Organic and Inorganic Biochemistry and the Cell

Overview of Biochemistry and Chemical Classification

• Biochemistry is defined as the scientific study of the chemical composition and reactions occurring within living matter.

• All chemical substances found in the body are classified as either inorganic compounds or organic compounds:

  • Inorganic compounds:

  • Include water, salts, and numerous acids and bases.

  • Do not contain carbon atoms (with minor exceptions such as carbon dioxide and carbon monoxide).

  • Organic compounds:

  • Include carbohydrates, lipids (fats), proteins, and nucleic acids.

  • Contain carbon, are typically large molecules, and are joined by covalent bonds.

• Both organic and inorganic compounds are equally essential for maintaining biological life.

Inorganic Compounds: Water and Its Vital Properties

• Water is the most abundant inorganic compound in living organisms, accounting for $60\%$ to $80\%$ of the total volume of living cells.

• It is considered the most important inorganic compound due to its distinct physicochemical properties:

  • High heat capacity:

  • Has the ability to absorb and release large amounts of heat with minimal change in its own temperature.

  • Serves to prevent sudden, drastic fluctuations in body temperature caused by environmental changes or metabolic activity.

  • High heat of vaporization:

  • The transition from liquid to gas (evaporation) requires the absorption of large quantities of heat.

  • Acts as an effective cooling mechanism for the body (e.g., thermal regulation via perspiration).

  • Reactivity:

  • Possesses a high chemical impulse to participate directly in metabolic reactions.

  • Serves as an essential reactant in hydrolysis (breakdown) and dehydration synthesis (building) reactions.

  • Cushioning:

  • Physical fluid buffer that protects soft internal organs from physical trauma and mechanical shock.

  • Example: Cerebrospinal fluid cushions delicate central nervous system organs such as the brain and spinal cord.

  • Polar solvent properties:

  • Function as a universal solvent that dissolves and dissociates ionic compounds.

  • Forms hydration layers (layers of water molecules) around large, charged biological molecules such as proteins, preventing them from settling out of solution.

  • Acts as the body's primary transport medium for nutrients, gases, and metabolic waste products.

Inorganic Compounds: Salts and Electrolytes

• Salts are ionic compounds that dissociate into their constituent ions when dissolved in water.

• Upon dissociation, they separate into:

  • Cations: Positively charged ions.

  • Anions: Negatively charged ions.

  • Note: Ions do not include hydrogen ions ($H^+$) or hydroxyl ions ($OH^-$).

• All dissociated ions are termed electrolytes because they are capable of conducting electrical currents in aqueous solution.

• Electrolyte ions fulfill specialized physiological functions throughout the body:

  • Major examples include sodium ($Na^+$), potassium ($K^+$), calcium ($Ca^{2+}$), and iron ($Fe$).

  • Common physiological salts include sodium chloride ($NaCl$), calcium carbonate ($CaCO_3$), potassium chloride ($KCl$), and calcium phosphates.

• Precise ionic balance across fluid compartments is vital for maintaining homeostasis.

Inorganic Compounds: Acids, Bases, and the pH Scale

• Both acids and bases are electrolytes that ionize and dissociate in water.

• Acids:

  • Defined as proton donors; they release hydrogen ions ($H^+$) into solution.

  • A hydrogen ion ($H^+$) is a bare proton lacking electrons.

  • Key physiological acids include:

  • Hydrochloric acid ($HCl$)

  • Acetic acid ($HC_2H_3O_2$, abbreviated as $HAc$)

  • Carbonic acid ($H_2CO_3$)

• Bases:

  • Defined as proton acceptors; they take up hydrogen ions ($H^+$) from solution.

  • When dissolved in water, bases typically release a hydroxyl ion ($OH^-$).

  • Key physiological bases include:

  • Bicarbonate ion ($HCO_3^-$)

  • Ammonia ($NH_3$)

• Concept of pH:

  • pH is a measure of the acid-base concentration, specifically representing the hydrogen ion concentration ($[H^+]$) of a solution.

  • The higher the concentration of hydrogen ions ($[H^+]$), the more acidic the solution.

  • Mathematical formula for pH:     $\text{pH} = -\log_{10}([H^+])$

  • Expressed in units of moles per liter ($M$), ranging from $0$ to $14$.

  • The pH scale is logarithmic; each whole pH unit shift represents a $10$--fold change in hydrogen ion concentration.

  • Example: A solution with a pH of $5$ is $10$ times more acidic than a solution with a pH of $6$.

  • Biological enzymes operate strictly within a very narrow pH range.

• Solution Classifications:

  • Acidic solutions:

  • Possess high $[H^+]$ and a low pH.

  • Acidic pH range: $0$ to $6.99$

  • Neutral solutions:

  • Possess equal numbers of $H^+$ and $OH^-$ ions.

  • Neutral pH value: Exactly $7$

  • Pure water is neutral, with a pH of $7$ where $[H^+] = 10^{-7}\,M$

  • Alkaline (Basic) solutions:

  • Possess low $[H^+]$ and a high pH.

  • Alkaline pH range: $7.01$ to $14$

Chemical Buffer Systems and Neutralization

• Neutralization Reactions:

  • Occurs when acids and bases are mixed together.

  • Displacement reactions take place to form water and a neutral salt:     $\text{Base} + \text{Acid} \rightarrow \text{Salt} + \text{Water}$

• Buffers:

  • Chemical systems composed of a combination of a weak acid and a weak base.

  • Function to resist abrupt and significant fluctuations in body fluid pH.

  • Dynamic Mechanism:

  • Release hydrogen ions ($H^+$) if the pH rises (when solution becomes too basic / fewer protons).

  • Bind hydrogen ions ($H^+$) if the pH falls (when solution becomes too acidic / excess protons).

  • Convert strong acids or strong bases (which dissociate completely) into weak acids or weak bases (which dissociate only slightly).

  • Carbonic Acid--Bicarbonate Buffer System:

  • Essential buffer system responsible for maintaining blood pH stability:       $H_2CO_3 \rightleftharpoons HCO_3^- + H^+$

  • Carbonic acid ($H_2CO_3$) acts as the weak acid (proton donor).

  • Bicarbonate ion ($HCO_3^-$) acts as the weak base (proton acceptor).

Organic Compounds: Carbon Chemistry, Polymerization, and Reactions

• Carbon Properties:

  • Organic molecules always contain carbon (exceptions include inorganic $CO_2$ and $CO$).

  • Carbon is electroneutral; it shares electrons rather than gaining or losing them.

  • Forms four covalent bonds with other elements, allowing complex structural branching unique to living systems.

• Polymerization:

  • Major classes: Carbohydrates, lipids, proteins, and nucleic acids.

  • Many organic molecules are polymers, which are long chains composed of repeating structural units called monomers (building blocks).

• Synthesis and Breakdown Reactions:

  • Dehydration Synthesis:

  • Process by which monomers are covalently linked together to form polymers.

  • Occurs via the removal of a hydroxyl group ($-OH$) from one monomer and a hydrogen atom ($-H$) from the adjacent monomer at the bond site, producing a water molecule ($H_2O$).

  • Hydrolysis:

  • Process by which polymers are cleaved into individual monomers.

  • Occurs via the addition of a water molecule ($H_2O$), which breaks the covalent bond by adding a hydroxyl group ($-OH$) to one monomer and a hydrogen atom ($-H$) to the other.

Carbohydrates: Structures, Monomers, and Polymers

• Carbohydrates comprise sugars and starches containing carbon ($C$), hydrogen ($H$), and oxygen ($O$).

  • Hydrogen and oxygen exist in a strictly maintained $2:1$ ratio.

  • Carbon and oxygen atom counts are frequently equal.

• Three Major Structural Classes:

  • Monosaccharides:

  • Single sugar molecules representing the fundamental monomers of carbohydrates.

  • Pentose sugars (5-carbon sugars):

    • Ribose

    • Deoxyribose

  • Hexose sugars (6-carbon sugars, general formula $C_6H_{12}O_6$):

    • Glucose (primary blood sugar)

    • Fructose

    • Galactose

  • Disaccharides:

  • Double sugars formed when two monosaccharides combine via dehydration synthesis.

  • Equations of formation:       $\text{Glucose} + \text{Fructose} \rightarrow \text{Sucrose} + H_2O$

  • Too large to pass passively through cell membranes.

  • Key examples: Sucrose, maltose, and lactose.

  • Polysaccharides:

  • Long polymers consisting of many linked monosaccharides formed by repeated dehydration synthesis reactions.

  • Possess low solubility in water.

  • Key examples:

    • Starch: Primary carbohydrate storage polymer utilized by plants.

    • Glycogen: Primary carbohydrate storage polymer utilized by animals.

Lipids: Triglycerides, Phospholipids, Steroids, and Eicosanoids

• Lipids contain carbon ($C$), hydrogen ($H$), and oxygen ($O$), but with significantly lower oxygen proportions relative to carbohydrates; some also contain phosphorus ($P$).

• Lipids are insoluble in water (hydrophobic).

• Four Primary Classes of Lipids:

  • Triglycerides:

  • Termed fats when solid at room temperature and oils when liquid at room temperature.

  • Composed of three fatty acid chains attached to a single glycerol backbone molecule via dehydration synthesis.

  • Primary physiological functions: High-density energy storage, thermal insulation, and mechanical protection.

  • Saturated Fatty Acids:

    • Contain only single covalent bonds between carbon atoms ($C-C$).

    • Saturated with the maximum possible number of hydrogen atoms.

    • Form straight, linear molecular structures that pack closely together, making them solid at room temperature (e.g., animal fats, butter).

    • High dietary intake is linked to the development of atherosclerosis.

  • Unsaturated Fatty Acids:

    • Contain one or more double covalent bonds between carbon atoms ($C=C$).

    • Possess a reduced number of hydrogen atoms.

    • Carbon double bonds introduce structural kinks that prevent tight molecular packing, rendering them liquid at room temperature (e.g., plant oils such as olive oil).

    • Trans fats: Industrially modified unsaturated oils altered to structurally resemble saturated fats; considered highly unhealthy.

    • Omega-3 fatty acids: Naturally occurring unsaturated fats providing significant biological benefits for metabolic, cerebral, and cardiovascular health.

  • Phospholipids:

  • Structurally modified triglycerides consisting of a glycerol molecule bound to two fatty acid tails and a charged phosphorus-containing head group.

  • Possess amphipathic properties:

    • Head: Polar and hydrophilic (attracted to water).

    • Tails: Nonpolar and hydrophobic (repelled by water).

  • Essential structural component forming cellular membranes.

  • Steroids:

  • Molecules constructed from four interlocking hydrocarbon ring structures.

  • Cholesterol is the most important bodily steroid:

    • Endogenously synthesized by the liver and ingested via animal diet sources (e.g., cheese, eggs, meat).

    • Acts as a critical structural component of cell membranes.

    • Serves as the precursor molecule for the synthesis of vitamin D, steroid hormones, and bile salts.

  • Eicosanoids:

  • Signaling lipids derived from arachidonic acid, a $20$--carbon fatty acid component of cell membranes.

  • Prostaglandins represent the premier eicosanoid subcategory:

    • Regulate physiological processes including blood clotting, blood pressure regulation, inflammatory responses, and labor contractions during childbirth.

    • Inflammatory actions of prostaglandins are therapeutically inhibited by non-steroidal anti-inflammatory drugs (NSAIDs, such as aspirin or ibuprofen).

Discussion Questions and Analytical Exercises

• Exercise 1: Lipid Solubilization and Solvent Polarity

  • Scenario: In a hurry one day, a person merely rinses a salad bowl with water. While drying the bowl, an oily residue from the dressing remains on the surface.

  • Mechanism / Explanation: Water is a polar solvent, whereas the oils in salad dressing are nonpolar lipid molecules. Polar solvents dissolve polar and ionic compounds through electrostatic interactions, but cannot dissolve nonpolar, hydrophobic substances. Because water molecules prefer to interact with each other rather than nonpolar hydrocarbon chains, water alone cannot solubilize or remove the oily film.

• Exercise 2: Quantitative pH Scale Calculations

  • Scenario: Lemon juice has a pH of $2$, and orange juice has a pH of $4$.

  • Question: Which substance is more acidic, and by what factor?

  • Calculation / Explanation:

  • Lemon juice (pH $2$) is more acidic than orange juice (pH $4$).

  • Because the pH scale is logarithmic ($\text{pH} = -\log_{10}([H^+])$), each single pH unit difference represents a $10$--fold change in hydrogen ion concentration ($[H^+]$).

  • The numerical difference between pH $2$ and pH $4$ is $4 - 2 = 2$ units.

  • Factor calculation:       $10^2 = 100$

  • Therefore, lemon juice contains $100$ times (a hundred-fold) more hydrogen ions ($[H^+]$) than orange juice.

• Exercise 3: Chemical Stoichiometry of Disaccharide Synthesis

  • Scenario: The disaccharide maltose is synthesized by joining two glucose monosaccharides (hexose sugars) together.

  • Question: How many total atoms of carbon, hydrogen, and oxygen are contained in a single maltose molecule?

  • Calculation / Explanation:

  • A hexose sugar monomer such as glucose has the empirical molecular formula $C_6H_{12}O_6$.

  • Combining two glucose molecules before reaction yields:       $2 \times (C_6H_{12}O_6) = C_{12}H_{24}O_{12}$

  • Disaccharide formation requires a dehydration synthesis reaction, which removes one water molecule ($H_2O$) to establish a glycosidic bond:       $2\,C_6H_{12}O_6 - H_2O \rightarrow C_{12}H_{22}O_{11}$

  • Atom count breakdown for maltose:

    • Carbon ($C$): $12$ atoms

    • Hydrogen ($H$): $22$ atoms

    • Oxygen ($O$): $11$ atoms