Comprehensive Study Guide: General Biology, Chemistry of Life, and Biomolecules

Foundations of Biology and the Major Themes of Life

• Definition of Biology: Biology is defined as the scientific study of life. Biologists continuously acquire new knowledge to understand the millions of species inhabiting Earth.
• Five Major Themes of Biology:
  • 1. Biological Systems Interact: Every living organism represents a biological system that is interdependent with numerous other biological systems across different scales.
  • 2. Structure and Function Are Inter-Related: The physical form and structural design of a biological feature directly dictate its functional capability.
    • Example: Both horses and wolves possess teeth, but a horse's teeth are flattened and designed to grind plant vegetation, whereas a wolf's sharp canine teeth are engineered to tear flesh.
  • 3. Information Must Be Transferred: Biological information must be transmitted within individual cells, between cells, among organisms, and across generations from parents to offspring.
  • 4. Life Depends on Continuous Energy Input and Transfer: All living cells and organisms require a non-stop supply and transformation of energy to maintain life processes.
  • 5. Populations Change Over Time Through Evolution: Evolution is the core unifying process explaining how the ancestry of diverse organisms traces back to common earlier forms of life.

Characteristics of Living Organisms

• Universal Features of Life: All living organisms display six fundamental characteristics:
  • 1. Cellular Composition: Every organism is composed of one or more cells surrounded by a plasma membrane (also called a cell membrane).
  • 2. Growth and Development:
    • Biological Growth: Defined as an increase in the size of individual cells of an organism, an increase in the total number of cells, or both.
    • Development: Encompasses all the structural, functional, and physiological changes that occur throughout an organism's life span.
  • 3. Metabolic Regulation and Homeostasis:
    • Metabolism: Organisms regulate all internal chemical reactions essential for nutrition, cellular growth, tissue repair, and energy conversion.
    • Homeostasis: Organisms self-regulate their internal biochemical environment to maintain stable, balanced conditions necessary for survival.
  • 4. Response to Stimuli: Organisms detect and respond to stimuli—physical or chemical changes in their internal or external environment that evoke a response.
  • 5. Reproduction: Living organisms reproduce to generate new organisms, operating via asexual reproduction (producing genetic clones) or sexual reproduction (combining genetic material).
  • 6. Adaptation and Evolution: Organisms exist within populations that adapt to their environment and evolve over time through changes in the frequencies of genetic variants.

Levels of Biological Organization

• Biological Hierarchy: Life is structured in a precise hierarchy where each higher level exhibits emergent properties—unique characteristics and complex functions not present at lower organizational levels.
• Chemical and Cellular Levels:
  • Atoms: Fundamental units of elements (e.g., Carbon, Hydrogen, Oxygen).
  • Small Molecules: Combinations of atoms bonded together (e.g., Glycerol, Glycine, Ribose).
  • Large Molecules (Macromolecules): Complex biological polymers (e.g., Phospholipids, Proteins, RNA, DNA).
  • Organelles: Subcellular functional structures composed of macromolecular complexes (e.g., Plasma membrane, Ribosomes composed of RNA and protein).
  • Cells: The fundamental structural and functional unit of life. Organisms can be unicellular, colonial, or multicellular with specialized cells.
• Organismal Levels:
  • Tissues: Associations of specialized cells working together to perform specific functions (in animals: connective, epithelial, nervous, and muscle tissue).
  • Organs: Organized structures composed of multiple tissue types (e.g., heart, liver, bone).
  • Organ Systems: Groups of coordinated organs performing major bodily functions (e.g., cardiovascular system, digestive system, skeletal system).
  • Multicellular Organism: A fully functional individual living system integrated across all organ systems (e.g., an elephant).
• Ecological Levels:
  • Ecology: The scientific study of how organisms interact with one another and their physical environment.
  • Population: A group of organisms belonging to the same species residing in a defined geographic area.
  • Community: All the interacting biotic populations of different species inhabiting a shared area.
  • Ecosystem: A biological community interacting alongside its non-living, physical (abiotic) environment.
  • Biosphere: The highest level, encompassing Earth and all its ecosystems and communities.

Energy Flow and Trophic Dynamics in Ecosystems

• Energy Input: All biological processes require a continuous input of energy.
• Thermodynamic Limits: Organisms can neither create energy nor convert it with $100\%$ efficiency. During every energy conversion, a portion of useful energy is lost as heat and dispersed into the surrounding environment.
• Trophic Categories in Self-Sufficient Ecosystems:
  • Autotrophs (Producers): Synthesize their own organic food molecules from inorganic raw materials, primary using light energy via photosynthesis (e.g., plants).
  • Heterotrophs (Consumers): Obtain energy and nutrients by consuming producers or other heterotrophs.
    • Primary Consumers: Herbivores that eat producers directly (e.g., caterpillars eating plant leaves).
    • Secondary Consumers: Carnivores or omnivores that consume primary consumers (e.g., birds eating caterpillars).
  • Decomposers: Heterotrophic organisms (such as bacteria and fungi) that break down non-living organic matter, including plant litter, wastes, and dead bodies, returning essential nutrients to the soil.

Scientific Inquiry, Methodology, and Reasoning

• Definition of Science: Science is a systematic way of thinking and investigating the natural world based on empirical evidence.
• Scientific Reasoning:
  • Deductive Reasoning: Begins with established general premises or supplied information and draws specific logical conclusions from them.
  • Inductive Reasoning: Begins with specific, detailed observations and synthesizes them to formulate a general conclusion or underlying principle.
• Steps of the Scientific Method:
  1. Make formal observations.
  2. Formulate specific questions.
  3. Develop hypotheses.
  4. Design and conduct controlled experiments to test hypotheses.
  5. Gather, record, and analyze experimental data.
  6. Draw logical conclusions based on the data.
• Hypotheses vs. Scientific Theories:
  • Hypothesis: A proposed, tentative explanation for a specific set of observations. A valid hypothesis must be testable, falsifiable, and supported by reproducible, quantifiable data.
  • Scientific Theory: A comprehensive, integrated explanation of an aspect of the natural world, built upon numerous hypotheses each consistently supported by extensive experimental results (e.g., Germ theory of disease, Cell theory, Theory of evolution).
• Experimental Design and Variables:
  • Controlled Experiments: Test hypotheses by isolating and changing specific factors while holding all other environmental conditions constant.
  • Independent Variable: The single factor deliberately altered or manipulated in the experimental group.
  • Dependent Variable: The measurable outcome or response variable recorded to evaluate the effect of the independent variable.
  • Control Group: The baseline group in which the independent variable is withheld or kept at normal status.
• Experimental Bias, Errors, and Statistics:
  • Avoiding Bias: Researchers utilize designs like double-blind studies (where neither the patient nor the examining physician knows who receives an experimental drug versus a placebo) to eliminate subjective bias.
  • Sampling Error: Occurs when a small or unrepresentative sample leads to inaccurate conclusions; experiments must be repeatable with adequate sample sizes.
  • Statistical Significance: Statistical tests (e.g., $t\text{-test}$, Chi-square) calculate the probability that experimental differences are mathematically significant rather than caused by random variation.
  • Paradigm Shifts: Major shifts in scientific consensus and theoretical frameworks occurring when new empirical facts contradict older concepts.
  • Ethical Considerations: Science supplies technical capabilities (e.g., cloning, stem cell engineering) but cannot resolve moral or societal questions regarding whether those capabilities should be executed. Science relies entirely on truthfulness and accurate reporting.

Atomic Structure, Subatomic Particles, and Isotopes

• Matter and Atoms:
  • Matter: Anything that occupies physical space and possesses mass.
  • Atom: The smallest fundamental unit of matter that retains all the unique chemical properties of an element.
  • Element: A chemical substance that cannot be broken down into simpler substances by ordinary chemical reactions. An element's identity is determined strictly by its proton count.
• Subatomic Particles:
  • Protons: Positively charged particles ($+1$) located inside the atomic nucleus, with a mass of approximately $1\,amu$ (atomic mass unit or Dalton).
  • Neutrons: Uncharged neutral particles ($0$) located inside the atomic nucleus, with a mass of approximately $1\,amu$ (Dalton).
  • Electrons: Negatively charged particles ($-1$) orbiting outside the nucleus, with negligible mass. Electrons dictate chemical bonding and reactivity.

• Atomic Numbers and Mass Metrics:
  • Atomic Number ($Z$): The exact number of protons in an atom's nucleus. Unique to each element and used to order the periodic table.
  • Mass Number: The total integer sum of protons plus neutrons in an individual atom ($\text{Mass Number} = \text{Protons} + \text{Neutrons}$). One $amu$ equals the mass of a single proton or neutron.
  • Atomic Mass of an Element: The weighted average mass of all naturally occurring isotopes of that element, expressed in amu$.\n * *Example (Carbon)*: Carbon has an atomic number of 6$. Carbon-12 ($^{12}\text{C}$) has 6 protons, 6 electrons, and 6 neutrons ($\text{mass number} = 12$). Carbon-13 ($^{13}\text{C}$) has 6 protons, 6 electrons, and 7 neutrons ($\text{mass number} = 13$). Carbon-14 ($^{14}\text{C}$) has 6 protons, 6 electrons, and 8 neutrons ($\text{mass number} = 14$). The collective atomic mass of carbon is$12.01\,amu.\n* **Isotopes and Radioactivity**:\n * *Isotopes*: Atoms of the exact same element containing identical proton counts but differing numbers of neutrons.\n * *Stable Isotopes*: Isotopes with stable nuclear structures that do not change subatomic composition over time.\n * *Radioisotopes*: Unstable isotopes that spontaneously decay into more stable forms, emitting radiation.\n * *Detection & Uses*: Radioactive decay is detected on photographic film via autoradiography. Radioisotopes serve as biological research tracers, diagnostic and therapeutic medical agents, and tools in archaeology and paleontology for radiometric age dating.\n\n# Electron Configuration, Orbitals, and the Octet Rule\n\n* **Bohr Models vs. Orbitals**:\n * *Bohr Model*: Simplistic model representing electron configurations as 2D concentric rings.\n * *Electron Orbitals*: 3D spatial regions surrounding the nucleus where a specific electron is found at least 90\%$of the time. Orbitals have distinct 3D shapes and orientations, and each orbital can hold a maximum of$2 electrons.\n* **Electron Shells (Energy Levels)**:\n * *First Shell*: Contains one spherical 1s$orbital (holds up to$2 electrons).\n * *Second Shell*: Contains one 2s$orbital and three dumbbell-shaped$2p$orbitals ($2p_x, 2p_y, 2p_z$), holding up to$8 electrons.\n * *Additional Shells*: Contain 4 orbital pairs holding up to 8 valence electrons in biologically important main-group elements.\n* **Valence Electrons and Reactivity**:\n * *Valence Shell*: The outermost concentric electron shell containing the most energetic electrons (valence electrons).\n * *Energy Levels*: An electron absorbs discrete energy to jump to a higher orbital, or releases energy to drop to a lower orbital—a core mechanism in biological energy conversions.\n * *The Octet Rule*: Atoms tend to lose, gain, or share electrons until their outer valence shell is completely filled with 8$electrons (or$2 for the first shell). Atoms with full valence shells are chemically unreactive.\n * *Periodic Trends*: Elements in the same vertical column (group) of the periodic table possess identical numbers of valence electrons and share similar chemical reactivity.\n\n# Chemical Formulas, Molecular Mass, and Stoichiometry\n\n* **Chemical Formulas**:\n * *Empirical Formula (Simplest Formula)*: Shows the simplest whole-number ratio of atoms in a compound (e.g., the empirical formula of glucose is \text{CH}2\text{O}).\n * *Molecular Formula*: Indicates the actual exact numbers of each atom type in a single molecule (e.g., the molecular formula of glucose is \text{C}_6\text{H}{12}\text{O}_6).\n * *Structural Formula*: Diagram showing the physical spatial arrangement and covalent connections between atoms.\n* **Molecular Mass and the Mole**:\n * *Molecular Mass*: The sum of the atomic masses of all component atoms in a single molecule, measured in amu$.
  • Mole (mol): The amount of a substance in grams numerically equivalent to its molecular mass in $amu$.\n * *Glucose (\text{C}_6\text{H}_{12}\text{O}_6$) Molecular Calculation*:\n * \text{Carbon}: 6 \times 12\,amu = 72\,amu\n * \text{Hydrogen}: 12 \times 1\,amu = 12\,amu\n * \text{Oxygen}: 6 \times 16\,amu = 96\,amu\n * \text{Molecular mass of 1 molecule of glucose} = 180\,amu\n * \text{Mass of 1 mole of glucose} = 180\,g\n* **Chemical Equations**: Describe chemical transformations, listing reactants on the left and products on the right.\n * *Cellular Respiration Equation*:\n        \text{C}6\text{H}{12}\text{O}_6 + 6\text{O}_2 \rightarrow 6\text{CO}_2 + 6\text{H}_2\text{O} + \text{energy}\n\n# Chemical Bonds and Intermolecular Forces\n\n* **Bond Energy**: The amount of energy required to break a specific chemical bond.\n* **Covalent Bonds**:\n * Formed when atoms share pairs of valence electrons to complete their outer shells.\n * *Molecule*: Two or more atoms held together by covalent bonds.\n * *Covalent Compound*: Unlike elements linked by covalent bonds (e.g., methane, \text{CH}_4).\n * *Bond Multiplicity*:\n * *Single Bond*: Sharing 1 pair of electrons (e.g., \text{C}-\text{H}).\n * *Double Bond*: Sharing 2 pairs of electrons (e.g., \text{C}=\text{C}).\n * *Triple Bond*: Sharing 3 pairs of electrons (e.g., \text{N}\equiv\text{N}).\n * *Carbon Covalent Bonding*: Carbon has 4 valence electrons and forms 4 covalent bonds to satisfy the octet rule.\n * *Lewis Structures*: Represent valence electrons as dots surrounding an element's symbol (e.g., \text{H}:\text{O}:\text{H}).\n * *Molecular Shape*: The 3D geometric arrangement of atoms optimizes distances to minimize electron pair repulsion; molecular shape directly determines biological function.\n * *Electronegativity*: The measure of atomic attractive force exerted by a nucleus on shared electrons in a bond. Depends on proton number and nuclear distance.\n * *Nonpolar Covalent Bond*: Covalent bond where electrons are shared equally between atoms with similar electronegativities.\n * *Polar Covalent Bond*: Covalent bond where electrons are shared unequally because one atom is significantly more electronegative, creating partial charges (\delta+$and$\delta-).\n * *Polar Molecule*: A molecule possessing a partial positive charge at one pole and a partial negative charge at another (e.g., \text{H}_2\text{O}).\n* **Ionic Bonds**:\n * *Ion*: An atom or molecule with an electric charge due to loss or gain of valence electrons.\n * *Cations*: Positively charged ions formed when atoms with 1, 2, or 3 valence electrons lose electrons (e.g., \text{H}^+$,$\text{Na}^+$,$\text{K}^+$,$\text{Ca}^{2+}$,$\text{Mg}^{2+}).\n * *Anions*: Negatively charged ions formed when atoms with 5, 6, or 7 valence electrons gain electrons (e.g., \text{Cl}^-$,$\text{I}^-$,$\text{O}^{2-}).\n * *Ionic Bond*: Formed by electrostatic attraction between a positive cation and a negative anion.\n * *Ionic Compound*: Substance composed of cations and anions held in a solid crystalline lattice by opposite charges (e.g., \text{NaCl}).\n * *Hydration*: In the absence of water, ionic bonds are extremely strong. When placed in water, ionic compounds undergo hydration and dissociate into individual hydrated ions:\n        \text{NaCl} \xrightarrow{\text{H}_2\text{O}} \text{Na}^+ + \text{Cl}^-\n* **Hydrogen Bonds**:\n * Relatively weak individually, but vital in biological systems.\n * Formed between a partial negative charge (\delta-$) on an electronegative atom (typically$\text{O}$or$\text{N}$) and a partial positive charge ($\delta+$) on a hydrogen atom covalently bonded to another$\text{O}$or$\text{N}.\n* **van der Waals Interactions**:\n * Transient, weak electrostatic forces operating over very short distances between nonpolar regions.\n * Driven by temporary, asymmetric electron distribution fluctuations. Individually weak, but collectively significant within protein interiors and cell membranes.\n\n# Physical and Chemical Properties of Water\n\n* **Biological Importance**: Water accounts for roughly 70\%$of total human body weight. It acts as the primary solvent for biological reactions, a reactant/product in metabolic pathways, a climate regulator, and the original source of atmospheric$\text{O}_2 and hydrogen used in organic molecules via photosynthesis.\n* **Solubility and Interactions**:\n * *Hydrophilic ("Water-Loving")*: Polar and ionic substances that dissolve readily in water due to charge attractions (e.g., amino acids, sugars, DNA, RNA).\n * *Hydrophobic ("Water-Fearing")*: Nonpolar, uncharged substances that are insoluble in water; nonpolar molecules cluster together in aqueous solution via hydrophobic interactions (e.g., lipid droplets in salad dressing).\n* **States of Water**: Exists naturally in three physical states: gas (steam/vapor), liquid (water), and solid (crystalline ice).\n* **Cohesion and Adhesion**:\n * *Adhesion*: Electrostatic attraction between water molecules and dissimilar polar/charged surfaces (causes water to wet surfaces).\n * *Cohesion*: Hydrogen bonding attraction between neighboring water molecules; creates high surface tension and drives liquid transport through plant vascular systems.\n* **Thermal Regulation**:\n * *High Specific Heat*: Water requires substantial heat absorption to change its temperature, stabilizing organismal internal temperatures and moderating ocean/coastal climates.\n * *High Heat of Vaporization*: Absorbs considerable environmental heat energy to convert liquid water into gas, resulting in evaporative cooling (e.g., sweating).\n * *Density Anomaly of Ice*: Ice is *less dense* than liquid water because each water molecule forms four stable hydrogen bonds in a rigid, open crystalline lattice. Consequently, ice floats, insulating aquatic life below.\n\n# Acids, Bases, pH, and Buffers\n\n* **Acids**: Proton donors; substances that dissociate in solution to yield hydrogen ions (\text{H}^+) and an anion:\n    \text{Acid} \rightarrow \text{H}^+ + \text{anion}\n* **Bases**: Proton acceptors; substances that dissociate in solution to yield hydroxide ions (\text{OH}^-$) and a cation, or directly accept free$\text{H}^+:\n    \text{NaOH} \rightarrow \text{Na}^+ + \text{OH}^-\n    \text{OH}^- + \text{H}^+ \rightarrow \text{H}_2\text{O}\n* **The pH Scale**: Logarithmic scale (0$to$14$) measuring relative hydrogen ion concentration ($[\text{H}^+]) in solution:\n * *Acidic Solution (pH < 7)*: [\text{H}^+] > [\text{OH}^-]$. Examples: Battery acid ($0.0$), Hydrochloric acid ($0.8$), Stomach acid ($1.0$), Gastric juice ($2.0$), Vinegar ($3.0$), Beer ($4.5$), Black coffee ($5.0$), Rainwater ($6.25$), Cow's milk ($6.5).\n * *Neutral Solution (pH = 7)*: [\text{H}^+] = [\text{OH}^-]$. Example: Pure distilled water ($7.0$). Human blood is kept slightly basic at$7.4\n * *Basic / Alkaline Solution (pH > 7)*: [\text{H}^+] < [\text{OH}^-]$. Examples: Seawater ($8.0$), Bleach ($9.0$), Mono Lake, CA ($9.9$), Household ammonia ($11.5$), Oven cleaner ($13.0$), Lye ($14.0).\n\n\n\n* **Buffers**: Homeostatic chemical systems comprising a weak acid or weak base that resist drastic pH changes when an acid or base is added. Maintain blood pH within extremely narrow physiological boundaries around 7.4\n\n# Organic Chemistry, Carbon Tetravalence, Isomers, and Functional Groups\n\n* **Carbon Backbone**: Biomolecules (macromolecules) consist of hundreds or thousands of atoms built around a carbon chain or backbone.\n* **Carbon Tetravalence**: Carbon has 4 valence electrons and forms 4 strong covalent bonds to achieve an octet. Forms straight chains, branched chains, or ring structures with single, double, or triple bonds.\n* **Isomerism**: Compounds possessing identical molecular formulas but displaying different chemical structures and properties.\n * *1. Structural Isomers*: Differ in the covalent arrangement of their constituent atoms (e.g., Ethanol vs. Dimethyl ether, both \text{C}_2\text{H}_6\text{O}).\n * *2. Geometric Isomers*: Differ in spatial arrangement around double bonds (cis$isomer: identical groups on same side;$trans$isomer: identical groups on opposite sides; e.g.,$cis\text{-2-butene}$vs$trans\text{-2-butene}).\n * *3. Enantiomers*: Chiral molecules that are non-superimposable mirror images of one another.\n\n\n\n* **Hydrocarbons vs. Functional Groups**:\n * *Hydrocarbons*: Nonpolar chains of carbon bonded exclusively to hydrogen. Lack charged regions, are insoluble in water, and aggregate via hydrophobic interactions.\n * *Functional Groups*: Polar or ionic atom groups that substitute for hydrogens on hydrocarbons, conferring hydrophilic properties and unique chemical reactivity.\n* **Major Functional Groups**:\n * *Methyl Group (R-\text{CH}_3)*: Nonpolar hydrocarbon group (e.g., methane, ethane, propane).\n * *Hydroxyl Group (R-\text{OH}$)*: Polar group containing strongly electronegative oxygen; characteristic of alcohols. (Not identical to inorganic hydroxide ion$\text{OH}^-).\n * *Carbonyl Group (\text{C}=\text{O})*: Carbon double-bonded to oxygen. Defines Aldehydes (carbonyl at chain end) and Ketones (carbonyl within chain).\n * *Carboxyl Group (R-\text{COOH}$)*: Carbon doubly bonded to oxygen and singly bonded to a hydroxyl group ($-\text{O}-\text{H}$). Weakly acidic; donates$\text{H}^+$to ionize as$R-\text{COO}^-. Component of amino acids and organic acids.\n * *Amino Group (R-\text{NH}_2$)*: Nitrogen covalently bonded to two hydrogens. Weakly basic; accepts$\text{H}^+$to ionize as$R-\text{NH}_3^+. Component of amino acids and nucleic acids.\n * *Phosphate Group (R-\text{PO}_4\text{H}_2$)*: Releases one or two$\text{H}^+ ions, generating negative charges ($R-\text{PO}_4^{2-}). Found in nucleic acids, ATP, and phospholipids.
  • Sulfhydryl Group ($R-\text{SH}$): Atom of sulfur covalently bonded to hydrogen; defines thiols. Forms covalent disulfide bonds ($-\text{S}-\text{S}-$) stabilizing protein tertiary/quaternary structure.

Polymer Synthesis and Degradation

• Monomers vs. Polymers: Monomers are small molecular subunits. Polymers are large molecules composed of repeating monomer units joined by covalent bonds. (Lipids are an exception, not following a strict monomer-polymer scheme).
• Condensation (Dehydration Synthesis) Reactions:
  • Builds polymers from monomers.
  • Consumes energy and requires enzymatic catalysis (e.g., Enzyme A).
  • Water is "lost"—one $\text{H}_2\text{O}$ molecule is removed per covalent bond formed ($-\text{OH}$ from one monomer, $-\text{H}$ from another).
• Hydrolysis Reactions:
  • Breaks polymers down into constituent monomers.
  • Releases energy, but still requires enzymatic catalysis (e.g., Enzyme B).
  • Water is added back—one $\text{H}_2\text{O}$ molecule is consumed per covalent bond cleaved.

Carbohydrates: Structure, Function, and Classification

• Chemical Ratio: Contain carbon, hydrogen, and oxygen in an approximate ratio of $1\text{C}:2\text{H}:1\text{O}$ ($(\text{CH}_2\text{O})_n$). Includes simple sugars and complex starches.
• Monosaccharides: Simple sugars containing 3 to 7 carbon atoms; names typically end in -ose.
  • Trioses (3 Carbons, $\text{C}_3\text{H}_6\text{O}_3$): Glyceraldehyde (aldehyde sugar), Dihydroxyacetone (ketone sugar).
  • Pentoses (5 Carbons): Ribose ($\text{C}_5\text{H}_{10}\text{O}_5$, RNA sugar component), Deoxyribose ($\text{C}_5\text{H}_{10}\text{O}_4$, DNA sugar component missing an oxygen at C2').
  • Hexoses (6 Carbons, $\text{C}<em>6\text{H}</em>{12}\text{O}_6$): Glucose (most abundant monosaccharide, primary cellular energy source; forms ring and linear structures; possesses $\alpha$ and $\beta$ ring isomers), Fructose (ketone hexose), Galactose (aldehyde hexose).

• Disaccharides: Two monosaccharide rings joined via condensation by a glycosidic linkage (covalent bond consisting of a central oxygen atom bonded to two carbons, one in each ring):
  • Maltose (Malt Sugar): 2 covalently linked $\alpha\text{-glucose}$ units.
  • Sucrose (Table Sugar): 1 glucose + 1 fructose (linked by an $\alpha\text{-1,2-glycosidic linkage}$).
  • Lactose (Milk Sugar): 1 glucose + 1 galactose.
• Polysaccharides: Giant polymers composed of long monosaccharide chains.
  • Starch: Polymer of $\alpha\text{-glucose}$ subunits used for energy storage in plants. Occurs as unbranched Amylose ($\alpha\text{-1,4-glycosidic linkages}$) and branched Amylopectin ($\alpha\text{-1,4}$ and $\alpha\text{-1,6}$ linkages).
  • Glycogen: Glucose storage polymer in animal tissues (stored mainly in liver and muscle cells). Highly branched and more water-soluble than plant starch.
  • Cellulose: Structural polymer in plant cell walls composed of linear $\beta\text{-glucose}$ chains ($\beta\text{-1,4-glycosidic linkages}$). Indigestible by human digestive enzymes; functions as dietary fiber creating waste bulk (e.g., Metamucil).
• Modified and Complex Carbohydrates:
  • Amino Sugars: Galactosamine and Glucosamine present in cartilage matrix.
  • Chitin: Structural polymer of N-acetylglucosamine subunits; forms arthropod exoskeletons and fungal cell walls.
  • Glycoproteins: Functional secreted proteins covalently linked to carbohydrates.
  • Glycolipids: Carbohydrate-bound recognition lipids on animal plasma cell membranes.

Lipids: Structure, Function, and Diversity

• Chemical Characteristics: Heterogeneous group of nonpolar compounds insoluble in water but soluble in nonpolar organic solvents. Composed mainly of carbon and hydrogen with few oxygen functional groups.
• Biological Functions: Fuel reserve energy storage, organ cushioning, waterproofing, cell membrane structural components, and major hormones.
• Major Lipid Groups:
  • 1. Triacylglycerols (Triglycerides / Fats):
    • Most abundant lipids in living organisms; function as reserve fuel storage.
    • Composed of 1 glycerol molecule (3-carbon alcohol) joined to 3 fatty acid chains by ester linkages (covalent bond between carboxyl of fatty acid and hydroxyl of glycerol).

    *   *Saturated Fatty Acids*: Contain the maximum number of hydrogen atoms with no $\text{C}=\text{C}$ double bonds. Straight chains pack tightly; solid at room temperature (e.g., Palmitic acid, animal fats, solid vegetable shortening).
    *   *Unsaturated Fatty Acids*: Contain one or more $\text{C}=\text{C}$ double bonds creating physical kinks in the chain. Liquid at room temperature (oils). Monounsaturated (1 double bond, e.g., Oleic acid); Polyunsaturated (2+ double bonds, e.g., Linoleic acid, omega-3 fatty acids).
    *   *Trans-Fatty Acids and Hydrogenation*: Hydrogen atoms are added to unsaturated fats to increase shelf life and make oils solid/creamy (partially hydrogenated oils). Replaces double bonds or converts them to *trans* spatial configurations, altering molecular shape. Sources include fast foods, fries, cakes, cookies, crackers, doughnuts, chips, candy. Excess consumption increases "bad" LDL cholesterol, promoting coronary artery plaque buildup and heart disease. FDA requires trans-fat content on food labels.
*   **2. Phospholipids**:
    *   Amphipathic membrane components consisting of 1 glycerol + 2 fatty acid chains (hydrophobic tails) + 1 phosphate group linked to an organic base like choline (hydrophilic head).
    *   Spontaneously form lipid bilayers in water, constructing cell membranes.

*   **3. Steroids**:
    *   Lipids composed of carbon atoms arranged in four attached/fused rings.
    *   Side chains distinguish individual steroids. Examples: Cholesterol (essential component of animal cell membranes), Estrogen, Testosterone, Cortisol (steroid hormone secreted by adrenal glands), Aldosterone. Plant cell membranes contain cholesterol-like sterols.

Proteins: Amino Acids, Structure, and Function

• Protein Composition: Polymers composed of 20 different amino acids linked into unbranched polypeptide chains.
• Biological Functions: Catalysis (enzymes), structural support (keratin), storage (ovalbumin in egg whites), protective immunity (antibodies), movement (myosin/actin), transport, and signaling.
• Amino Acid Structure: Central alpha-carbon ($\text{C}_\alpha$) covalently bound to:
  1. An Amino group ($-\text{NH}_2$).
  2. A Carboxyl group ($-\text{COOH}$).
  3. A Hydrogen atom ($-\text{H}$).
  4. A Variable Side Chain ($R\text{-group}$).
• Ionization: At neutral physiological pH, amino acids exist as dipolar zwitterions—carboxyl groups donate a proton ($-\text{COO}^-$) and amino groups accept a proton ($-\text{NH}_3^+$).
• R-Group Classification:
  • Nonpolar Side Chains: Hydrophobic (e.g., Leucine).
  • Polar Side Chains: Hydrophilic, uncharged (e.g., Asparagine).
  • Acidic Side Chains: Contain carboxyl groups; negatively charged at pH 7 (e.g., Aspartic acid).
  • Basic Side Chains: Accept hydrogen ions; positively charged at pH 7 (e.g., Arginine).
• Peptide Bonds: Covalent bonds linking amino acids into polypeptide chains. Formed via condensation reactions between the carboxyl carbon of one amino acid and the amino nitrogen of another.

• Four Levels of Protein Structure:
  • 1. Primary Structure: The specific linear sequence of amino acids linked by peptide bonds, determined by genetic code.
  • 2. Secondary Structure: Regular spatial conformations along the polypeptide backbone stabilized by hydrogen bonds between N–H and C=O groups:
    • $\alpha\text{-Helix}$: Helical coil.
    • $\beta\text{-Pleated Sheet}$: Sheet formed between adjacent aligned polypeptide chains.
  • 3. Tertiary Structure: Overall 3D shape of a single polypeptide chain determined by R-group interactions:
    • Hydrogen bonds (between polar R-groups).
    • Ionic bonds (between acidic and basic R-groups).
    • Hydrophobic interactions (nonpolar R-groups clustering internally).
    • Disulfide Bonds: Covalent bonds ($-\text{S}-\text{S}-$) formed between sulfhydryl groups ($-\text{SH}$) of two Cysteine side chains.

*   *4. Quaternary Structure*: Conformation resulting from the interaction of two or more independent polypeptide subunits held by hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide linkages. Examples: Hemoglobin (composed of 4 subunits: 2 $\alpha\text{-globin}$ and 2 $\beta\text{-globin}$ chains with heme groups) and Collagen (triple helix).

• Denaturation: Unfolding and loss of a protein's native 3D shape and biological activity caused by heat, acids, bases, salts, or organic solvents. Misfolded proteins lose function and cause disease.
• Food Allergy Trivia: Protein molecules are the major cause of food allergies, affecting $1\% - 2.5\%$ of U.S. adults. Worldwide, $90\%$ of food allergies stem from proteins in eight foods: peanuts, soybeans, tree nuts, milk, eggs, fish, shellfish, and wheat.

Nucleic Acids and Energy-Transfer Nucleotides

• Nucleic Acid Polymers: Long polymers composed of monomer units called nucleotides joined by covalent phosphodiester linkages (bonds connecting carbon 3' of one sugar to the phosphate group at carbon 5' of the adjacent sugar, forming a sugar-phosphate backbone).
• Nucleotide Components: Every nucleotide consists of:
  1. A 5-carbon pentose sugar (Ribose in RNA, Deoxyribose in DNA).
  2. One or more phosphate groups (imparting acidic character).
  3. A nitrogenous base (nitrogen-containing ring compound).
• Nitrogenous Bases:
  • Purines (Double-Ring): Adenine (A), Guanine (G).
  • Pyrimidines (Single-Ring): Cytosine (C), Thymine (T, in DNA only), Uracil (U, in RNA only).

• DNA vs. RNA:
  • DNA (Deoxyribonucleic Acid): Double-stranded helix containing Deoxyribose sugar and bases A, G, C, T. Encodes hereditary material (genes). Human cells contain $3\text{ billion}$ nucleotides per cell.
    • Complementary Base Pairing: Purines pair with Pyrimidines via hydrogen bonds: Adenine pairs with Thymine ($\text{A}=\text{T}$, 2 hydrogen bonds); Guanine pairs with Cytosine ($\text{G}\equiv\text{C}$, 3 hydrogen bonds).
  • RNA (Ribonucleic Acid): Single-stranded chain containing Ribose sugar and bases A, G, C, U (Uracil replaces Thymine). Links amino acids into polypeptides.
• Energy Nucleotides:
  • Adenosine Triphosphate (ATP): Composed of Adenine, Ribose, and 3 phosphate groups. Primary energy transfer molecule of all cells; used in RNA synthesis.
  • Guanosine Triphosphate (GTP): Composed of Guanine, Ribose, and 3 phosphate groups. Transfers energy via phosphate transfer; used in RNA synthesis.

Biological Taxonomy, Classification, and Evolution

• Taxonomy: The scientific discipline of naming, describing, and classifying organisms.
• Linnaean Taxonomy: Hierarchical system established in the 18th century by Carolus Linnaeus utilizing a binomial system of nomenclature.
  • Binomial Name: Two-part scientific name consisting of the Genus (capitalized) followed by the specific epithet (lowercase).
  • Examples: Canis familiaris (domestic dog), Canis lupus (timber wolf), Felis catus (domestic cat), Homo sapiens (human), Quercus alba (white oak).
• Taxonomic Hierarchy (Broadest to most specific): Domain $\rightarrow$ Kingdom $\rightarrow$ Phylum (Subphylum) $\rightarrow$ Class $\rightarrow$ Order $\rightarrow$ Family $\rightarrow$ Genus $\rightarrow$ Species.
• Taxonomic Classification Table:
  • Cat: Domain Eukarya, Kingdom Animalia, Phylum Chordata, Subphylum Vertebrata, Class Mammalia, Order Carnivora, Family Felidae, Genus Felis, Species Felis catus.
  • Human: Domain Eukarya, Kingdom Animalia, Phylum Chordata, Subphylum Vertebrata, Class Mammalia, Order Primates, Family Hominidae, Genus Homo, Species Homo sapiens.
  • White Oak: Domain Eukarya, Kingdom Plantae, Phylum Anthophyta, Subphylum None, Class Eudicotyledones, Order Fagales, Family Fagaceae, Genus Quercus, Species Quercus alba.
• Species Definition: A group of organisms with similar structure, function, and behavior capable of interbreeding with one another; represents a population sharing a common gene pool and ancestry.
• Evolutionary Common Origin:
  • All living organisms descended from a common origin of life that occurred almost $4\text{ billion}$ years ago.
  • Cladogram: A branching diagram showing proposed evolutionary relationships among organisms supported by fossil and molecular evidence.
  • Clade: A group of organisms sharing a common ancestor.

• The Three Domains of Life:
  • Domain Bacteria: Unicellular prokaryotic organisms.
  • Domain Archaea: Unicellular prokaryotic organisms distinct from bacteria, often inhabiting extreme environments.
  • Domain Eukarya: Eukaryotic organisms possessing membrane-bound nuclei and organelles. Divided into four main groups/kingdoms:
    • Protists: Unicellular, colonial, or simple multicellular eukaryotes.
    • Plants (Kingdom Plantae): Multicellular autotrophic photosynthetic organisms.
    • Fungi (Kingdom Fungi): Heterotrophic decomposers that absorb nutrients.
    • Animals (Kingdom Animalia): Multicellular heterotrophic organisms that ingest other organisms.