9-11-25 lecture 4 Biology Notes on Free Radicals, Bonding, Water, and Metabolism

Free Radicals, Antioxidants, and Health

Free radicals are
- defined as an electrically charged atom or grouped atoms with an unpaired electron in its outermost shell. $ext{Outer shell unpaired electron}$
- are very unstable and reactive.
- damage molecules by taking or giving electrons, potentially harming DNA, proteins, fats, RNA, etc.
Oxygen free radicals are especially dangerous because they are continually produced during normal metabolism.
- Oxygen radicals are produced during processes like aerobic cellular respiration and via energy absorption, ultraviolet light, X-rays, and breakdown of harmful substances.
Health implications:
- abundance of free radicals is linked to diseases such as cancer, diabetes, Alzheimer's disease, atherosclerosis, and arthritis.
Combatting free radicals:
- Antioxidants (e.g., vitamin C, vitamin E, selenium) act to neutralize free radicals.
- Antioxidants often work together to form larger protective networks, acting like a glue that holds molecules together to stabilize cellular environments.
Key metabolic context:
- Many free radicals are oxygen-based; metabolism and exposure to energy sources contribute to radical formation.
- Aerobic cellular respiration is a normal metabolic process that can generate oxygen free radicals.
Important takeaways:
- Free radicals can destabilize and damage other molecules if not controlled.
- Antioxidants are critical for slowing radical-induced damage and maintaining cellular health.

Bonding: Atoms, Shells, and Bond Formation

Atomic structure and valence:
- The likelihood of bond formation depends largely on the outermost electron shell (the valence shell).
- Innermost shell capacity: $2$ electrons.
- Next shell capacity: up to $8$ electrons.
- The outermost shell is the valence shell; filling it leads to chemical stability.
How atoms fill outer shells:
- Atoms with incompletely filled outer shells tend to combine to achieve stable configurations with filled outer shells.
- This can involve gaining electrons, losing electrons, or sharing electrons with other atoms.
Covalent bonds (sharing electrons):
- Very strong bonds formed when two atoms share electrons.
- Types of covalent bonds:
- Single covalent bond: share one pair of electrons. Example: $ext{H}_2$ with a single covalent bond. Represented by a single line between atoms.
- Double covalent bond: share two pairs of electrons. Example: $ext{O}_2$ . Represented by two lines between atoms.
- Triple covalent bond: share three pairs of electrons. Example: $ext{N}_2$ . Represented by three lines between atoms.
- Carbon valence:
- Carbon has four electrons in its outermost shell and can form up to four covalent bonds. This makes carbon-based chemistry central to biology (proteins, DNA, carbohydrates, fats).
- Carbon-centered structures can form ring or chain arrangements, creating a vast diversity of biological molecules.
Polar vs nonpolar covalent bonds:
- Nonpolar covalent bonds: electrons are shared equally; identical atoms have identical electronegativity (e.g., $ext{H-H}$ , $ext{C-H}$ ).
- Polar covalent bonds: electrons are shared unequally due to different electronegativities; result in partial charges (
 oldsymbol{C C}
)
- Example: water, ext{H}_2 ext{O} $, where oxygen is more electronegative than hydrogen, leading to a partial negative charge on O (δ−) and partial positive charges on H (δ+).</li></ul></li><li>Ionic bonds:<ul><li>Formed by transfer of electrons from one atom to another, creating oppositely charged ions that attract (electrostatic attraction).</li><li>Example: sodium chloride, NaCl. Na transfers its outer electron to Cl, forming Na⁺ and Cl⁻, which lattice together in a crystal.</li><li>Ionic compounds are typically solid and form crystals; they can dissociate in water to form electrolytes that are essential for cellular processes.</li></ul></li><li>Hydrogen bonds:<ul><li>Weak bonds formed between a hydrogen atom covalently bonded to a highly electronegative atom (like O or N) and another electronegative atom.</li><li>Very weak individually, but numerous hydrogen bonds collectively are significant (e.g., holding the two strands of DNA together).</li><li>Hydrogen bonds contribute to DNA structure, protein folding, and water’s properties.</li></ul></li><li>Summary of bond types:<ul><li>Ionic bonds: attraction between oppositely charged ions; e.g., Na⁺–Cl⁻ in NaCl crystals; dissolves in water to form electrolytes.</li><li>Covalent bonds: atoms share electrons; strongest type among bonds discussed.</li><li>Nonpolar covalent bonds: equal sharing (e.g., C–H, H–H).</li><li>Polar covalent bonds: unequal sharing leading to partial charges (e.g., O–H in H₂O).</li><li>Hydrogen bonds: weak, but numerous bonds between molecules or within large molecules; critical for DNA, proteins, and water properties.</li></ul></li></ul><h3 id="6c1f611a-4b63-41ab-a84c-246b77861d11" data-toc-id="6c1f611a-4b63-41ab-a84c-246b77861d11" collapsed="false" seolevelmigrated="true">Water: Polarity, Bonding, and Biological Roles</h3><ul><li>Water polarity and structure:<ul><li>Water is a polar molecule with partial negative charge on the oxygen and partial positive charges on the hydrogens due to polar covalent bonds. The molecule$ ext{H}_2 ext{O} $forms two polar covalent bonds.</li><li>The polarity arises because the outer electrons are not shared equally between O and H.</li></ul></li><li>Hydrogen bonds in water:<ul><li>Hydrogen bonds are weak, about$ 5\% $as strong as covalent bonds, but collectively very important for properties of water.</li><li>Hydrogen bonding leads to cohesion (water molecules sticking to each other) and adhesion (water sticking to other surfaces).</li></ul></li><li>Water’s unique properties due to hydrogen bonding:<ul><li>Cohesion: surface tension; allows phenomena like water striders skimming water surfaces.</li><li>Adhesion and capillary action: water climbs small tubes due to attraction to surfaces and between water molecules.</li><li>High heat capacity: water absorbs and retains heat, aiding in temperature regulation in organisms.</li><li>Water’s solvent properties: water dissolves many substances due to its polarity; often called the universal solvent.</li></ul></li><li>Hydration spheres and dissolution:<ul><li>Water forms hydration shells around ions (e.g., Na⁺, Cl⁻) and polar molecules (like sugars), preventing ions from recombining and enabling dissolution.</li><li>Example of hydration: a hydrated sodium ion is surrounded by water molecules oriented with the partial negative oxygen toward the Na⁺, stabilizing the ion in solution.</li></ul></li><li>Organic vs inorganic solvents:<ul><li>Organic solvents (e.g., ethanol, acetone) are carbon-containing and can dissolve many organic compounds.</li><li>Water is an inorganic solvent because it lacks carbon; it dissolves many inorganic salts and polar organics.</li></ul></li><li>Importance of electrolytes:<ul><li>Electrolytes are inorganic ions dissolved by water (e.g., Na⁺, K⁺, Ca²⁺, Mg²⁺, bicarbonate) and are essential for nerve signaling, muscle function, and pH balance.</li></ul></li><li>Water in biology:<ul><li>About$ 65\%$- $70\%$ of body weight is water; most organisms have heavy water content (humans ~66%, jellyfish ~90%).
- Water participates in hydrolysis and dehydration synthesis reactions (see next section) and acts as a reactant or product in many metabolic processes.
Hydration and pH balance:
- Sodium bicarbonate (NaHCO₃) and other electrolytes help maintain acid-base balance in the body when dissolved in water.

Chemical Reactions, Metabolism, and Energy

Metabolism overview:
- All biological reactions involve making or breaking chemical bonds (chemical reactions).
- Law of conservation of mass: the total mass of reactants equals the total mass of products; matter is conserved.
- Reactants are converted into products; in enzymatic reactions, reactants are often called substrates.
Energy and its forms:
- Energy is the capacity to do work (e.g., moving objects, muscle contraction, transporting substances across membranes).
- Kinetic energy: energy of motion. Temperature is an indirect measure of molecular motion. Higher temperature means faster molecular motion.
- Potential energy: stored energy, e.g., a boulder on a hill, water behind a dam, a charged battery.
- Chemical energy: a form of potential energy stored in chemical bonds; energy stored in bonds can be released by breaking bonds and captured in new bonds.
Energy content of biological molecules:
- Carbohydrates, proteins, and fats store energy in their bonds; fats store more energy per unit mass than carbohydrates or proteins (often cited as fats providing more energy per gram).
Exergonic vs Endergonic reactions:
- Exergonic: energy is released; often involves breaking bonds; downhill energetics; examples include digestion of starch to sugars (catabolism). Represented as ΔG < 0.
- Endergonic: energy is required; energy input drives the reaction to form bonds (anabolism).
- In cells, exergonic reactions often provide the energy to drive endergonic reactions, enabling energy coupling.
Activation energy:
- Activation energy (Ea) is the energy barrier that must be overcome to start a reaction.
- Even exergonic reactions may require an initial input of energy to proceed.
- Ways to overcome Ea:
- Increase reactant concentration (more collisions).
- Increase temperature (more molecular motion).
- Use a catalyst to lower Ea.
Catalysts and enzymes:
- Catalysts speed up reactions by lowering the activation energy without changing the overall energy difference between reactants and products.
- The catalyst brings reactants into proper orientation and/or stresses bonds to facilitate reaction; it is unchanged by the reaction and can be reused.
- Enzymes are biological catalysts (protein-based) that speed reactions by enormous factors (often millions-fold) and are highly specific for substrates.
- Example: lactase digests lactose into glucose and galactose; sucrase digests sucrose; different enzymes are required for different substrates.
Decomposition vs synthesis (catabolism vs anabolism):
- Catabolic reactions break large molecules into smaller parts, releasing energy (e.g., starch to glucose).
- Anabolic reactions build larger molecules from smaller subunits, requiring energy (e.g., amino acids to proteins, glucose to polysaccharides like starch or glycogen).
Hydrolysis vs dehydration synthesis:
- Hydrolysis: large molecule is split by adding water; a water molecule contributes H to one fragment and OH to the other.
- Dehydration synthesis (condensation): two smaller molecules join, releasing water, to form a larger molecule.
Redox chemistry: Oil and rig
- Oxidation: loss of electrons; energy is typically released.
- Reduction: gain of electrons; energy is stored in the reduced form.
- ***O2 Is Lost
- Reduction is Gained
Organic vs inorganic compounds:
- Organic compounds contain carbon and hydrogen; if a molecule contains both C and H, it is considered organic.
- Inorganic compounds may lack carbon or hydrogen (e.g., CO₂ is inorganic).

Practical Implications and Connections

Why this matters:
- Understanding free radicals and antioxidants informs health decisions related to aging, cancer risk, and chronic diseases.
- Knowledge of bonding and water properties underpins biochemistry, physiology, and pharmacology.
- Enzymes and energy metabolism are central to how organisms grow, move, and maintain homeostasis.
Real-world relevance:
- Antioxidants are common in diets (fruits, vegetables) and supplements; their effectiveness depends on many factors and is a topic of ongoing research.
- Proper hydration and electrolyte balance are essential for nerve and muscle function and for maintaining pH homeostasis.
- Water’s solvent properties affect drug delivery, digestion, and cellular processes.

Quick Reference: Key Terms and Concepts

Free radical: an atom or group with an unpaired electron in the outer shell, making it highly reactive.
Antioxidant: a molecule that neutralizes free radicals.
Ionic bond: electrostatic attraction between oppositely charged ions (e.g., Na⁺ and Cl⁻).
Covalent bond: sharing of electrons between atoms; includes nonpolar and polar covalent bonds.
Nonpolar covalent bond: equal sharing of electrons; often occurs when electronegativities are similar (e.g., C–H).
Polar covalent bond: unequal sharing of electrons; results in partial charges (δ⁺, δ⁻).
Hydrogen bond: weak attraction between a hydrogen atom and another electronegative atom; critical for DNA structure and water properties.
Hydration sphere/shell: layer of water molecules around an ion or polar molecule that stabilizes it in solution.
Solvent: the dissolving medium in a solution (water is a major biological solvent).
Solute: substance dissolved in a solvent.
Electrolyte: inorganic ions dissolved in water that conduct electricity in solution.
Hydrolysis: chemical reaction that uses water to break a bond.
Dehydration synthesis: reaction that forms a bond by removing water.
Oxidation: loss of electrons.
Reduction: gain of electrons.
ATP: adenosine triphosphate, the primary energy currency of the cell (to be discussed further).
Catabolism: metabolic pathways that break down molecules to release energy.
Anabolism: metabolic pathways that build larger molecules from smaller units.
Exergonic: reactions that release energy (ΔG < 0).
Endergonic: reactions that require energy input (ΔG > 0).
Activation energy (Ea): energy barrier that must be overcome to start a reaction.
Enzyme: protein-based biological catalyst that speeds a chemical reaction.
Substrate: molecule that is acted upon by an enzyme.
Organic compound: contains both carbon and hydrogen.
Inorganic compound: lacks one or both of carbon or hydrogen.