Biomolecules and Macromolecules (2.4-2.6)

Carbon and the Chemistry of Life

• Carbon is central to life because of its unique bonding capabilities: tetravalent and capable of forming diverse structures (chains, branches, rings) that serve as backbones for complex biomolecules.

• Carbon forms single, double, and triple bonds and can bond with other carbons and heteroatoms to create a vast array of molecules.

• Example of carbon compound: methane with chemical formula $CH_4$.

• Structural arrangement example: tetrahedral geometry around carbon in methane.

• The molecular orbitals of methane orient toward four corners of a tetrahedron, enabling diverse bonding patterns.

Macromolecules: Overview

• The major macromolecules are carbohydrates, lipids, proteins, and nucleic acids.

• These carbon-based polymers are built from monomers linked by covalent bonds (e.g., peptide bonds in proteins, phosphodiester bonds in nucleic acids).

• Functional groups provide chemical character and reactivity to biomolecules.

• Biomolecules can originate from inorganic precursors via environmental processes (e.g., Miller–Urey experiments). Evidence suggests organic molecules can arise from inorganic components under early Earth-like conditions.

Vocab and Key Terms (selected)

• Organic molecule, isomer, polymer, monomer, functional group

• Carbohydrate, Lipid, Protein, Nucleic acid

• Monosaccharide, Polysaccharide, Saccharide

• Amino acid, Nucleotide, Sugar

• Amino group ($-NH_2$), Carboxyl group ($-COOH$), R group (side chain)

• Glycosidic bond, Peptide bond, Phosphodiester bond

• Nucleotide base: Pyrimidines (Cytosine C, Thymine T, Uracil U); Purines (Guanine G, Adenine A)

• Double helix, Complementary base pairing

• Lipids: Triacylglycerol, Fatty acid, Glycerol, Saturated, Unsaturated, Trans fats

• Other lipids: Steroid, Phospholipid

Carbon Structures: Length, Branching, Rings, and Multiple Bonds

• Carbon skeletons vary by:

  • Length (number of carbon atoms)

  • Position of double bonds

  • Branching (branched vs unbranched)

  • Presence of ring structures

• Examples:

  • Ethane ( C₂H₆ ) vs Propane ( C₃H₈ )

  • 1-Butene and 2-Butene differ in double-bond position

  • Cyclohexane (ring) and Benzene (aromatic ring)

  • Butane (no rings) vs 2-Methylpropane (isobutane, branched)

• Concept: Constitutional isomers share the same molecular formula but have different structures.

Constitutional Isomers in Biology and Medicine

• Isomer examples: Isoleucine vs Leucine share the same formula, e.g., $ext{C}<em>6 ext{H}</em>{13} ext{NO}_2$ but differ in structure.

• In medicinal chemistry: Enflurane vs Isoflurane are constitutional isomers with the same formula (differences in halogenated ethyl groups) and different pharmacological profiles.

• Enflurane (older inhaled anesthetic) was associated with adverse effects (convulsions, kidney damage) and was largely replaced by Isoflurane.

Biomolecules (Overview)

• Life’s macromolecules are carbon-based chains with functional groups that confer chemical properties and reactivity.

• Major classes: Carbohydrates, Lipids, Proteins, Nucleic Acids.

• The Amoeba Sisters (educational video) summarizes these concepts conceptually.

Carbohydrates

• Monosaccharides: simplest sugars; often exist in ring form in aqueous solutions.

• Common monosaccharide: Glucose (most common, energy source).

• Chemical formula: $C<em>6H</em>{12}O_6$

• Functional groups in monosaccharides: Aldehyde group (aldoses) or Ketone group (ketoses) and multiple hydroxyl groups.

• Example structure of glucose shows multiple hydroxyl groups and an aldehyde or hemiacetal form in ring structures.

• Polysaccharides: storage (starch in plants; glycogen in animals) and structural (cellulose in plants).

  • Amylose: unbranched component of starch

  • Amylopectin: branched component of starch

  • Glycogen: highly branched storage in animals

  • Cellulose: unbranched polymer forming plant cell walls; hydrogen bonds stabilize microfibrils

• Storage granules: starch granules in potato cells; glycogen granules in muscle tissue

Storage and Structural Polysaccharides (Plants and Animals)

• Amylose (unbranched) and Amylopectin (branched) are forms of starch used for energy storage in plants.

• Glycogen is the animal storage polysaccharide, highly branched for rapid mobilization.

• Cellulose forms plant cell walls; cellulose molecules are unbranched and form strong microfibrils via hydrogen bonding.

• Hydrogen bonds contribute to the high strength and rigidity of cellulose fibers.

Proteins: Structure and Function

• Proteins account for a large fraction of cell mass and perform diverse functions:

  • Enzymatic proteins: act as catalysts; example: digestive enzymes hydrolyze bonds in food molecules.

  • Defensive proteins: antibodies that inactivate/destroy viruses and bacteria.

  • Storage proteins: Casein (milk) provides amino acids for offspring; ovalbumin (egg white) as a nutrient source.

  • Transport proteins: Hemoglobin transports oxygen; transport across membranes.

  • Hormonal proteins: Insulin coordinates glucose uptake and blood sugar regulation.

  • Receptor proteins: respond to chemical stimuli (e.g., nerve cell receptors).

  • Contractile and motor proteins: Actin and myosin enable muscle contraction and ciliary/flagellar movement.

  • Structural proteins: Keratin (hair, nails), collagen and elastin in connective tissues; silk fibers in insects/spiders.

• Protein composition:

  • Proteins are polymers of amino acids linked by peptide bonds forming peptide/protein backbones.

  • A protein is a polymer (polypeptide) built from monomers: amino acids linked by peptide bonds.

Amino Acids: Building Blocks of Proteins

• All amino acids share a common structure:

  • An amino group ($-NH_2$) and a carboxyl group ($-COOH$) bonded to a central (alpha) carbon, with a variable side chain (R group).

• Amino acids vary in their chemical properties based on the R group.

• All amino acids are chiral except glycine (often drawn as having a single hydrogen as the side group).

• Classification by side chain properties:

  • Nonpolar (hydrophobic): e.g., Glycine (Gly, G), Alanine (Ala, A), Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I), Methionine (Met, M)

  • Polar, uncharged: e.g., Serine (Ser, S), Threonine (Thr, T), Cysteine (Cys, C), Tyrosine (Tyr, Y), Asparagine (Asn, N), Glutamine (Gln, Q)

  • Electrically charged (polar): Acids (acidic) – Aspartic acid (Asp, D), Glutamic acid (Glu, E); Bases (basic) – Lysine (Lys, K), Arginine (Arg, R), Histidine (His, H)

• Essential amino acids are those that cannot be synthesized by the body and must be supplied by diet; complete proteins contain all nine essential amino acids in sufficient amounts.

• Amino acids can be categorized into three groups: nonpolar, polar uncharged, and charged.

Protein Structure and Peptide Bonds

• Amino acids link via peptide bonds to form polypeptides/proteins.

• A peptide bond links the carboxyl group of one amino acid to the amino group of the next amino acid, releasing a molecule of water (condensation reaction).

• Proteins fold into three-dimensional structures driven by interactions among R groups, including hydrogen bonds, ionic bonds, hydrophobic effects, and disulfide bridges (in cysteine).

Nucleic Acids: DNA and RNA

• Nucleic acids are polymers composed of nucleotides, each consisting of three parts:

  • A sugar (pentose): ribose in RNA, deoxyribose in DNA

  • A phosphate group

  • A nitrogenous base (A, G, C, T, U)

• Nucleotides link via phosphodiester bonds to form polynucleotides (nucleic acids).

• Sugar-phosphate backbone runs along the length of the molecule with bases projecting to the interior (RNA) or forming base pairs (DNA).

• Nucleobases:

  • Pyrimidines: Cytosine (C), Thymine (T, in DNA), Uracil (U, in RNA)

  • Purines: Adenine (A), Guanine (G)

  • Pyrimidines have a single ring; Purines have a double ring.

• Base pairing:

  • DNA: A pairs with T, and C pairs with G (through hydrogen bonds) to form the double helix.

  • RNA: A pairs with U; RNA is typically single-stranded but can form secondary structures via intramolecular base pairing.

DNA vs RNA: Form and Function

• DNA (Deoxyribonucleic acid): carries genetic information; double-stranded, helical structure; sugar is deoxyribose; bases A, G, C, T; base pairing is A-T and C-G via hydrogen bonds; the backbone is formed by alternating sugar and phosphate groups connected by phosphodiester bonds.

• RNA (Ribonucleic acid): single-stranded; sugar is ribose; bases A, G, C, U; functions in transcription, translation, and regulation; can fold into complex three-dimensional structures via intramolecular base pairing.

Lipids: Hydrophobic Biomolecules

• Lipids are hydrophobic or amphipathic molecules that include fats, phospholipids, steroids, and glycolipids.

• Functions: energy storage (fats), membrane structure (phospholipids), signaling (steroids, lipids like prostaglandins).

Fats (Triglycerides)

• Structure: triacylglycerols formed by glycerol backbone linked to three fatty acids via ester bonds (carboxyl groups of fatty acids).

• Components:

  • Glycerol (glycerin) backbone: HO–CH2–CHOH–CH2–OH

  • Three fatty acids: long hydrocarbon chains with a terminal carboxyl group

• Saturation:

  • Saturated fatty acids have no C=C double bonds; chains straight and pack tightly.

  • Unsaturated fatty acids contain one or more C=C double bonds; causes kinks that prevent tight packing.

  • Trans fats are unsaturated fats with trans double bonds; have different physical properties and health effects compared to cis forms.

• Physical interactions: triglycerides stay together in tissues via van der Waals forces between hydrocarbon chains.

• Common fatty acids examples include palmitic acid (saturated) and palmitoleic acid (unsaturated).

Phospholipids and Membranes

• Structure: hydrophilic (polar) head group and hydrophobic (nonpolar) tails; typically a glycerol backbone with two fatty acids and a phosphate-containing head (often with a choline group).

• The phospholipid bilayer forms the fundamental structure of cellular membranes, with a hydrophobic core that acts as a barrier to most polar molecules.

• Membrane composition includes phospholipids, glycolipids, cholesterol, transmembrane (integral) proteins, and membrane-associated proteins (glycoproteins).

Steroids and Cholesterol

• Steroids are lipid molecules composed of four fused carbon rings (sterane skeleton).

• Cholesterol is a steroid important for membrane fluidity and as a precursor for steroid hormones.

• Lipoproteins: LDL (bad cholesterol) stores cholesterol in the bloodstream; HDL (good cholesterol) helps remove cholesterol and promotes excretion.

• Hormones example: Estrogen and Testosterone are steroids derived from cholesterol;

  • Estrogen tends to have protective cardiovascular effects; excessive LDL can contribute to atherosclerosis when cholesterol accumulates in arteries.

Membrane Organization: Lipids, Proteins, and Carbohydrates

• The cell membrane comprises a phospholipid bilayer with embedded proteins and surrounding glycoproteins and glycolipids.

• The arrangement supports selective permeability, signaling, and interactions with the extracellular environment.

Origin of Life: Miller–Urey Experiments

• Demonstrated that organic molecules could arise from inorganic precursors under early Earth-like conditions.

• Experimental setup: water vapor simulated ocean; hydrogen, methane, ammonium (and other gases) fed into a chamber with electric sparks to simulate lightning.

• Products were condensed and analyzed, revealing formation of simple organic molecules and amino acids.

• This supports the hypothesis that life’s building blocks could form abiotically in a reducing atmosphere.

Practical and Ethical/Philosophical Implications

• Understanding the origin of organic molecules informs debates about abiogenesis and the likelihood of life’s emergence elsewhere in the universe.

• The study of biomolecules guides biotechnology, medicine, and nutrition, with ethical considerations around genetic engineering and dietary recommendations.

Important Equations and Formulas (selected)

• Methane: $CH_4$

• Glucose (most common monosaccharide): $C<em>6H</em>{12}O_6$

• General formula for many sugars and some lipids involves repeating units; for example, a typical triglyceride backbone combines glycerol with three fatty acids via ester bonds.

Summary of Connections to Foundational Principles

• Structure determines function: functional groups, bond types, and three-dimensional shape dictate biomolecule behavior (e.g., enzyme catalysis, membrane formation, nucleic acid base pairing).

• Polymerization and monomer diversity enable vast biodiversity: different monomers (amino acids, nucleotides, monosaccharides) assemble into proteins, nucleic acids, and polysaccharides with varied properties.

• Metabolic and signaling roles: proteins act as enzymes, transporters, receptors; nucleic acids encode information; lipids form membranes and signaling molecules; carbohydrates provide energy and structural support.

Quick Reference: Essential Concepts

• Major macromolecules: Carbohydrates, Lipids, Proteins, Nucleic Acids

• Monomers: Monosaccharides, amino acids, nucleotides, glycerol + fatty acids

• Bonds: Peptide bonds, glycosidic bonds, phosphodiester bonds, ester bonds in lipids

• Functional groups: Amino, Carboxyl, Phosphate, Hydroxyl, Carbonyl, Sulfhydryl, Methyl, etc.

• DNA vs RNA: Double-stranded vs single-stranded; sugar differences; base pairing rules; backbone structure

• Saturation and geometry of fatty acids influence membrane dynamics and health implications of fats (saturated, unsaturated, cis/trans)

• Miller–Urey: Abiotic synthesis of organic molecules from inorganic precursors under early Earth-like conditions

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