Chapter 2: Chemistry Comes Alive Flashcards

Fundamentals of Matter, Energy, and Atomic Structure

• Chemical reactions underlie all physiological processes in living organisms.
• Matter is defined as anything that occupies space and has mass. It exists in three distinct states:
  • Solid: Rigid state with a definite shape and volume.
  • Liquid: Fluid state with a definite volume that takes the shape of its container.
  • Gaseous: Fluid state with neither a definite shape nor a definite volume.
• Energy is defined as the capacity to do work or put matter into motion. Energy exists in two primary states:
  • Kinetic Energy: Energy in active motion.
  • Potential Energy: Stored energy capable of doing work when released.
• Forms of Energy in Living Organisms:
  • Chemical Energy: Energy stored directly within the chemical bonds of molecular substances.
  • Electrical Energy: Energy resulting from the movement of charged particles (ions).
  • Mechanical Energy: Energy directly involved in physically moving matter.
• Thermodynamic Principles:
  • Energy conversions in biological systems are never $100\,\%$ efficient; a portion of the initial energy supply is always converted into thermal energy (heat) and lost to the surrounding environment.
  • Thermal energy given off as heat is unusable for driving biological processes.
  • All natural processes adhere to the Second Law of Thermodynamics, which dictates that physical systems tend spontaneously toward disorder (entropy).
  • Biological life represents a continuous metabolic effort to maintain order against the Second Law of Thermodynamics.

Elements and Subatomic Structure

• Elements are unique chemical substances that cannot be broken down into simpler substances by ordinary chemical methods.
• Every element is composed of fundamental units called atoms.
• The physical and chemical properties of an element are determined by the specific atomic structure of its constituent atoms.
• Properties of Elements:
  • Physical Properties: Characteristics detectable by human senses (e.g., color, texture) or measurable physical constants (e.g., boiling point, freezing point).
  • Chemical Properties: Characteristics determining how atoms interact, bond, and react with other atoms.
• Atomic Symbols: One- or two-letter chemical abbreviations derived from an element's English name (e.g., Carbon = $\text{C}$, Oxygen = $\text{O}$, Calcium = $\text{Ca}$) or Latin name (e.g., Natrium/Sodium = $\text{Na}$).
• Subatomic Particles: Atoms consist of three primary subatomic particles:
  • Protons ($\text{p}^+$): Positively charged particles situated in the central atomic nucleus, carrying a mass unit of approximately $1\,\text{amu}$.
  • Neutrons ($\text{n}^0$): Electrically neutral particles situated in the central nucleus, carrying a mass unit of approximately $1\,\text{amu}$.
  • Electrons ($\text{e}^-$): Negatively charged particles orbiting the nucleus within designated electron shells; an electron possesses only about $\frac{1}{2000}$ the mass of a proton.
• Atomic Neutrality and Mass Distribution:
  • Almost the entire mass of an atom is concentrated within its dense central nucleus.
  • All isolated atoms are electroneutral because the total number of positively charged protons in the nucleus precisely equals the total number of orbiting negatively charged electrons.
• Atomic Models:
  • Planetary Model: A simplified visualization depicting electrons orbiting the central nucleus in fixed circular pathways (shells).
  • Orbital Model: A probabilistic quantum mechanical model depicting electron clouds, representing regions of high probability for locating electrons.
• Atomic Profiles of Specific Elements:
  • Hydrogen ($\text{H}$): The simplest and smallest atom, containing $1\,\text{proton}$, $0\,\text{neutrons}$, and $1\,\text{electron}$.
  • Helium ($\text{He}$): Contains $2\,\text{protons}$, $2\,\text{neutrons}$, and $2\,\text{electrons}$ filling its single electron shell.
  • Lithium ($\text{Li}$): Contains $3\,\text{protons}$, $4\,\text{neutrons}$, and $3\,\text{electrons}$ ($2$ in the filled inner shell, $1$ in the outer valence shell).

Elemental Composition of the Human Body

• Four major elements compose approximately $96.1\,\%$ of total body mass (calculated as percentage of wet body mass including water):
  • Oxygen ($\text{O}$): Symbol $\text{O}$; accounts for approx. $65.0\,\%$ of body mass. Essential component of organic and inorganic molecules; required as a gas for cellular respiration and ATP synthesis.
  • Carbon ($\text{C}$): Symbol $\text{C}$; accounts for approx. $18.5\,\%$ of body mass. The primary structural backbone of all organic molecules (carbohydrates, lipids, proteins, nucleic acids).
  • Hydrogen ($\text{H}$): Symbol $\text{H}$; accounts for approx. $9.5\,\%$ of body mass. Present in all organic molecules; as a free hydrogen ion (proton, $\text{H}^+$), it dictates the pH of bodily fluids.
  • Nitrogen ($\text{N}$): Symbol $\text{N}$; accounts for approx. $3.2\,\%$ of body mass. Structural component of all amino acids, proteins, and nucleic acids.
• Nine lesser elements compose approximately $3.9\,\%$ of total body mass:
  • Calcium ($\text{Ca}$): Symbol $\text{Ca}$; accounts for approx. $1.5\,\%$ of body mass. Present as mineral salts in bones and teeth; ionic form ($\text{Ca}^{2+}$) is mandatory for muscle contraction, nerve impulse transmission, and blood coagulation.
  • Phosphorus ($\text{P}$): Symbol $\text{P}$; accounts for approx. $1.0\,\%$ of body mass. Forms calcium phosphate salts in bone structure; component of nucleic acids, cell membrane phospholipids, and ATP.
  • Potassium ($\text{K}$): Symbol $\text{K}$; accounts for approx. $0.4\,\%$ of body mass. Its cation ($\text{K}^+$) is the primary intracellular positive ion; crucial for nerve impulse conduction and muscle contraction.
  • Sulfur ($\text{S}$): Symbol $\text{S}$; accounts for approx. $0.3\,\%$ of body mass. Key component of functional proteins, particularly structural muscle proteins and cysteine residues.
  • Sodium ($\text{Na}$): Symbol $\text{Na}$; accounts for approx. $0.2\,\%$ of body mass. Its cation ($\text{Na}^+$) is the major extracellular positive ion; essential for fluid volume balance, nerve conduction, and muscle cell excitability.
  • Chlorine ($\text{Cl}$): Symbol $\text{Cl}$; accounts for approx. $0.2\,\%$ of body mass. Its anion (chloride, $\text{Cl}^-$) is the primary extracellular negative ion.
  • Magnesium ($\text{Mg}$): Symbol $\text{Mg}$; accounts for approx. $0.1\,\%$ of body mass. Structural component of bone tissue; critical enzymatic cofactor for metabolic reactions.
  • Iodine ($\text{I}$): Symbol $\text{I}$; accounts for approx. $0.1\,\%$ of body mass. Required for the biosynthesis of functional thyroid hormones.
  • Iron ($\text{Fe}$): Symbol $\text{Fe}$; accounts for approx. $0.1\,\%$ of body mass. Core metallic component of hemoglobin (oxygen transport in red blood cells) and metabolic cytochromes/enzymes.
• Trace elements make up less than $0.01\,\%$ of total body mass:
  • Includes Chromium ($\text{Cr}$), Cobalt ($\text{Co}$), Copper ($\text{Cu}$), Fluorine ($\text{F}$), Manganese ($\text{Mn}$), Molybdenum ($\text{Mo}$), Selenium ($\text{Se}$), Silicon ($\text{Si}$), Tin ($\text{Sn}$), Vanadium ($\text{V}$), and Zinc ($\text{Zn}$).
  • Function predominantly as vital enzyme active site cofactors or structural components of metabolic enzymes.

Molecules, Compounds, and Mixtures

• Molecule: Combination of two or more identical or different atoms held together by chemical bonds.
• Compound: Chemical substance formed when two or more different types of atoms bond together (e.g., $\text{H}_2\text{O}$). A molecule represents the smallest structural unit of a compound that retains its distinct chemical identity.
• Mixture: Physical blend consisting of two or more components that are intermixed without chemical bonding:
  • Individual properties of mixed substances remain completely unchanged.
  • Components can be physically separated using non-chemical methods.

• Three Primary Classes of Biological Mixtures:
  • Solutions: Homogeneous mixtures containing extremely small solute particles (atoms, ions, or small molecules) that do not settle out and do not scatter light.
  • Solvent: The substance present in the greatest volume (water is the universal biological solvent).
  • Solutes: Substances present in smaller amounts dissolved within the solvent.
  • Examples: Mineral water, air, saline solution.
  • Colloids (Emulsions): Heterogeneous mixtures containing larger solute particles that scatter light but do not settle out over time.
  • Colloids exhibit sol-gel transformations (reversible transitions between fluid sol states and gelled states).
  • Example: Cytosol of biological cells, gelatin.
  • Suspensions: Heterogeneous mixtures containing large, visible solute particles that do not stay dissolved and gradually settle out over time due to gravity.
  • Example: Whole blood (blood cells settle out from liquid plasma when left undisturbed).

Chemical Bonds and Energy Relationships

• A chemical bond is an energy relationship between the valence shell electrons of interacting atoms, rather than a physical structure.
• Electron Shells and Energy Levels:
  • Electrons occupy specific energy shells surrounding the nucleus.
  • The innermost electron shell holds a maximum capacity of $2\,\text{electrons}$.
  • Subsequent outer shells hold maximum capacities in multiples of $8\,\text{electrons}$ (Rule of Octets).
  • The Valence Shell is an atom's outermost energy level containing chemically active electrons.
• Chemically Inert vs. Reactive Elements:
  • Inert Elements: Atoms with a completely filled valence shell (e.g., Helium with $2$ valence electrons, Neon with $8$ valence electrons) are chemically stable and unreactive.
  • Reactive Elements: Atoms with incomplete valence shells (e.g., Hydrogen, Carbon, Oxygen, Sodium) tend to gain, lose, or share electrons to attain maximum stability.

• Types of Chemical Bonds:
  • Ionic Bonds: Formed by the complete chemical transfer of valence electrons from one atom to another.
  • Cation: A positively charged ion formed when an atom loses one or more electrons (e.g., $\text{Na}^+$).
  • Anion: A negatively charged ion formed when an atom gains one or more electrons (e.g., $\text{Cl}^-$).
  • Oppositely charged ions attract electrostatic forces to form crystalline salt lattices (e.g., Sodium Chloride, $\text{NaCl}$).
  • Covalent Bonds: Formed when reacting atoms share electron pairs in shared orbital paths.
  • Single Covalent Bond: Sharing of one electron pair (e.g., Methane, $\text{CH}_4$).
  • Double Covalent Bond: Sharing of two electron pairs (e.g., Oxygen Gas, $\text{O}_2$).
  • Nonpolar Covalent Bonds: Equal sharing of electrons among constituent atoms, resulting in balanced spatial distribution of charge (e.g., $\text{CO}_2$, $\text{CH}_4$).
  • Polar Covalent Bonds: Unequal sharing of electrons due to differing electronegativity between atoms.
    • Results in spatial dipole orientation: a partial negative charge ($\delta^-$) at the electronegative end and a partial positive charge ($\delta^+$) at the opposite end (e.g., Water, $\text{H}_2\text{O}$).
  • Hydrogen Bonds: Weak intermolecular or intramolecular attractions occurring when a hydrogen atom covalently bound to an electronegative atom (like oxygen or nitrogen) is simultaneously attracted to another electronegative atom.
  • Intermolecularly creates high surface tension and solvent properties in water.
  • Intramolecularly maintains complex secondary and tertiary folding structures in proteins and holds complementary nucleic acid strands together in DNA.

Inorganic Chemistry: Properties of Water

• Water ($\text{H}_2\text{O}$) is the most abundant inorganic compound in living tissue, accounting for $60\,\%$ to $80\,\%$ of total cell volume.
• Physiological Functions and Properties of Water:
  • Polar Solvent Properties: Functions as the universal solvent in biological systems.
  • Water dipole ends orient around individual charged ions or polar solute molecules, creating hydration shells that separate and dissolve ionic salts and polar compounds.
  • Acts as the primary transport medium in blood plasma for delivering nutrients, respiratory gases, and metabolic waste products.
  • Chemical Reactivity: Serves as a direct chemical reactant in key biological pathways:
  • Hydrolysis Reactions: Decomposition reactions consuming water to split complex polymers.
  • Dehydration Synthesis: Anabolic reactions releasing water as a byproduct when combining monomers.
  • Cushioning: Forms a non-compressible, resilient fluid barrier around critical body organs to absorb mechanical physical trauma (e.g., cerebrospinal fluid protecting the central nervous system).

Organic Chemistry: Carbohydrates

• Organic compounds are carbon-containing molecules unique to living organisms, characterized by covalent carbon backbones and active functional groups.

• Carbon is tetravalent (contains $4$ valence electrons) and electroneutral, forming $4$ stable covalent bonds with other atoms or neighboring carbon atoms.

• Major classes of organic macromolecules include Carbohydrates, Lipids, Proteins, and Nucleic Acids.

• Carbohydrates: Composed of carbon, hydrogen, and oxygen, typically in a ratio near $1:2:1$; comprise $1\,\%$ to $2\,\%$ of overall cell mass.

  • Monosaccharides (Simple Sugars): Single-ring structures containing $3$ to $7$ carbon atoms. Building blocks (monomers) of carbohydrates.
  • Hexose Sugars ($\text{C}_6\text{H}_{12}\text{O}_6$ Isomers): Glucose, Fructose, and Galactose.
  • Pentose Sugars ($\text{C}_5\text{H}_{10}\text{O}_5$ / $\text{C}_5\text{H}_{10}\text{O}_4$): Ribose and Deoxyribose.
  • Disaccharides (Double Sugars): Formed when two monosaccharide monomers undergo dehydration synthesis.
  • Sucrose: Glucose + Fructose.
  • Lactose: Glucose + Galactose.
  • Maltose: Glucose + Glucose.
  • Polysaccharides: Long, complex polymers of linked monosaccharide units formed by sequential dehydration synthesis reactions.
  • Glycogen: Highly branched glucose storage polymer found in animal liver and skeletal muscle tissue.
  • Starch: Glucose storage polymer synthesized by plants; principal digestive carbohydrate source for humans.
  • Cellulose: Structural plant cell wall polysaccharide; digestible fiber aiding human gastrointestinal motility.

Organic Chemistry: Lipids

• Lipids are organic compounds containing carbon, hydrogen, and oxygen (with oxygen proportions significantly lower than in carbohydrates), and sometimes phosphorus. Insoluble in polar solvents (water) but highly soluble in nonpolar organic solvents and other lipids.

• Major Subclasses of Lipids:

  • Triglycerides (Neutral Fats): Composed of a single Glycerol molecule covalently bound to $3$ Fatty Acid chains via dehydration synthesis.
  • Form solid fats or liquid oils depending on fatty acid saturation.
  • Location & Function: Concentrated in subcutaneous adipose tissue and surrounding major visceral organs; provide primary energy storage, thermal insulation, and mechanical organ protection.
  • Phospholipids: Amphipathic molecules composed of a Glycerol backbone attached to $2$ nonpolar hydrophobic Fatty Acid tails and $1$ polar hydrophilic Phosphorus-containing head group (e.g., Phosphatidylcholine).

• Phospholipid Orientation: Hydrophilic polar heads interact with aqueous environments, while hydrophobic nonpolar tails orient away from water toward nonpolar lipids, assembling the fundamental lipid bilayer framework of all cellular membranes.
• Steroids: Flat, nonpolar molecules built from a core framework of four interlocking hydrocarbon rings.
  • Cholesterol: Structural component of cell membranes; foundational molecule required for synthesizing all body steroids.
  • Bile Salts: Liver-derived cholesterol breakdown products released into the intestine to emulsify dietary fats.
  • Vitamin D: Fat-soluble steroid derivative synthesized in skin upon exposure to UV radiation; essential for calcium absorption and bone metabolism.
  • Sex Hormones: Estrogen, Progesterone (female), and Testosterone (male) produced in gonads; control reproductive system development.
  • Adrenocortical Hormones: Cortisol (glucocorticoid maintaining glucose metabolism) and Aldosterone (mineralocorticoid regulating renal salt/water balance).
• Other Lipoid Substances:
  • Vitamin A: Ingested in orange fruits/vegetables; converted in retina to retinal (photoreceptor visual pigment).
  • Vitamin E: Plant-derived fat-soluble antioxidant; neutralizes free radicals in tissues.
  • Vitamin K: Synthesized by enteric gut bacteria; necessary for hepatic synthesis of blood clotting factors.
  • Eicosanoids: Fatty-acid derivatives synthesized from membrane arachidonic acid:
    • Prostaglandins: Direct uterine contractions, regulate blood pressure, control GI motility, mediate inflammation.
    • Leukotrienes: Mediate inflammatory and allergic immune signaling.
    • Thromboxanes: Potent cellular vasoconstrictors and platelet activators.
  • Lipoproteins: Lipid and protein complexes transporting hydrophobic fatty acids and cholesterol through the blood (classified as High-Density Lipoproteins [HDLs] and Low-Density Lipoproteins [LDLs]).

Organic Chemistry: Proteins and Structure

• Proteins comprise $10\,\%$ to $30\,\%$ of total cellular mass and serve as the main structural and functional machinery of the body.
• Contain carbon, hydrogen, oxygen, nitrogen, and frequently sulfur ($\text{S}$) or phosphorus ($\text{P}$).
• Amino Acids: The amphipathic building block monomers of proteins. All $20$ natural amino acids contain an identical core backbone with two primary functional groups:
  • Amine Group: Basic end ($-\text{NH}_2$).
  • Acid / Carboxyl Group: Acidic end ($-\text{COOH}$).
  • Central Carbon Atom: Bound to a single hydrogen atom ($-\text{H}$) and a variable functional $\text{R}$ Group.
• Specific Amino Acid Examples:
  • Glycine: Simplest amino acid ($\text{R} = -\text{H}$).
  • Aspartic Acid: Acidic amino acid possessing an additional carboxyl group ($-\text{COOH}$) in its $\text{R}$ group.
  • Lysine: Basic amino acid possessing an additional amine group ($-\text{NH}_2$) in its $\text{R}$ group.
  • Cysteine: Contains a sulfhydryl group ($-\text{SH}$) in its $\text{R}$ group, enabling covalent intramolecular disulfide bridge formation.
• Peptide Bonds: Covalent bonds linking amino acids into long polymer chains. Formed via dehydration synthesis when the acid carboxyl end of one amino acid joins the basic amine end of another.

• Four Hierarchical Levels of Protein Organization:
  • Primary Structure: Linear polypeptide backbone sequence of amino acids linked together by peptide bonds.
  • Secondary Structure: Localized spatial bending or coiling of the primary chain, stabilized by hydrogen bonds between amino acid $\text{N}-\text{H}$ and $\text{C}=\text{O}$ groups:
  • $\alpha$-Helix: Spiral coil held together by intramolecular hydrogen bonds parallel to the axis.
  • $\beta$-Pleated Sheet: Pleated zigzag sheet formed by lateral hydrogen bonds joining adjacent strand segments.
  • Tertiary Structure: Superimposed 3D folding of secondary structural elements producing a compact, globular ball. Maintained by hydrogen bonding, ionic interactions, hydrophobic folding, and covalent disulfide bridges between distant $\text{R}$ groups (e.g., Transthyretin/Prealbumin monomer).
  • Quaternary Structure: Complex formed when two or more distinct polypeptide subunits aggregate into a single functional unit (e.g., Hemoglobin, Prealbumin dimer consisting of two identical subunits joining head-to-tail).

Functional Classification of Proteins

• Fibrous (Structural) Proteins: Extended, strand-like insoluble structural proteins providing mechanical support and tensile strength:
  • Collagen: The single most abundant protein in the human body; provides high tensile strength in bones, tendons, ligaments, and connective tissue.
  • Keratin: Structural protein of hair, nails, and water-resistant epidermal skin layers.
  • Elastin: Provides elastic recoil and flexibility in articular ligaments and blood vessel walls.
  • Spectrin: Reinforces and stabilizes the internal plasma membrane surface of red blood cells.
  • Dystrophin: Stabilizes the sarcolemma plasma membrane of skeletal muscle fibers.
  • Titin: Organizes intracellular muscle sarcomeres and maintains passive elasticity.
  • Actin and Myosin: Contractile filaments causing muscle shortening, cell division cleavage, and intracellular axonal transport.
• Globular (Functional) Proteins: Compact, spherical water-soluble proteins that execute biochemical physiological functions:
  • Catalysis: Metabolic protein enzymes (e.g., Salivary Amylase breaking down starch; Oxidase enzymes oxidising fuels).
  • Transport: Circulatory and membrane transport molecules (e.g., Hemoglobin carrying oxygen; Lipoproteins transporting lipids; Plasma membrane channels/carriers).
  • pH Regulation: Plasma proteins acting as reversible amphoteric buffers to stabilize blood pH (e.g., Albumin).
  • Metabolic Regulation: Peptide and protein hormones regulating endocrine physiology (e.g., Growth Hormone; Insulin regulating blood glucose).
  • Body Defense: Immune defense proteins recognizing and inactivating pathogens (e.g., Antibodies/Immunoglobulins; Complement system blood proteins).
  • Protein Management: Molecular chaperones directing proper polypeptide folding, metal ion transport, and targeted destruction of damaged cellular proteins.

Enzymatic Catalysis

• Enzymes are specialized globular proteins that function as biological catalysts.
• Catalysts accelerate chemical reaction rates by at least a millionfold ($10^6$) without being consumed or altered in the process.
• Enzymes accelerate reactions that would naturally occur extremely slowly by lowering the required Activation Energy ($E_a$).

• Enzyme Properties and Specificity:
  • Highly chemical- and stereospecific: Active sites strictly distinguish spatial configuration, selectively binding specific molecular isomers (e.g., distinguishing $\text{L}$-amino acids from $\text{D}$-amino acids, or $\text{D}$-monosaccharides from $\text{L}$-monosaccharides).
  • Named according to the specific substrate or reaction catalyzed, typically ending in the suffix -ase (e.g., Hydrolases, Lactase, ATPase).
• Three-Step Mechanism of Enzyme Action:
  1. Substrate Binding: Substrates ($\text{S}$) bind with exact spatial orientation to the enzyme's active site, forming a temporary Enzyme-Substrate Complex ($\text{E-S}$).
  2. Catalytic Rearrangement: The $\text{E-S}$ complex undergoes internal conformational shape changes that align substrate bonds, lowering activation energy and facilitating bond formation or cleavage.
  3. Product Release: The resulting product ($\text{P}$) no longer fits the active site structure and is released. The unaltered enzyme returns to its original conformation, ready to catalyze subsequent reactions.
• Example: Lactase binds lactose and lowers activation energy to cleave it into glucose and galactose.

Chemical Reaction Patterns

• Synthesis (Anabolic) Reactions: Smaller molecules or atoms combine to form larger, more complex structures. Involves chemical bond formation ($\text{A} + \text{B} \rightarrow \text{AB}$).
  • Example: Amino acid monomers joining via dehydration synthesis to form a structural protein.
• Decomposition (Catabolic) Reactions: Complex molecules are broken down into simpler, smaller molecules or constituent atoms. Involves breaking chemical bonds ($\text{AB} \rightarrow \text{A} + \text{B}$).
  • Example: Glycogen polymers undergoing hydrolysis to release individual glucose monomers.
• Exchange (Displacement) Reactions: Bonds are both broken and formed, resulting in the exchange of molecular components ($\text{AB} + \text{C} \rightarrow \text{AC} + \text{B}$ or $\text{AB} + \text{CD} \rightarrow \text{AD} + \text{CB}$).
  • Example: ATP transferring its terminal phosphate group to glucose, producing Glucose-Phosphate and Adenosine Diphosphate (ADP).

Nucleic Acids and Nucleotides

• Nucleic acids are the largest organic macromolecules in the body, composed of Carbon, Hydrogen, Oxygen, Nitrogen, and Phosphorus.
• Structural monomeric units are Nucleotides, which consist of three components:
  1. A nitrogenous base (Purine or Pyrimidine).
  2. A pentose sugar (Ribose or Deoxyribose).
  3. A phosphate group.
• Five Major Nitrogenous Bases:
  • Purines (Two-Ring Structure): Adenine ($\text{A}$) and Guanine ($\text{G}$).
  • Pyrimidines (One-Ring Structure): Cytosine ($\text{C}$), Thymine ($\text{T}$ - DNA only), and Uracil ($\text{U}$ - RNA only).

• Deoxyribonucleic Acid (DNA):
  • Localization & Function: Confined to the cell nucleus; constitutes the genome/genetic material, directing cellular protein synthesis and replicating prior to cell division.
  • Structure: Double-stranded polymer twisted into a coiled Double Helix ladder.
  • Composition: Deoxyribose pentose sugar, phosphate backbone, and bases $\text{A}$, $\text{T}$, $\text{G}$, and $\text{C}$.
  • Complementary Base Pairing: Hydrogen bonds selectively join nitrogenous bases across strands:
  • Adenine pairs exclusively with Thymine ($\text{A}=\text{T}$ via $2$ hydrogen bonds).
  • Guanine pairs exclusively with Cytosine ($\text{G}\equiv\text{C}$ via $3$ hydrogen bonds).
• Ribonucleic Acid (RNA):
  • Localization & Function: Found primarily in the cytoplasm outside the nucleus; carries out nuclear genetic instructions to execute cytoplasmic protein synthesis.
  • Structure: Single-stranded polymer (straight or folded).
  • Composition: Ribose pentose sugar, phosphate backbone, and bases $\text{A}$, $\text{U}$, $\text{G}$, and $\text{C}$ (Uracil replaces Thymine).
  • Three Functional Varieties: Messenger RNA (mRNA), Ribosomal RNA (rRNA), and Transfer RNA (tRNA).

Adenosine Triphosphate (ATP)

• Glucose catabolism releases bond energy that is captured and stored within Adenosine Triphosphate (ATP) molecules.
• Structure of ATP: An Adenine-containing RNA nucleotide (Adenosine = Adenine + Ribose) linked to a chain of three phosphate groups.
• Energy Transfer Mechanism:
  • The terminal high-energy phosphate bonds are unstable because the three closely packed, negatively charged phosphate groups repulsively stress the chemical bond.
  • Hydrolysis of the terminal phosphate bond by the enzyme ATPase releases a large packet of usable chemical energy, forming Adenosine Diphosphate (ADP) and Inorganic Phosphate ($\text{P}_i$):

$\text{ATP} + \text{H}_2\text{O} \xrightarrow{\text{ATPase}} \text{ADP} + \text{P}_i + \text{Energy (Exergonic)}$

• Reversibly, ATP Synthase captures energy released from cellular fuel oxidation to re-attach inorganic phosphate to ADP via an endergonic synthesis reaction:

$\text{ADP} + \text{P}_i + \text{Energy} \xrightarrow{\text{ATP Synthase}} \text{ATP} + \text{H}_2\text{O} \quad (\text{Endergonic})$

Summary of Macromolecular Monomers and Polymers

• Carbohydrates:
  • Monomer: Monosaccharides (e.g., Glucose, Fructose).
  • Polymer: Polysaccharides (e.g., Glycogen, Starch, Cellulose).
• Proteins:
  • Monomer: Amino acids (e.g., Glycine, Lysine, Cysteine).
  • Polymer: Polypeptides and functional proteins (e.g., Collagen, Enzymes, Hemoglobin).
• Nucleic Acids:
  • Monomer: Nucleotides (Base + Pentose Sugar + Phosphate).
  • Polymer: Nucleic acid strands (e.g., DNA, RNA).