Chapter 3: Macromolecules - Study Notes

Polymers, Monomers, and Bond Formation

  • Macromolecules are built from repeating subunits called monomers to form polymers.

  • Key processes:

    • Dehydration synthesis (condensation): monomers are joined by removal of OH from one monomer and removal of H from the other at the site of bond formation, releasing water (H₂O).

    • Monomer 1 + Monomer 2 → covalently linked monomers + H₂O.

    • Hydrolysis: polymers are broken into monomers by the addition of a water molecule, adding OH to one monomer and H to the other.

    • Polymer + H₂O → Monomer 1 + Monomer 2.

  • These reactions link and break covalent bonds between monomer units to form polymers such as carbohydrates, proteins, nucleic acids, and lipids.

Carbohydrates: Monosaccharides, Disaccharides, and Polysaccharides

  • Carbohydrates have general formula often summarized as (CH₂O)ₙ and are produced from CO₂ and H₂O via photosynthesis in plants.

  • Size range: from glyceraldehyde (Mw ≈ 90 g/mol) to amylopectin (Mw ≈ 2.0×10⁸ g/mol).

  • General functions:

    • Energy source and storage (e.g., glucose, starch, glycogen).

    • Structural components of cell walls and exoskeletons (e.g., cellulose, chitin).

    • Informational molecules in cell-cell signaling.

    • Covalent linkage to proteins to form glycoproteins and proteoglycans.

  • Carbohydrates are polyhydroxy aldehydes/ketones; basic unit is a sugar (saccharide).

  • Monosaccharide: single sugar unit.

  • Disaccharide: two sugar units covalently bound.

  • Oligosaccharide: short chains of sugars.

  • Polysaccharide: >20 sugar units.

Monosaccharides

  • Most common biological monosaccharide: D-glucose (dextrose).

  • Most biologically relevant monosaccharides have 3–6 carbons; >4 C easily form cyclic structures.

  • Naming convention: many mono- and disaccharide names end in “-ose.”

  • Common carbon-count designations:

    • 3 = triose

    • 4 = tetrose

    • 5 = pentose

    • 6 = hexose

    • Rare: heptoses, octoses, nonoses in biology.

  • Notable monosaccharides:

    • Glucose (D-glucose)

    • Fructose

    • Galactose

    • Deoxyribose (DNA sugar; lacks one oxygen compared to ribose)

    • Ribose (RNA sugar)

  • Structural representations in diagrams show hydroxyl groups oriented around the carbon backbone (D-configuration is common).

Glycogen, Starch, and Structural Polysaccharides

Glycogen

  • Glycogen is a branched homopolysaccharide of glucose.

  • Linkages:

    • Main chains: (α1→4) glycosidic bonds.

    • Branch points: (α1→6) linkers every 8–12 residues.

  • Molecular weight: reaches several millions.

  • Function: main storage polysaccharide in animals.

Starch

  • Starch is a mixture of two glucose homopolysaccharides:

    • Amylose: unbranched polymer with (α1→4) linkages.

    • Amylopectin: branched like glycogen but branch points occur every 24–30 residues with (α1→6) linkers.

  • Molecular weight of amylopectin: up to ≈ 2.0×10⁸ g/mol.

  • Function: main storage polysaccharide in plants.

Glycosidic Linkages in Glycogen and Starch

  • Branching pattern: main chains with occasional branches.

  • In diagrams, reducing and nonreducing ends are indicated; branch points involve (α1→6) linkages.

  • Key terms: nonreducing end (terminal ends where the terminal glucose has a blocking anomeric carbon) and reducing end (end with a free anomeric carbon able to open to form an aldehyde).

Structural Polysaccharides

Cellulose

  • Structural component of plants.

  • Linkages are β instead of α: β(1→4) linkages.

  • Forms long, straight chains capable of extensive hydrogen bonding between adjacent chains.

  • Results in a tough, water-insoluble structure; cellulose is the most abundant polysaccharide in nature.

  • Cotton is nearly pure fibrous cellulose.

Chitin

  • Homopolymer of N-acetylglucosamine (GlcNAc) with β linkages.

  • Present in exoskeletons of insects and in some fungi.

Cellulose and Chain Interactions

  • Hydrogen bonding between adjacent glucose chains contributes to the high tensile strength and water-insolubility of cellulose.

Lipids: Hydrophobic Compounds

  • Major classes shown: fats & oils, waxes, phospholipids, and steroids.

  • Lipids are generally hydrophobic and serve multiple roles.

  • Differences between saturated and unsaturated lipids:

    • Saturated fatty acids have no double bonds; chains are more extended and pack tightly.

    • Unsaturated fatty acids contain cis or trans double bonds; cis introduces kinks, reducing packing efficiency.

  • FIGURES illustrate saturated vs unsaturated chains and the presence of cis vs trans double bonds.

Functions of Lipids

  • Energy storage: fats store more energy per carbon because they are more reduced.

  • Water content: fats store less water per gram because they are nonpolar.

  • Membrane structure: phospholipids form lipid bilayers; hydrophobic tails face inward, hydrophilic heads face outward.

  • Insulation and protection: low thermal conductivity, shock absorption, buoyancy, etc.

  • Hydrophobic properties: help keep surfaces dry and prevent excessive water loss in organisms.

Major Lipid Types

  • Fats and oils: triacylglycerols (TAGs) as main storage form; fats are saturated, oils are unsaturated.

  • Waxes: esters of long-chain fatty acids and long-chain alcohols; provide protective coatings.

  • Phospholipids: glycerol or sphingosine-based backbones with two fatty acids and a phosphate-containing head group; form membranes.

  • Steroids: four-ring sterol nucleus; include cholesterol and steroid hormones.

Fatty Acids

  • Carboxylic acids with hydrocarbon chains ranging from 4 to 36 carbons.

  • Most natural fatty acids have an even number of carbons; most are unbranched.

  • Conformation:

    • Saturated chains tend to be extended.

    • Natural unsaturated fatty acids have cis double bonds that kink the chain.

  • Melting behavior is influenced by saturation and configuration of double bonds:

    • Saturated fatty acids pack well and have higher melting points.

    • Unsaturated cis fatty acids pack less densely and have lower melting points.

Trans Fats

  • Formed by partial dehydrogenation of unsaturated fatty acids (industrial hydrogenation).

  • A trans double bond allows the chain to adopt an extended conformation, enabling tighter packing and higher melting points than cis forms.

  • Health impact: consumption of trans fats increases risk of cardiovascular disease.

  • Regulatory trends: many foods reducing trans fats due to health concerns.

Plasma Membrane and Sterols

  • Plasma membrane: fundamental membrane in both prokaryotic and eukaryotic cells; encloses cellular contents and separates from the environment.

  • Animal membranes: rich in phospholipids, proteins, and cholesterol (a sterol).

  • Structure: lipid bilayer with polar, hydrophilic heads and nonpolar, hydrophobic tails.

Sterols and Cholesterol

  • Sterol: steroid nucleus with four fused rings and a polar hydroxyl head group; relatively planar.

  • Physiological roles:

    • Modulate membrane fluidity and permeability; thicken the plasma membrane.

    • Most bacteria lack sterols.

    • Mammals synthesize cholesterol in the liver and obtain some from food.

    • Sterols are precursors to many hormones.

Steroid Hormones

  • Steroids are oxidized derivatives of sterols with the sterol nucleus.

  • More polar than cholesterol.

  • Synthesized from cholesterol in gonads and adrenal glands.

  • Transported in the bloodstream, usually attached to carrier proteins.

  • Many steroid hormones serve as sex hormones (e.g., androgens, estrogens).

Amino Acids and Proteins

Amino Acids

  • There are 20 standard amino acids with unique side chains (R groups).

  • General amino acid structure:

    • Amino group (–NH₃⁺ in physiological pH) and carboxyl group (–COO⁻) attached to central α-carbon, plus a hydrogen and an R group.

  • Side chain classifications by R group:

    • Nonpolar, aliphatic

    • Polar, uncharged

    • Negatively charged (acidic)

    • Positively charged (basic)

    • Aromatic (special cases like phenylalanine, tyrosine, tryptophan)

  • Example structures (selected):

    • Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline

    • Serine, Threonine, Cysteine

    • Asparagine, Glutamine

    • Lysine, Arginine, Histidine

    • Phenylalanine, Tyrosine, Tryptophan

    • Aspartate, Glutamate

Peptide Bonds and Protein Polymerization

  • A covalent peptide bond forms when the carboxyl group of one amino acid is joined to the amino group of the next amino acid via a condensation reaction.

  • The resulting chain is a polypeptide.

Protein Structure: Four Levels

  • Primary structure: amino acid sequence of the polypeptide.

  • Secondary structure: regular sub-structures (e.g., α-helix, β-sheet) formed by hydrogen bonding between backbone atoms.

  • Tertiary structure: three-dimensional folding of a single polypeptide, driven by hydrophobic interactions, hydrogen bonds, ionic interactions, and disulfide bonds; hydrophobic R groups tend to be buried inside, hydrophilic R groups on the outside.

  • Quaternary structure: assembly of multiple polypeptide chains into a functional protein.

  • Examples: hemoglobin (quaternary structure with multiple subunits).

Protein Folding and Function

  • Proteins must fold into native conformations to function properly.

  • Folding is influenced by the environment; denaturation disrupts structure and function.

  • Native conformation is the functional state of the protein.

Enzymes: Biological Catalysts

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

  • Most are globular proteins; some catalytic RNAs (ribozymes) exist.

  • Enzyme nomenclature and function:

    • Enzymes catalyze the conversion of substrates into products.

    • Substrates bind to the active site.

    • The binding lowers the activation energy, increasing reaction rate.

  • Models of catalysis:

    • Induced fit model: binding of substrate induces a conformational change to optimize catalysis.

  • Key properties:

    • Enzymes do not change the equilibrium of reactions; they alter the rate (kinetics).

    • They can be inhibited by factors such as heat and pH; severely denatured enzymes lose activity.

Nucleotides and Nucleic Acids

Nucleotides

  • Nucleotides consist of:

    • Nitrogenous base (purine: A, G; pyrimidine: C, T, U)

    • Pentose sugar (ribose in RNA, deoxyribose in DNA)

    • Phosphate group(s) that link nucleotides together

  • Nucleotides polymerize to form nucleic acids (DNA and RNA).

  • Functions include storage and transmission of genetic information, processing of genetic information (ribozymes), and involvement in protein synthesis (tRNA and rRNA).

Nitrogenous Bases

  • Purines: Adenine (A), Guanine (G)

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

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

Nucleic Acids: DNA and RNA

  • Nucleotides are connected by phosphodiester linkages between the 5' phosphate of one nucleotide and the 3' hydroxyl of the next, forming a sugar-phosphate backbone with nitrogenous bases as side chains.

  • Structure:

    • DNA is a double helix with two antiparallel strands.

    • The bases pair via hydrogen bonds to form the complementary strands.

  • Nucleic acids can be linear polymers with directionality from 5' to 3' ends; strands are complementary and antiparallel.

Phosphodiester Backbone: 5' to 3' Orientation

  • In DNA, the backbone consists of alternating phosphate and sugar units: the linkage is between the 5' phosphate and the 3' hydroxyl of the next nucleotide.

  • Base pairing and helical geometry drive the double-stranded structure.

Key Concepts Across Macromolecules (Cross-links and Significance)

  • Glycosidic linkages determine branching and digestibility in polysaccharides:

    • Glycogen: α(1→4) main chains with α(1→6) branches; branches every 8–12 residues.

    • Starch: mixture of amylose (α(1→4)) and amylopectin (α(1→4) with α(1→6) branches every 24–30 residues).

  • β-linkages in cellulose confer rigidity and insolubility, forming structural fibers.

  • Lipid hydrophobicity and nonpolarity drive membrane formation and energy storage efficiency; cis/trans configurations influence melting points and packing.

  • Proteins require precise folding into native structures to function; disruptions can lead to loss of activity or misfolding-related diseases.

  • Nucleic acids store and transmit genetic information; the antiparallel, complementary nature of DNA enables predictable sequence relationships and replication fidelity.