Lecture Review: Buffers, pH, and Organic Molecules

Administrative Reminders, Course Schedule, and Safety Protocol

• Upcoming Laboratory Requirements:

  • Topic: Scientific Method, Buffers, and $pH$.

  • Required Materials: Bring a printed hard copy of the lab handout (located in the "lab handouts folder"). Bring the lab manual as a backup resource.

  • Preparation: Browse over the lab handout and watch the assigned recorded video titled "The Scientific Method Buffers and pH" under Course Content prior to class.

  • Safety Attire: Long pants or sweatpants and closed-toe shoes or sneakers are mandatory due to chemical use. Shorts, flip-flops, and sandals are strictly prohibited.

  • Lab Quiz 2: Due by $8:00\,\text{AM}$ on the morning of the lab.

• Exam and Quiz Deadlines:

  • Lecture Quiz 1: Extended until Tuesday, September 1st at $12:00\,\text{PM}$ (noon), providing $5$ extra days to complete the quiz and prepare for the lecture exam.

  • Lecture Exam 1: Tuesday, September 8th.

  • Lab Exam 1: Friday, September 11th.

• Study Blueprint and References:

  • Textbook Figure 2.24: An integrated diagram covering biological molecules that should be studied thoroughly.

  • Review Guide: Learning Objective $14$ marks the starting point for this material. Typed answers to learning objectives should be completed continuously outside of class.

Properties of Water, Chemical Bonding, and Blood pH Homeostasis

• Structure and Polarity of Water ($H_2O$):

  • Chemical Formula: $H_2O$, consisting of two hydrogen atoms covalently bonded to one oxygen atom.

  • Bond Polarity: The two covalent bonds are polar due to unequal sharing of electrons between oxygen and hydrogen.

  • Charge Distribution: Oxygen attracts shared electrons more strongly, gaining a partial negative charge ($\delta^-$). Hydrogen atoms hold electrons less tightly, gaining a partial positive charge ($\delta^+$). The Greek symbol delta ($\delta$) denotes a partial charge.

• Non-Covalent Intermolecular Attractions:

  • Hydrogen Bonds: Weak attractions formed between a partial negative charge on an oxygen atom (or nitrogen atom) of one molecule and a partial positive charge on a hydrogen atom of another molecule. Every water molecule forms multiple hydrogen bonds with surrounding water molecules.

  • Van der Waals Forces: Very weak, highly numerous non-covalent attractive forces occurring between any two neutrally charged atoms situated close together in space.

• Physiological Blood $pH$ Ranges:

  • Normal Range: Maintained within a narrow range between $7.35$ and $7.45$.

  • Acidosis: A pathological condition where blood $pH$ drops below $7.35$. It is life-threatening if uncorrected.

  • Alkalosis: A pathological condition where blood $pH$ rises above $7.45$. It is life-threatening if uncorrected.

• Questions & Discussion: Water and Chemical Bonds:

  • Question: Are the covalent bonds within a water molecule polar or nonpolar, and how do partial charges arise?

  • Response: The covalent bonds are polar because electrons are shared unequally. Electrons spend more time near the oxygen atom, giving it a partial negative charge ($\delta^-$), and less time near the hydrogen atoms, giving them partial positive charges ($\delta^+$).

  • Question: What is the difference between hydrogen bonds and Van der Waals forces?

  • Response: Hydrogen bonds occur specifically between partial positive hydrogen atoms and partial negative atoms like oxygen or nitrogen. Van der Waals forces are generalized, weak attractions between any two close, neutrally charged atoms.

Buffer Systems and the Carbonic Acid-Bicarbonate System

• Universal Features of All Buffers:

  1. Resist $pH$ Changes: All buffers maintain $pH$ stability by either binding to or releasing hydrogen ions ($H^+$).

  2. Unique $pH$ Range: Every buffer functions within its own specific, unique $pH$ range (e.g., neutral $pH \approx 7.0$, acidic $pH \approx 4.0$, or basic $pH \approx 9.0$ to $10.0$).

  3. Limited Buffering Capacity: Buffers do not have infinite capacity; they can only absorb or release a finite number of $H^+$ ions before their buffering capacity is exceeded.

• The Carbonic Acid-Bicarbonate Buffer System:

  • Primary Function: The main buffer system regulating human blood $pH$ within the $7.35$ to $7.45$ range.

  • Key Chemical Components:

  • Carbonic Acid: Weak acid with the chemical formula $H_2CO_3$.

  • Bicarbonate Ion: Weak base with the chemical formula $HCO_3^-$.

• Equilibrium and Reversible Chemical Reactions:

  • Dissociation Reaction:

  • Equation: $H_2CO_3 \rightarrow HCO_3^- + H^+$

  • Mechanism: Carbonic acid breaks apart to release a hydrogen ion ($H^+$) and a bicarbonate ion ($HCO_3^-$).

  • Response to Added Base: When a base is added to the system, the dissociation reaction replaces lost $H^+$ ions by releasing additional hydrogen ions.

  • Association Reaction:

  • Equation: $HCO_3^- + H^+ \rightarrow H_2CO_3$

  • Mechanism: Bicarbonate binds with a free hydrogen ion ($H^+$) to reform carbonic acid ($H_2CO_3$).

  • Response to Added Acid: When an acid is added to the system, the association reaction binds and removes excess $H^+$ ions released by the acid.

  • Dynamic Equilibrium: The balance between dissociation and association reactions maintains a stable concentration of $H^+$ ions, preventing significant shifts in $pH$.

• Questions & Discussion: Buffer Dynamics:

  • Question: Where is the hydrogen located in the bicarbonate solution?

  • Response: Bicarbonate ions and hydrogen ions are dissolved in solution, constantly moving and diffusing. When they come close enough together, they react to form carbonic acid via the association reaction.

Principles of Organic Chemistry and Functional Groups

• Carbon Skeletons:

  • Organic molecules contain the element carbon ($C$).

  • Carbon Skeleton: The structural framework of carbon atoms within an organic molecule, forming linear chains, branched chains, or closed ring structures.

• Six Essential Functional Groups:

  1. Hydroxyl Group: Symbolized as $-OH$. Consists of an oxygen atom bonded to a hydrogen atom.

  2. Sulfhydryl Group: Symbolized as $-SH$. Consists of a sulfur atom bonded to a hydrogen atom.

  3. Methyl Group: Symbolized as $-CH_3$. Consists of a carbon atom single-bonded to three hydrogen atoms.

  4. Carboxyl Group: Symbolized as $-COOH$. Consists of a carbon atom double-bonded to an oxygen atom and single-bonded to a hydroxyl group.

  5. Amino Group: Symbolized as $-NH_2$. Consists of a nitrogen atom single-bonded to two hydrogen atoms.

  6. Phosphate Group: Contains a central phosphorus atom bonded to oxygen atoms and hydroxyl groups.

  • Biological Roles: Functional groups govern a molecule's water solubility (hydrophilicity) and influence its chemical reactivity and $pH$.

• Monomers, Polymers, and Chemical Reactions:

  • Monomers: Individual structural subunits or building blocks (e.g., amino acids).

  • Polymers: Long chains of repeating monomers linked together (e.g., proteins).

  • Dehydration Synthesis Reaction:

  • Function: Joins monomers together to lengthen a polymer.

  • Bonding: Forms strong covalent bonds between monomers.

  • Byproduct: Produces a molecule of water ($H_2O$) as a product.

  • Hydrolysis Reaction:

  • Function: Cleaves covalent bonds between monomers to shorten a polymer.

  • Reactants: Consumes a molecule of water ($H_2O$) as a reactant to split the bond.

• Macromolecules:

  • Definition: Large, complex organic molecules, most of which are polymers.

  • Examples: Deoxyribonucleic acid (DNA) and proteins.

Carbohydrates: Structural Classes and Biological Roles

• General Characteristics:

  • Commonly referred to as sugars.

  • Primary Function: Energy storage (with specific exceptions providing structural support).

• Classes of Carbohydrates:

  • Monosaccharides ($1$ sugar unit):

  • Structure: Single ring structure composed of $5$ or $6$ carbon atoms with attached hydroxyl ($-OH$) groups.

  • Examples:

    • Glucose: Primary sugar in human blood.

    • Fructose: Sugar found in fruits.

    • Deoxyribose: Five-carbon monosaccharide in DNA.

    • Ribose: Five-carbon monosaccharide in RNA.

  • Disaccharides ($2$ sugar units):

  • Structure: Two monosaccharide ring units joined by a covalent bond known as a glycosidic bond.

  • Examples:

    • Sucrose: Table sugar.

    • Lactose: Milk sugar.

  • Polysaccharides (Long chains of sugar units):

  • Structure: Polymer chains of monosaccharides linked together by strong covalent glycosidic bonds.

  • Examples:

    • Glycogen: Energy storage polysaccharide in animals; stored predominantly in the liver.

    • Starch: Energy storage polysaccharide in plants (e.g., abundant in potatoes).

    • Cellulose: Structural polysaccharide in plants providing structural support; constitutes dietary fiber in human nutrition (e.g., found in oatmeal).

Lipids I: Fatty Acids and Triglycerides

• General Characteristics of Lipids:

  • Hydrophobic Nature: All lipids are hydrophobic ("water-fearing") and do not dissolve in water because they cannot form attractive forces or hydrogen bonds with water molecules.

  • Diversity: Lipids display highly diverse structures and biological functions.

• Fatty Acids:

  • Building Blocks: Simple lipids used to construct complex lipids like triglycerides and phospholipids.

  • Structure: A long hydrocarbon chain (chain of carbon and hydrogen atoms) attached to a carboxyl group ($-COOH$).

  • Types of Fatty Acids:

  • Saturated Fatty Acids: Contain only single covalent bonds between carbon atoms in the hydrocarbon chain.

  • Unsaturated Fatty Acids: Contain one or more double covalent bonds between carbon atoms in the hydrocarbon chain.

  • Trans Fatty Acids: Unhealthy unsaturated fatty acids found in fast food, fried foods, and baked goods that increase the risk of cardiovascular (CV) disease.

  • Omega-3 Fatty Acids: Healthy unsaturated fatty acids that lower the risk of cardiovascular disease. Natural sources include fish (e.g., salmon, albacore tuna), walnuts, spinach, and fish oil supplements.

• Triglycerides (Fats):

  • Functions: Energy storage, thermal insulation of the body, and mechanical cushioning/protection for internal organs.

  • Storage Location: Stored in specialized adipose tissue.

  • Chemical Structure: Consists of one $3$-carbon glycerol backbone (containing $3$ hydroxyl groups) covalently linked to $3$ fatty acid chains via ester bonds.

  • Classification of Fats:

  • Saturated Fats: Composed mostly of saturated fatty acids. Derived from animal sources (e.g., meat, dairy, cheese, butter, ice cream) and increase CV disease risk.

  • Unsaturated Fats: Composed mostly of unsaturated fatty acids. Derived from plant and fish sources (e.g., olive oil, nuts, legumes).

  • Metabolic Processes:

  • Lipogenesis: The anabolic process of building a triglyceride by forming ester bonds between glycerol and $3$ fatty acids.

  • Lipolysis: The catabolic process of breaking down a triglyceride into glycerol and free fatty acids.

Lipids II: Phospholipids, Steroids, and Lipoproteins

• Phospholipids:

  • Biological Function: Primary structural component of cell membranes.

  • Chemical Nature: Amphipathic (possesses both polar/hydrophilic and nonpolar/hydrophobic regions).

  • Chemical Structure:

  • One $3$-carbon glycerol backbone.

  • Two fatty acid chains forming the nonpolar tails (hydrophobic hydrocarbon chains).

  • One phosphate group attached to a polar molecule forming the polar head (hydrophilic region, which includes glycerol, phosphate, and the attached polar molecule).

• Steroids:

  • Structural Framework: All steroids are constructed from a four-ring carbon backbone derived from cholesterol.

  • Structural Features of Cholesterol: Four hydrocarbon ring structures, a hydrocarbon tail, methyl groups ($-CH_3$), and a hydroxyl group ($-OH$).

  • Functions: Primarily serve as chemical signaling messengers (hormones).

  • Key Examples:

  • Estradiol: A type of estrogen and primary female sex hormone.

  • Testosterone: The primary male sex hormone.

  • Cortisol: A key stress hormone.

  • Vitamin D: A steroid derivative.

• Lipoproteins and Cholesterol Transport:

  • Function: Protein-lipid complexes that transport hydrophobic lipids (such as cholesterol) through the bloodstream.

  • Low-Density Lipoprotein (LDL):

  • "Bad Cholesterol".

  • Delivers cholesterol from the liver to blood vessels.

  • Excess LDL causes cholesterol accumulation in blood vessel walls, leading to atherosclerosis (narrowing of blood vessels) and increasing the risk of heart attacks and CV disease.

  • High-Density Lipoprotein (HDL):

  • "Good Cholesterol".

  • Delivers excess cholesterol from blood vessels back to the liver, lowering the risk of atherosclerosis.

• Pharmacological Interventions:

  • Statins: Pharmaceutical drugs that lower blood levels of LDL ("bad cholesterol") and reduce the risk of atherosclerosis.

  • Examples of Statin Medications: Rosuvastatin, Lovastatin, Atorvastatin (Lipitor), Simvastatin (Zocor).