Comprehensive Notes: Inorganic Molecules, Biomolecules, and Metabolism

Electrolytes and Electrical Charge

• Inorganic portions of the body include water, oxygen, carbon dioxide, and electrolytes (ions).

• Electrolytes are ions that carry an electrical charge in the body.

• Electrical charges in the body can be carried by:

  • Positive ions (cations) flowing

  • Negative ions (anions) flowing

  • Electrons flowing (in certain contexts)

• Concept of electrical conduction in the body demonstrated with a simple energy stick and a closed circuit:

  • A closed circuit is a circle that allows electrons to flow from one point back to itself.

  • Conduction means that charges can pass through a material.

  • In the body, conduction can occur through tissues and fluids, especially water.

• Experimental thought: if a finger is dipped in water and touches a circuit, conduction still occurs because water conducts.

• Sodium chloride (table salt) in water dissociates into Na⁺ and Cl⁻ because water is polar and attracts the charges, enabling electrical conduction.

• Summary: electrolytes release ions that carry electrical charges in water and enable conduction in biological systems.

Acids, Bases, and pH

• Acids: substances that release hydrogen ions (H⁺) into solution.

• Bases: substances that release hydroxide ions (OH⁻) or that accept H⁺; e.g., potassium hydroxide releases K⁺ and OH⁻.

• The pH scale measures hydrogen ion concentration; it runs from 0 to 14 and is a log scale: every unit change represents a tenfold change in [H⁺].

• Neutral pH is 7; higher than 7 is basic/alkaline; lower than 7 is acidic.

• Examples (from lecture):

  • Pure water: neutral (~7)

  • Milk: acidic

  • Rainwater: acidic

  • Tomatoes: ~4.5

  • Lemon: ~2.3

  • Stomach acid: ~1.5

  • Baking soda (NaHCO₃): ~8.3

  • Antacids: ~10.5

  • Easy Off oven cleaner: ~13.5

• Key relationship: as pH decreases, the solution becomes more acidic (more H⁺); as pH increases, more basic (more OH⁻).

• Important equation (pH concept):

  • $\text{pH} = -\log_{10}[H^+]$

  • A difference of 1 pH unit corresponds to a 10-fold change in hydrogen ion concentration:

  • $\frac{[H^+]<em>2}{[H^+]</em>1} = 10^{\text{pH}<em>1 - \text{pH}</em>2}$

• Relationship between H⁺ and OH⁻ is governed by water and buffering; extremely high or low H⁺/OH⁻ concentrations disrupt bonding in biomolecules.

• Acid and base definitions:

  • Acid: releases H⁺ into solution.

  • Base: releases OH⁻ or accepts H⁺.

  • Salt (e.g., KCl): formed from a metal cation and a nonmetal anion; not inherently an acid or base.

Buffers and the Carbonic-Acid–Bicarbonate System

• Buffers are substances that resist pH changes by:

  • Accepting hydrogen ions when there are excess H⁺

  • Donating hydrogen ions when they are depleted

• Buffers help convert strong acids/bases into weaker acids/bases, thereby stabilizing pH.

• Prime buffer system in the blood: the bicarbonate system with carbon dioxide (CO₂) and water forming carbonic acid (H₂CO₃) and bicarbonate (HCO₃⁻):

  • $\text{CO}<em>2 + \text{H}</em>2\text{O} \leftrightarrow \text{H}<em>2\text{CO}</em>3 \leftrightarrow \text{H}^+ + \text{HCO}_3^-$

• Role of lungs: exhale CO₂ to reduce carbonic acid and lower acidity; multiple routes for managing blood pH, but the bicarbonate system is prime.

• In summary, buffers maintain pH and prevent drastic shifts that could disrupt biochemical processes.

Anabolism and Catabolism

• Anabolism: building larger molecules from smaller units (monomers → polymers) using energy and water; energy stored in chemical bonds (ATP).

• Monomer and polymer concepts:

  • Monomer: basic building block (e.g., amino acids, simple sugars).

  • Polymer: long chain of monomers linked together.

• Dehydration synthesis (condensation): joins monomers by removing water; forms covalent bonds and stores energy in the new bonds.

  • General form: $\text{Monomer-}OH + \text{Monomer-}H \rightarrow \text{Polymer} + \text{H}_2\text{O}$

  • Example from lecture: A–OH + B–H → AB + H₂O

• Hydrolysis: breaks bonds by adding water; releases energy and monomers can be used elsewhere.

  • General form: $\text{Polymer} + \text{H}_2\text{O} \rightarrow \text{Monomer-}OH + \text{Monomer-}H$

• Catabolism: the breakdown of polymers into smaller units; releases energy.

• ATP as cellular energy currency: energy from food is stored as ATP; used to power reactions.

• Summary: all major biomolecules (carbohydrates, proteins, fats, nucleic acids) are built or broken down via dehydration synthesis or hydrolysis, with ATP providing the energy currency for many reactions.

Carbohydrates

• Function: provide cellular energy.

• General composition: carbon, hydrogen, oxygen with a characteristic pattern: typically

  • twice as many hydrogen atoms as oxygen atoms in the formula, i.e., C:H:O ≈ 1:2:1 for many simple sugars.

  • Example formula: $\mathrm{C<em>6H</em>{12}O_6}$

• Monosaccharides (monomers): glucose, fructose, galactose, ribose, and deoxyribose.

• Ring vs linear form: glucose can polymerize in water and form a ring structure used to simplify drawing; ring representation often used in diagrams.

• Structural isomers:

  • Glucose vs fructose share the same empirical formula (C₆H₁₂O₆) but differ in structure (glucose typically in a hexose ring; fructose is a ketohexose with a different arrangement).

  • Five-carbon sugars: ribose and deoxyribose (deoxyribose lacks one oxygen compared to ribose).

• Disaccharides (two monosaccharides):

  • Sucrose = glucose + fructose

  • Maltose = glucose + glucose

  • Lactose = galactose + glucose

• Polysaccharides: multiple sugars linked by dehydration synthesis; used for energy storage or structural roles.

• How they form/break down:

  • Dehydration synthesis builds polysaccharides by linking monosaccharides; each bond formation releases water.

  • Hydrolysis breaks polysaccharides into monosaccharides by adding water.

• Relevance for DNA/RNA: ribose vs deoxyribose in nucleic acids are influenced by which sugar is present.

Lipids

• General properties: nonpolar, largely insoluble in water; lipids are hydrophobic and play roles in energy storage, membranes, and signaling.

• Major types:

  • Triglycerides (fats): energy storage and structure; glycerol backbone with three fatty acids.

  • Phospholipids: glycerol backbone with two fatty acids and a phosphate-containing head; amphipathic (hydrophobic tails, hydrophilic head); essential for cell membranes.

  • Steroids: based on cholesterol with four-ring structure; precursors to steroid hormones (e.g., testosterone and estrogen).

• Fatty acids:

  • Saturated: all carbon–carbon bonds are single; straight chains; typically solid at room temperature.

  • Unsaturated: contain one or more carbon–carbon double bonds; kinked chains; typically liquid at room temperature.

• Triglyceride structure and derivatives:

  • Fatty acids attached to glycerol form triglycerides when three fatty acids are present.

  • Monoglycerides and diglycerides have one or two fatty acids, respectively.

• Phospholipid structure:

  • Glycerol backbone, two fatty acid tails (hydrophobic), and a phosphate-containing head (hydrophilic and polar).

• Steroids and cholesterol:

  • Cholesterol skeleton forms the four-ring structure; functional groups attached determine its conversion into hormones like testosterone and estrogen.

  • Small structural changes (functional groups) can drastically change biological activity (e.g., gender-determining hormones).

Organic Molecules: Functional Groups and the Role of R Groups

• Functional groups and the R group (side chain) on amino acids determine chemical behavior and reactivity.

• In proteins, nitrogen-containing groups (amino group) and carboxyl group participate in peptide bond formation.

Proteins

• Composition: made of carbon, hydrogen, oxygen, nitrogen; some also contain sulfur.

• Functions: structural (hair, nails, keratin), storage, contractile, transport, enzymes, hormones, receptor signaling, antibodies (defense).

  • Structural proteins: keratin, collagen, elastin, hair, nails, skin.

  • Contractile proteins: muscle fibers.

  • Transport proteins: carry substances in blood and across membranes.

  • Enzymes: catalytic proteins.

  • Hormonal proteins: signaling molecules.

  • Receptor proteins: receive signals.

  • Antibodies: immune defense.

• Building blocks: amino acids.

  • General amino acid structure: central carbon (alpha carbon) with a carboxyl group (COOH), an amino group (NH₂), a hydrogen, and an R group (side chain).

  • Cysteine contains sulfur; phenylalanine has a complex aromatic R group.

  • Humans have 20 standard amino acids.

• Bonding and polymerization:

  • Amino acids polymerize via dehydration synthesis forming peptide bonds (a covalent bond) between the carboxyl carbon of one amino acid and the amino nitrogen of the next.

  • This creates a polypeptide chain; chains can range from ~100 to ~5,000 amino acids.

• Protein structure levels:

  • Primary structure: linear sequence of amino acids linked by peptide bonds (covalent).

  • Secondary structure: local folding stabilized primarily by hydrogen bonds; includes:

  • Alpha helix (spiral)

  • Beta-pleated sheet (crinkle)

  • Tertiary structure: three-dimensional folding stabilized by ionic, covalent, hydrogen bonds, and hydrophobic interactions.

  • Quaternary structure: multiple polypeptide chains (subunits) come together to form a functional protein.

• Types of proteins by morphology:

  • Globular proteins: functional, folded 3D shapes with active sites (e.g., enzymes, antibodies, hormones, molecular chaperones).

  • Fibrous proteins: long strand-like structures (keratin, collagen, elastin, some contractile fibers).

• Protein shape and function:

  • Shape is critical; the same amino acid sequence folded differently may alter function.

  • Denaturation: disruption of protein folding resulting in loss of function.

  • Denaturation can be reversible or irreversible depending on conditions.

  • Causes include pH changes, high temperature, salts, radiation, and other chemicals.

  • Severe or prolonged denaturation can disrupt secondary, tertiary, and even primary structure (primary is covalent bonds; if primary is broken, function cannot be recovered).

• Importance of body temperature: around 98.6°F (37°C) is optimal; fever above ~103°F for long periods can denature proteins.

Enzymes

• Enzymes are biological catalysts that speed up chemical reactions without being consumed.

• Characteristics:

  • Highly specific for substrates; each enzyme acts on a particular substrate (substrate specificity).

  • Active site is the region where the substrate binds; the fit is complementary in shape.

  • Enzyme–substrate complex forms and lowers the activation energy required for the reaction.

  • After the reaction, products are released and the enzyme is free to catalyze more reactions.

• Analogy: a blender (enzyme) makes it easier to break down an onion (substrate) than breaking it by hand; the enzyme reduces energy required to reach the transition state.

• Mechanism:

  • Substrate binds to the active site, forming the enzyme–substrate complex.

  • The reaction occurs, producing products, which are released.

  • The enzyme remains unchanged and can catalyze additional reactions.

• Complexity: enzymes are globular proteins that may require cofactors and coenzymes:

  • Apoenzyme: the protein part without the bound cofactor/coenzyme.

  • Cofactor: typically a metal ion that assists catalysis.

  • Coenzyme: often a vitamin-derived molecule that participates in the reaction.

  • Holoenzyme: the active enzyme comprising apoenzyme + cofactor + coenzyme.

• Consequences: enzymes enable millions of reactions per minute rather than a few per minute.

Nucleic Acids

• Nucleic acids are polymers built from nucleotides (monomers).

  • Each nucleotide consists of a nitrogenous base, a sugar, and a phosphate group.

• Two major types:

  • RNA (ribonucleic acid): ribose sugar; typically single-stranded; roles include mRNA, tRNA, and rRNA.

  • DNA (deoxyribonucleic acid): deoxyribose sugar; typically double-stranded; stores genetic information.

• Bases and pairing:

  • Purines: adenine (A) and guanine (G)

  • Pyrimidines: cytosine (C) and thymine (T) in DNA; uracil (U) in RNA replaces T.

  • Complementary base pairing: A pairs with T (2 hydrogen bonds in DNA); C pairs with G (3 hydrogen bonds in DNA).

  • In RNA: A pairs with U; C pairs with G.

• DNA structure:

  • Double helix with two anti-parallel strands; sugar–phosphate backbone on the outside; bases paired across from each other.

• RNA structure:

  • Usually single-stranded; can fold into complex shapes via intramolecular base pairing; serves as a template and functional molecule.

• Gene and transcription/translation concept:

  • Gene: a segment of double-stranded DNA that codes for a single polypeptide or protein.

  • Transcription: copying the gene into messenger RNA (mRNA) which leaves the nucleus and travels to the cytoplasm.

  • Translation: ribosomes read mRNA to synthesize a polypeptide (protein) guided by codons.

• Nucleotides and energy: Adenosine triphosphate (ATP) is a nucleotide that carries energy due to its three phosphate groups; energy release occurs when phosphates are cleaved:

  • General idea: high-energy phosphate bonds provide energy for cellular work; energy currency in metabolism.

• Summary of DNA/RNA roles:

  • DNA: genetic material, instructions for making proteins.

  • RNA: intermediary (mRNA) and functional roles (tRNA, rRNA) in protein synthesis.

DNA details and RNA overview (recap)

• DNA:

  • Double-stranded, deoxyribose sugar, phosphate backbone, bases A, G, C, T.

  • Complementary base pairing: A with T; C with G.

  • Forms a stable double helix; genetic material in cells.

• RNA:

  • Single-stranded, ribose sugar, bases A, G, C, U.

  • Types: mRNA (messenger RNA) carries genetic information from DNA to ribosomes; tRNA (transfer RNA) brings amino acids to the ribosome; rRNA (ribosomal RNA) forms part of the ribosome's structure.

• Transcription and translation interplay:

  • A gene on DNA is transcribed to mRNA.

  • mRNA leaves the nucleus and is translated by ribosomes into a polypeptide, guided by tRNA and rRNA interactions.

• ATP as a nucleotide energy donor:

  • ATP has three phosphate groups; energy stored in the bonds; removing a phosphate yields ADP and Pi, releasing energy for cellular processes.

Closing: Interconnections and Real-World Relevance

• The energy methods (ATP) link metabolism to all other biomolecules (carbohydrates, fats, proteins).

• Buffer systems (bicarbonate, phosphate) interconnect respiratory and renal systems to maintain pH homeostasis critical for enzyme activity and protein structure.

• Protein structure-function relationship explains how slight changes in environment (pH, temperature) can disrupt enzyme activity and protein stability, affecting metabolism and signaling.

• The lipid bilayer concept (phospholipids with hydrophilic heads and hydrophobic tails) underpins cell membranes and transport functions.

• The complementary base pairing rule ensures faithful transmission of genetic information and accurate protein synthesis.

• Overall, chemistry of life (inorganic ions and molecules, organic macromolecules, and energy currencies) forms the foundation for physiology and medicine.

Quick reference of key formulas and concepts

• pH and hydrogen ion concentration: $\text{pH} = -\log_{10}[H^+]$

• Tenfold change per pH unit: $\frac{[H^+]<em>2}{[H^+]</em>1} = 10^{\text{pH}<em>1 - \text{pH}</em>2}$

• Water dissociation and buffers (carbonic acid–bicarbonate system):

  • $\text{CO}<em>2 + \text{H}</em>2\text{O} \leftrightarrow \text{H}<em>2\text{CO}</em>3 \leftrightarrow \text{H}^+ + \text{HCO}_3^-$

• Dehydration synthesis (example form): $\text{A-OH} + \text{B-H} \rightarrow \text{AB} + \text{H}_2\text{O}$

• Hydrolysis (example form): $\text{AB} + \text{H}_2\text{O} \rightarrow \text{A-OH} + \text{B-H}$

• Carbohydrate formula example: $\mathrm{C<em>6H</em>{12}O_6}$

• Triglyceride structure: glycerol + 3 fatty acids; saturated vs. unsaturated fatty acids (single vs. double bonds)

• Phospholipid structure: glycerol + 2 fatty acids + phosphate-containing head

• Steroid structure: four fused rings (cholesterol base) related to hormone synthesis

• Protein synthesis: amino acids → peptide bonds (dehydration synthesis) → primary structure; folding into secondary (α-helix, β-pleated sheet), tertiary, and quaternary structures; denaturation concepts

• Gene expression: DNA → transcription to mRNA → translation to protein; amino acid sequence determines protein shape and function

• Enzyme concepts: active site, substrate specificity, enzyme–substrate complex, cofactors, coenzymes, holoenzyme vs apoenzyme

• Nucleic acids: bases, sugar, phosphate backbone; DNA double helix; RNA single strand; base-pairing rules (A–T, C–G in DNA; A–U, C–G in RNA)

• ATP as energy currency: three phosphates, energy release upon phosphate removal