-Mediated Endocytosis: Extracellular ligands bind membrane receptors, pinching off into an endocytic vesicle that matures from an early endosome (acidified via proton pumps) into a late endosome and lysosome.
Phagocytosis: The plasma membrane engulfs large external food particles or cells, forming a phagosome that fuses directly with a lysosome for digestion.
Autophagy: An internal membrane encapsulates damaged internal organelles, forming an autophagosome that fuses with a lysosome to recycle molecular subunits.
4. Cytoskeleton & Cellular Motility
Comparison of Cytoskeletal Elements
Actin Filaments (Microfilaments):
Structure: Two coiled strands of actin subunits (7 nm diameter).
Functions: Resists tension (pulling forces); drives cell crawling, cytokinesis in animal cells, and cytoplasmic streaming in plant cells via myosin motor interaction.
Intermediate Filaments:
Structure: Fibers wound into thicker cables (10 nm diameter; e.g., keratins, lamins).
Functions: Resists tension; anchors the nucleus and other organelles in place; maintains cell shape.
Microtubules:
Structure: Hollow tubes consisting of α- and β-tubulin dimers (25 nm diameter).
Functions: Resists compression (pushing forces); provides tracks for intracellular transport; forms spindle apparatus during cell division.
Motor Proteins & Movement
Kinesin: A motor protein that uses ATP hydrolysis to "walk" along microtubule tracks toward the positive (+) end, carrying transport vesicles.
Dynein: A motor protein that moves along microtubules toward the negative (−) end.
Structure and Function of Cilia and Flagella
Prokaryotic vs. Eukaryotic Flagella:
Prokaryotic flagella are naked protein rods (flagellin) that rotate like a propeller.
Eukaryotic flagella are membrane-bound structures that move in a whipping motion.
The Axoneme:
Structure consists of a "9 + 2" arrangement (9 outer microtubule doublets surrounding 2 central single microtubules).
Originates from a basal body (identical in structure to a centriole).
Bending Mechanism: Dynein arms attached to doublets attempt to "walk" toward the minus end of adjacent doublets. Because the doublets are structurally linked, this sliding motion is constrained, causing the entire axoneme to bend and create movement.