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The Chemical Basis of Life - Organic Molecules (Video)

The Chemical Basis of Life

  • Molecules containing carbon are organic; almost all organic compounds associated with life also contain hydrogen atoms. Examples listed include CH4, H2O, C2H6, CaCl2, C6H12O6, CO2, C5H10O5, NaCl.
  • Organic molecules are abundant in living organisms; macromolecules are large, complex organic molecules.
  • Carbon’s versatility:
    • Carbon can form up to 4 covalent bonds because it has 4 electrons in its outer shell and needs 4 more electrons to fill the shell.
    • The number of covalent bonds equals the number of electrons required to complete the valence shell.
    • Bonds can be single or double covalent bonds.
  • Polarity and solubility:
    • Molecules with nonpolar bonds (e.g., hydrocarbons) are poorly water soluble.
    • Molecules with polar bonds are more water soluble.
    • Carbon can form both nonpolar and polar bonds (e.g., propionic acid demonstrates polar groups).
  • Hydrocarbons:
    • Organic molecules with a high proportion of C–H bonds.
    • Many organic molecules (e.g., fats) have hydrocarbon components.
    • Hydrocarbons can release a large amount of energy when broken/oxidized.
    • Question: Are C–H bonds polar or nonpolar? They are generally nonpolar (hydrophobic).
  • Functional groups:
    • Chemical groups that replace one or more hydrogens on a carbon skeleton.
    • Functional groups have special chemical features and are functionally important.
    • Each type of functional group exhibits the same properties in all molecules where it occurs.
  • The seven functional groups most important in the chemistry of life (you should be able to identify them in molecules):
    • hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl groups (typical lifecycle in biochemistry courses).
  • Isomers: two molecules with the same molecular formula but different structures and properties.
    • Structural isomers: atoms arranged differently within the molecule (same formula, different bonding relationships).
    • Stereoisomers: identical bonding connections but different spatial arrangement.
    • Cis-trans isomers: around double bonds with different spatial arrangement of substituents.
    • Enantiomers: mirror-image isomers.
  • Biologically relevant examples:
    • D-glucose vs L-glucose (enantiomers).
    • D-alanine vs L-alanine (mirror images with different biological activity).
  • Macromolecules and polymers:
    • Macromolecules are polymers built from monomers.
    • A polymer is a long molecule consisting of many similar building blocks (monomers).
    • Some monomers also have functions of their own.
    • Enzymes facilitate the polymerization and depolymerization reactions, speeding up chemical reactions.
  • Formation of organic molecules and macromolecules:
    • Condensation (dehydration) reactions: links monomers to form polymers; one molecule of water is removed per monomer; catalyzed by enzymes.
    • Hydrolysis reactions: polymers broken down into monomers; one molecule of water is added per monomer released; catalyzed by enzymes.
  • Major macromolecule classes:
    • Four main classes: carbohydrates, lipids, proteins, nucleic acids.
    • For each macromolecule, you should know the monomer, the type of bonds that hold them together, their primary functions, and where in the cell they can be found.

Carbohydrates

  • Roles:
    • Serve as fuel and building material for organisms.
    • Include sugars and the polymers (chains) of sugars.
  • Composition and formula:
    • Composed of carbon, hydrogen, and oxygen.
    • General formula: Cn(H2O)_n
    • Most carbon atoms in carbohydrates are linked to a hydrogen atom and a hydroxyl group (-OH).
  • Monosaccharides:
    • Simplest sugars; commonly pentoses (5 carbons) and hexoses (6 carbons).
    • Glucose is the most common hexose: C6H{12}O_6.
    • Sugars can be depicted in ring or linear forms; many sugars form rings in solution.
  • Glucose isomers:
    • Structural isomers: different arrangement of the same elements (e.g., glucose vs galactose).
    • Stereoisomers: α- and β- glucose (orientation of the hydroxyl group on carbon 1).
    • D- and L- glucose: enantiomers with mirror-image structures.
  • Disaccharides:
    • Two monosaccharides joined by a dehydration (condensation) reaction forming a glycosidic bond; hydrolyzed back to monosaccharides.
    • Examples:
    • Sucrose = glucose + fructose
    • Lactose = galactose + glucose
    • Maltose = glucose + glucose
  • Polysaccharides:
    • Many monosaccharides linked to form long polymers; structure and function depend on sugar monomers and glycosidic bond positions.
    • Energy storage: starch (plants) and glycogen (animals).
    • Structural: cellulose (plants), chitin (exoskeletons), glycosaminoglycans (cartilage), peptidoglycan (bacteria cell walls).
    • Examples of linkages:
    • a-1,4-glycosidic linkages in linear chains (e.g., starch).
    • a-1,6-glycosidic linkages create branching (glycogen, some starch).
    • β-1,4-glycosidic linkages in cellulose form long, unbranched chains.
    • Plant vs animal: starch is storage in plants; glycogen is storage in animals; cellulose and chitin provide structural support.
  • Visual/structural notes:
    • Glycogen granules are visible in cells (e.g., in cardiac muscle).
    • Structural variation (branching) influences digestibility and storage efficiency.

Lipids

  • General properties:
    • A diverse group of hydrophobic molecules composed predominantly of carbon and hydrogen.
    • Nonpolar and thus largely insoluble in water.
    • Include fats, phospholipids, steroids, and waxes.
    • Lipids account for about 40% of the organic matter in the human body.
  • Fats (triacylglycerols):
    • Constructed from glycerol and three fatty acids.
    • Fatty acid: carboxyl group attached to a long hydrocarbon tail.
    • Formation via dehydration reactions; three ester bonds form with three water molecules released:
    • ext{Glycerol} + 3 ext{ Fatty Acids}
      ightarrow ext{Triacylglycerol} + 3 H_2O
    • Fatty acids vary by length (carbon number) and by the number/location of double bonds.
    • Saturated fats: all C–C bonds are single; typically solid at room temperature.
    • Unsaturated fats: contain one or more C=C double bonds; typically liquid at room temperature (oils).
    • Cis forms occur naturally; trans fats are formed artificially and are linked to disease.
    • Dietary note: fats store more energy per gram than glycogen or starch.
    • Structural role: fats provide cushioning and insulation beyond energy storage.
  • Phospholipids:
    • Two fatty acids and a phosphate group attached to glycerol.
    • Amphipathic: hydrophobic tails and hydrophilic head.
    • Major constituents of cell membranes; form a phospholipid bilayer that acts as a boundary between aqueous compartments.
  • Steroids:
    • Lipids with four fused carbon rings.
    • Generally insoluble in water.
    • Example: cholesterol.
    • Small structural changes can lead to very different biological properties (e.g., estrogen vs. testosterone).

Proteins

  • Overview:
    • Proteins display a wide range of structures and functions.
    • Composed of carbon, hydrogen, oxygen, nitrogen, and smaller amounts of sulfur.
    • Amino acids are the monomers.
    • 20 standard amino acids with side chains (R groups) determine each amino acid’s properties and how it influences protein structure and function.
  • Amino acids:
    • Core structure includes an amino group, a carboxyl group, a central (α) carbon, and a variable side chain (R).
    • The α-carbon is chiral for all except glycine.
    • The slide lists examples and key properties (polar, nonpolar, charged groups).
  • Polypeptides:
    • Amino acids are joined by dehydration reactions forming peptide bonds.
    • A polypeptide ranges from a few to more than a thousand monomers.
    • Proteins may consist of a single polypeptide or multiple polypeptides.
    • Hydrolysis can break polypeptides back into amino acids.
  • Protein structure levels:
    • Primary structure: linear sequence of amino acids; ends are the N-terminus (amino end) and C-terminus (carboxyl end).
    • Secondary structure: local folding due to hydrogen bonds between the carbonyl (C=O) and amino (N–H) groups; typical forms include alpha helices and beta sheets.
    • Tertiary structure: three-dimensional folding driven by interactions among R groups (electrostatic, hydrogen bonding, Van der Waals, hydrophobic effects).
    • Quaternary structure: assembly of two or more polypeptide chains into a functional protein; can be identical or different subunits.
  • Stability and folding factors:
    • Hydrogen bonds, ionic/polar interactions, hydrophobic effects, Van der Waals forces, and disulfide bridges contribute to proper folding and stability.
  • Protein-protein interactions:
    • Many cellular processes rely on specific interactions between proteins; binding involves the same noncovalent forces that stabilize folded structures.
  • Functional implications:
    • Protein structure determines function; misfolding or mutations can lead to loss of function or disease.

Nucleic Acids

  • Functions:
    • DNA stores and transmits hereditary information.
    • RNA decodes DNA into instructions for linking amino acids to form polypeptides; also participates in regulation and catalysis in some contexts.
  • Monomers: nucleotides.
  • Components of a nucleotide:
    • A five-carbon sugar (deoxyribose in DNA, ribose in RNA).
    • A nitrogenous base (A, T, C, G in DNA; A, U, C, G in RNA).
    • One or more phosphate groups.
  • Backbone and bonding:
    • Nucleotides are joined by phosphodiester bonds, forming a sugar-phosphate backbone.
    • The dehydration reaction creates the linkage; this backbone provides structural stability to nucleic acids.
    • The bond is a phosphodiester bond.
  • Structures:
    • DNA: two polynucleotides spiraling around an axis to form a double helix.
    • RNA: typically single-stranded.
    • Complementary base pairing:
    • In DNA: A pairs with T; G pairs with C.
    • In RNA: A pairs with U (not T).
    • Complementary pairing can occur between two RNA molecules or within a single molecule (folding).
  • Orientation and forms:
    • DNA has 5' to 3' ends on both strands in antiparallel orientation.
    • RNA is generally single-stranded and can fold into complex shapes.
  • The slide also references tRNA (transfer RNA) as an RNA form involved in translating mRNA into amino acids during protein synthesis.

Key formulas, notations, and concise references

  • General carbohydrate formula: Cn(H2O)_n
  • Glucose: C6H{12}O_6
  • Condensation (dehydration) joining of two monomers: ext{Monomer} + ext{Monomer}
    ightarrow ext{Polymer} + H_2O
  • Dehydration in triglyceride formation: ext{Glycerol} + 3 ext{Fatty Acids}
    ightarrow ext{Triacylglycerol} + 3 H_2O
  • Fatty acid relationships:
    • Saturated: only single C–C bonds; tend to be solid at room temperature.
    • Unsaturated: one or more C=C bonds; tend to be liquid at room temperature; cis forms natural, trans forms can be artificially produced.
  • Phospholipid backbone: glycerol + 2 fatty acids + phosphate group; forms bilayer membranes due to amphipathic nature.
  • Peptide bond: formed by dehydration between the carboxyl of one amino acid and the amino group of the next; type of bond is a peptide bond; polymers are polypeptides.
  • Nucleotides and nucleic acids:
    • Phosphodiester bonds connect nucleotides into a sugar-phosphate backbone.
    • DNA base pairing rules: A-T, ext{ } G-C; RNA base pairing rules: A-U, ext{ } G-C.

Connections to foundational principles and real-world relevance

  • The chemical basis of life hinges on carbon’s versatility to form diverse, stable, energy-rich molecules used for structure, metabolism, information storage, and signaling.
  • Understanding functional groups helps explain reactivity and the behavior of biomolecules across different environments (e.g., aqueous cellular compartments).
  • The distinction between polar and nonpolar bonds underpins solubility, membrane formation, and transport of nutrients.
  • Isomerism (structural, stereochemical, and enantiomeric) has profound biological implications, influencing enzyme specificity, receptor binding, and metabolism.
  • The condensation and hydrolysis reactions explain how macromolecules are built and recycled, tying into metabolism and enzyme function.
  • The four major macromolecule classes together cover every major cellular function: energy storage (carbohydrates and lipids), information storage/transfer (nucleic acids), catalysis and structure (proteins).
  • The architecture of macromolecules (primary to quaternary structure in proteins; DNA/RNA tertiary structures; carbohydrate branching patterns) directly influences function, regulation, and interaction networks in cells.
  • Real-world relevance includes nutrition (carb and fat metabolism), cellular membranes (lipids), genetic information flow (DNA/RNA), and disease implications stemming from protein misfolding or cholesterol balance.