Biochemistry: Inorganic and Organic Compounds

Laboratory Logistics and Practical Preparation

• Laboratory Practical 1 Overview:

  • Materials for Lab Practical 1 include cell models, tissues, and skin models.

  • The skin lab constitutes the final piece of new material required for Lab Practical 1.

  • The skin lab is relatively brief, and its accompanying study guide is intentionally minuscule.

  • Microscopes and study models are shared between specialized Anatomy and Physiology (A&P) and general A&P courses.

  • Study key and access materials (including index cards) have been retrieved by Noah and placed out for student access.

  • Models and scopes will be jumbled up one final time at the start of next week for practical preparation.

• Student Action Plan and Schedule:

  • A lab quiz takes place during the current week.

  • The first lab practical is scheduled for the following week during regular lab time.

  • Students must dedicate study time on campus, specifically on Mondays and Wednesdays, to review cell models, tissue slides, and skin models prior to the practical.

Classification of Chemical Compounds: Organic vs. Inorganic

• Biochemistry Focus:

  • Basic atomic structure and general introductory chemistry are assumed prerequisites and are omitted from lecture review.

  • Chemical compounds in A&P are divided into two fundamental families: Organic Compounds and Inorganic Compounds.

• Organic Compounds:

  • Definition: Carbon-containing compounds that almost universally possess Carbon ($\text{C}$), Hydrogen ($\text{H}$), and Oxygen ($\text{O}$).

  • Characteristics: Tend to be structurally complex and larger molecules.

  • Example: Glucose ($\text{C}_6\text{H}_{12}\text{O}_6$), referred to clinically as blood sugar in A&P.

    • Contains exactly $6$ carbon atoms arranged in a ring structure.

• Inorganic Compounds:

  • Definition: Compounds that do not contain carbon in their molecular formula.

  • Characteristics: Structurally simpler than organic compounds, but essential for life and physiological function.

  • Example: Water ($\text{H}_2\text{O}$), which contains zero carbon atoms and is the most abundant inorganic compound on Earth.

Chemical and Physical Properties of Water

• Water as the Universal Solvent:

  • Definitions:

    • Solvent: The liquid medium into which a solute dissolves to form a uniform solution.

    • Solute: Any molecule or particle (e.g., glucose, salts, isolated ions) that dissolves into a solvent.

  • Water is designated as the universal solvent due to its extreme polarity and high chemical reactivity.

  • The human body consists of almost $90\%$ water by weight.

  • Water acts as a highly social molecule, constantly interacting and forming bonds with surrounding chemicals regardless of chemical type.

• Molecular Polarity of Water:

  • Definition: A polar molecule possesses two distinct poles or regions exhibiting opposite electrical charges (unevenly charged).

  • Structural Geometry:

    • Resembles a tilted asymmetrical head (resembling a Mickey Mouse face).

    • The single Oxygen atom forms the central head region, carrying a net negative partial charge ($\delta^-$).

    • The two Hydrogen atoms form the ear regions, carrying net positive partial charges ($\delta^+$).

  • Chemical Interactions:

    • Opposites attract electrostatically.

    • The partial negative charge of the oxygen region attracts positively charged chemical entities.

    • The partial positive charges of the hydrogen regions attract negatively charged chemical entities.

    • This dual polarity grants water its universal chemical reactivity with both cations and anions.

• Physiological Properties of Water:

  1. Chemical Reactivity: Polarity enables water to participate in synthesis and breakdown reactions throughout the body.

  2. High Heat Capacity: Water retains thermal energy extremely well and resists rapid temperature fluctuations.

     • Environmental Analogy: River water in April or May remains freezing cold because it has retained low winter temperatures. Conversely, river water in October or November stays warm despite cool air temperatures because it has retained summer heat.

  3. Cushioning Factor: Fluid layers of water surrounding internal organs and bathing the interior and exterior of cells absorb physical shock and protect cellular structures from blunt force trauma.

Salts, Dissociation, and Electrolyte Homeostasis

• Dissociation of Salts:

  • Salts placed in water undergo dissociation, breaking their chemical bonds via interactions with polar water molecules.

  • Mechanism: The negative oxygen pole of water surrounds positively charged components of the salt, while the positive hydrogen poles surround negatively charged components, pulling the salt lattice apart into individual aqueous ions.

  • Historical Context: In the 1960s and 1970s, athletes consumed solid salt tablets without adequate water hydration, which severely impaired performance and health compared to modern electrolyte fluids (e.g., Gatorade).

• Classification of Ions:

  • An ion is any atom or molecule with a net electrical charge.

  • Cations:

    • Positively charged ions.

    • Key Physiological Examples: Sodium ion ($\text{Na}^+$), Potassium ion ($\text{K}^+$), Calcium ion ($\text{Ca}^{2+}$).

    • Physiological Functions: Required for neuronal action potential generation, skeletal and cardiac muscle contraction, and blood coagulation pathways (blood clotting specifically requires $\text{Ca}^{2+}$).

  • Anions:

    • Negatively charged ions.

    • Key Physiological Example: Chloride ion ($\text{Cl}^-$).

    • Physiological Functions: Participates in inhibitory neurotransmitter signaling pathways in the nervous system.

• Electrolyte Homeostasis:

  • In physiology, cations and anions are collectively referred to as electrolytes.

  • Replenishing electrolytes via fluids supports nervous system transmission, muscular contractions, digestive motility, and renal function.

  • Renal Regulation: The kidneys in the urinary system act as the primary homeostatic regulators of electrolytes, controlling the precise reabsorption and secretion flows of $\text{Na}^+$, $\text{H}^+$, $\text{Cl}^-$, and $\text{K}^+$.

Acids, Bases, and Neutralization Reactions

• Acids (Proton Donors):

  • Definition: Acids are proton donors or electron donors that dissociate in solution to release hydrogen ions ($\text{H}^+$).

  • Atomic Rationale: A hydrogen atom consists of precisely one proton and one electron. Stripping the electron leaves a single bare proton ($\text{H}^+$); thus, tracking hydrogen ions is equivalent to tracking protons.

  • Strong Acid Example: Hydrochloric Acid ($\text{HCl}$).

    • Caustic compound capable of causing severe chemical burns through the skin epidermis.

    • Dissociates fully into hydrogen ions and chloride ions: $\text{HCl} \rightarrow \text{H}^+ + \text{Cl}^-$

  • Other Physiological Acids: Acetic acid, Carbonic acid ($\text{H}_2\text{CO}_3$).

• Bases (Proton Acceptors):

  • Definition: Bases are proton, hydrogen, or electron acceptors that bind free hydrogen ions in solution.

  • Strong Base Example: Sodium Hydroxide ($\text{NaOH}$).

    • Caustic alkaline substance that induces severe chemical burns on contact with tissue.

    • Dissociates into sodium ions and hydroxyl/hydroxide ions: \text{NaOH} \n\rightarrow \text{Na}^+ + \text{OH}^-

  • Other Physiological Bases: Bicarbonate ion ($\text{HCO}_3^-$), Ammonia ($\text{NH}_3$).

    • Ammonia is filtered out of blood by the kidneys and contributes directly to the characteristic odor of urine.

• Neutralization Reactions:

  • Occur when a strong acid reacts with a strong base to produce a neutral salt and water.

  • Reaction Formula: $\text{NaOH} + \text{HCl} \rightarrow \text{NaCl} + \text{H}_2\text{O}$

  • Rearranges dangerous, caustic reactants into harmless table salt ($\text{NaCl}$) and water ($\text{H}_2\text{O}$), maintaining homeostatic safety in living tissues.

Quantitative Interpretation of the pH Scale

• pH Definition:

  • $\text{pH}$ is a quantitative measure of hydrogen ion concentration in a solution.

  • Represented shorthand as $[\text{H}^+]$, where outer square brackets denote concentration.

• Scale Dynamics and Values:

  • Neutral Point ($\text{pH} = 7$):

    • Represents an equal balance of $\text{H}^+$ and $\text{OH}^-$ ions.

    • Physiological Benchmark: Human blood is a slightly neutral-to-alkaline physiological fluid ranging from $\text{pH} = 7.2$ to $\text{pH} = 7.6$ (standard average reference value is $\text{pH} = 7.4$).

  • Acidic Range ($\text{pH} < 7$):

    • Solutions with a $\text{pH}$ less than $7$ are acidic.

    • As $\text{pH}$ numerical value decreases, solution acidity increases.

    • As $\text{pH}$ numerical value decreases, hydrogen ion concentration $[\text{H}^+]$ increases.

    • Mathematical Note: An exponent of $10^{-5}\,mol\,dm^{-3}$ represents a higher hydrogen ion concentration than $10^{-7}\,mol\,dm^{-3}$.

    • Acidic Fluid Examples:

      • Milk: $\text{pH} \approx 6.3$

      • Wine: $\text{pH} = 2 - 3.5$

      • Lemon Juice: $\text{pH} \approx 2$

      • Gastric Juice: $\text{pH} \approx 2$

      • Hydrochloric Acid: $\text{pH} = 0$

  • Basic / Alkaline Range ($\text{pH} > 7$):

    • Solutions with a $\text{pH}$ greater than $7$ are basic or alkaline.

    • As $\text{pH}$ numerical value increases, hydrogen ion concentration $[\text{H}^+]$ decreases, and hydroxyl ion concentration $[\text{OH}^-]$ increases.

    • Basic Fluid Examples:

      • Egg Whites: $\text{pH} \approx 8$

      • Household Ammonia: $\text{pH} \approx 11$

      • Household Bleach: High alkaline range

      • Oven Cleaner: $\text{pH} \approx 13$

      • Sodium Hydroxide ($\text{NaOH}$): $\text{pH} = 14$

Questions & Discussion

• Question: Is wine more acidic than lemon juice?

  • Answer: False. Lemon juice has a $\text{pH}$ of approximately $2$, whereas wine has a $\text{pH}$ between $2$ and $3.5$, making lemon juice further down the acidic scale.

• Question: Is sodium hydroxide a strong acid?

  • Answer: False. Sodium hydroxide ($\text{NaOH}$) is a strong base with a $\text{pH}$ near 14$.\n* **Question**: Which contains a higher concentration of hydrogen ions ([\text{H}^+]): egg whites or household ammonia?\n * **Answer**: Egg whites. Egg whites have a \text{pH}$of$\approx 8$($10^{-8}\,mol\,dm^{-3}$), which represents a higher hydrogen ion concentration than household ammonia at$\text{pH} \approx 11$($10^{-11}\,mol\,dm^{-3}).\n* **Question**: What is an example of a liquid with an acidic \text{pH}?\n * **Answer**: Black coffee, wine, lemon juice, stomach gastric juice, or hydrochloric acid.\n* **Question**: Which contains a higher concentration of hydroxyl ions ([\text{OH}^-]): oven cleaner or household ammonia?\n * **Answer**: Oven cleaner. Oven cleaner sits at a hydroxyl concentration of \approx 10^{-1}\,mol\,dm^{-3}$, compared to household ammonia at$\approx 10^{-3}\,mol\,dm^{-3}.\n\n# Physiological Buffering Systems and Enzyme Protection\n\n* **Reversible Carbonic Acid-Bicarbonate Buffer System**:\n * Buffering chemical reactions are fully reversible dynamic equilibria.\n * If \text{pH}$rises (becomes basic), the reaction shifts right to release$\text{H}^+ ions.\n * If \text{pH}$drops (becomes acidic), the reaction shifts left to bind free$\text{H}^+ ions.\n* **Carbon Dioxide (\text{CO}2) Homeostasis**:\n * \text{CO}_2 is generated as metabolic waste by thousands of daily intracellular chemical reactions.\n * Unbuffered \text{CO}_2$drastically decreases the$\text{pH} of any aqueous solution it enters, including blood plasma and interstitial fluid.\n * **Enzymatic Sensitivity**:\n * Enzymes are specialized protein catalysts that accelerate chemical reactions.\n * *Speed Analogy*: Cellular reactions without enzymes proceed at 5\text{ mph}$; functioning enzymes accelerate metabolism to$55\text{ mph}$or$65\text{ mph}.\n * Decreasing \text{pH} denatures enzymes, preventing them from functioning. Enzyme failure impairs cellular operations, causing organ dysfunction, disease, or death.\n * **\text{CO}_2 Transport Mechanism**:\n * Active tissues (such as contracting skeletal muscle) generate high volumes of \text{CO}_2\n * To prevent tissue damage during vascular transit, \text{CO}_2$is converted and buffered in blood as safe carbonic acid ($\text{H}_2\text{CO}_3).\n * Upon reaching the pulmonary capillaries in the lungs, carbonic acid unbuffers back into \text{CO}_2 gas and is exhaled.\n* **Gastrointestinal Protection**:\n * Stomach gastric juice maintains an extreme acidity of \text{pH} \approx 2\n * Upon exiting the stomach into the small intestine, acidic gastric juice threatens to burn and erode the intestinal epithelium.\n * The pancreas secretes sodium bicarbonate (\text{NaHCO}_3) directly into the small intestine to neutralize incoming gastric acid.\n* **Artificial Buffering**:\n * Over-the-counter antacids (e.g., Tums, Rolaids) act as artificial chemical buffers to neutralize stomach acids creeping upward into the esophagus during gastroesophageal reflux (heartburn).\n\n# Macromolecules and Chemical Synthesis Mechanisms\n\n* **The Four Families of Macromolecules**:\n 1. Carbohydrates (Sugars, starches, cellulose)\n 2. Lipids (Fats and oils: solid lipids vs. liquid lipids)\n 3. Proteins (Functional cellular workers/enzymes)\n 4. Nucleic Acids (DNA and RNA)\n* **Polymers and Monomers**:\n * Macromolecules are polymers ("poly" = many).\n * Polymers are constructed from repeating single subunit building blocks called monomers ("mono" = one).\n* **Dehydration Synthesis Reactions**:\n * Anabolic process used to build polymers from individual monomer reactants.\n * *Mechanism*: A hydroxyl group (-\text{OH}$) is cleaved from reactant A, and a hydrogen atom ($-\text{H}) is cleaved from reactant B.\n * Removal of these groups allows reactant A and reactant B to form a covalent bond, producing a combined polymer while releasing water (\text{H}_2 ext{O}) as a byproduct.\n * *Reaction Formula*: \text{Reactant A-OH} + \text{Reactant B-H} \rightarrow \text{Complex Product A-B} + \text{H}_2\text{O}\n* **Hydrolysis Reactions**:\n * Catabolic process used to break down complex polymers into monomer units.\n * *Mechanism*: A molecule of water (\text{H}_2\text{O}) is consumed to break (lyse) the covalent bond holding the polymer together.\n * Water is split, reattaching an -\text{OH}$group to one monomer and an$-\text{H} atom to the second monomer.\n * *Etymology*: *Hydro* = water; *lysis* = to cut or break apart.\n* **Chemical Example (Sucrose Synthesis and Breakdown)**:\n * *Synthesis*: Monosaccharide Glucose + Monosaccharide Fructose \xrightarrow{\text{Dehydration Synthesis}}$Disaccharide Sucrose +$\text{H}_2\text{O}\n * *Breakdown*: Disaccharide Sucrose + \text{H}_2\text{O}$$\xrightarrow[\text{Sucrase Enzyme}]{\text{Hydrolysis}} Glucose + Fructose\n* **Macromolecule Mastery Framework**:\n 1. Identify monomer building blocks.\n 2. Identify cellular and anatomical locations.\n 3. Provide structural and functional examples.\n 4. Detail cellular and physiological functions (e.g., energy nutrient, structural identity markers, blood typing markers).\n\n# Carbohydrate Classification and Monosaccharide Isomers\n\n* **Carbohydrate Overview**:\n * Macromolecule family encompassing single sugars, double sugars, complex starches (ingested by humans), and structural cellulose.\n * Classified fundamentally according to molecular chain length and size.\n* **Monosaccharides (Single Sugars)**:\n * Monosaccharides serve as the monomer building blocks for all carbohydrate polymers.\n * *Etymology*: *Saccharide* means sugar.\n * *Historical Note*: Saccharin was a synthetic artificial sweetener popular in the 1970s and 1980s (used in diet sodas like Tab) that was later removed from major markets due to carcinogenic concerns.\n * **Hexose Sugars**:\n * Monosaccharides containing exactly 6 carbon atoms organized in a ring structure.\n * *The Three Primary Hexoses*: Glucose, Galactose, and Fructose.\n * *Chemical Formula*: All three hexoses share the identical molecular formula of \text{C}_6\text{H}{12}\text{O}6\n * *Isomerism*: Because Glucose, Galactose, and Fructose share identical molecular formulas (\text{C}_6\text{H}{12}\text{O}_6) but possess different spatial arrangements of their constituent atoms, they are chemical **isomers** of one another.\n * **Pentose Sugars**:\n * Monosaccharides containing exactly 5$$ carbon atoms.

    • Key Examples: Deoxyribose and Ribose (which form the structural backbone of nucleic acids DNA and RNA).

• Disaccharides (Double Sugars):

  • Structures formed when two single monosaccharides are covalently bound together via dehydration synthesis.

• Polysaccharides:

  • Complex long chains consisting of three or more monosaccharides covalently linked together (typically composed of long branched glucose chains).