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Chapter 5: Organic Molecules — Comprehensive Study Notes

POLYMERS AND MONOMERS

  • Polymers are long chains or branched chains made of repeating subunits called monomers.

  • Macromolecules are very large polymers (typically 100+ subunits).

  • Examples of polymers in biology: proteins (polymers of amino acids) and nucleic acids (polymers of nucleotides).

  • Hydrolysis: polymers can be broken down into monomers by adding water; it often requires an enzyme for a reasonable rate.

    ◦ Water’s hydrogen attaches to one monomer, and the hydroxyl attaches to the other.

    ◦ General form: polymer + H₂O → monomers.

    • Condensation (dehydration synthesis): monomers covalently bond to form polymers; usually, water is removed.

    ◦ Water is a product: polymer formation with the removal of a water molecule.

    • Enzymes often speed up both hydrolysis and condensation reactions.

    CLASSES OF ORGANIC MOLECULES

  • Carbohydrates: starches, sugars, cellulose

  • Lipids: fats and fat-like substances

  • Proteins: macromolecules that are polymers formed from amino acid monomers

  • Nucleic acids: transmit hereditary information by determining what proteins a cell produces

  • Polypeptides: when 2+ amino acids are joined together by peptide bonds

  • Nucleotides: monomers of nucleic acids

CARBOHYDRATES

  • General roles: energy sources and structural components

  • Carbon skeletons: can have 3–7 carbons (trioses, tetroses, pentoses, hexoses, heptoses)

  • Ring structures are common in solution; monosaccharides often exist as rings in aqueous solutions.

  • Important monosaccharides:

    • Pentoses: ribose, deoxyribose (in RNA and DNA)

    • Hexoses: glucose, fructose

  • Monosaccharide notation:

    • Molecular formula: C6H{12}O_6 (example for glucose)

  • Linear vs. cyclic representations: glucose can be shown in linear form (e.g., ext{D-Glucose}) or cyclic forms.

  • Aldehyde vs. cyclic formation:

    • In solution, the carbonyl group at C1 reacts with a hydroxyl group at C5 to form rings; two ring forms exist depending on the orientation of the −OH on C1 (anomers: α and β). In symbols: ring formation yields ext{α-D-Glucose} and ext{β-D-Glucose}.

DISACCHARIDES AND POLYSACCHARIDES

  • Disaccharides: two monosaccharide units joined by a glycosidic bond (a condensation reaction).

  • Polysaccharides: macromolecules made of repeating monosaccharide units; can be branched or unbranched; typically >1000 subunits.

  • Some polysaccharides are easily broken down (energy storage), others are structural.

STORAGE POLYSACCARIDES

  • Starch: main storage component in plants.

    • Plants store starch in amyloplasts.

    • Types: amylose (unbranched) and amylopectin (branched).

  • Glycogen: main storage component in animals; highly branched and water-soluble; stored mainly in liver and muscle cells; used as quick energy.

  • Quick notes:

    • Starch and glycogen are used for energy storage.

    • Glycogen is more branched and more rapidly mobilized than starch.

STRUCTURAL POLYSACCHARIDES

  • Cellulose: main structural component of plant cell walls; strong and insoluble.

    • Most organisms cannot digest cellulose; many herbivores rely on gut microorganisms to break it down.

  • Chitin: main structural component in fungal cell walls and exoskeletons of insects, spiders, and crustaceans; second most abundant polysaccharide after cellulose; strong and insoluble.

LIPIDS

  • Lipids are fats and fat-like substances; principally hydrophobic and relatively insoluble in water.

  • Some lipids have polar and non-polar regions (amphipathic).

  • General composition: mainly hydrogen and carbon; some contain oxygen and/or phosphorus.

  • Biological roles:

    • Membrane structure components (phospholipids)

    • Signaling molecules (eicosanoids as lipid signaling molecules in inflammation)

    • Long-term energy storage (fats)

  • Classes of lipids:

TRIACYLGLYCEROLS (TRIGLYCERIDES, TAGs)

  • Structure: glycerol backbone with 3 fatty acids attached.

  • Glycerol: ext{C}3 ext{H}8 ext{O}_3

  • Fatty acids: long hydrocarbon chains with a carboxyl group at one end; most contain an even number of carbons.

  • Primary role: energy storage; energy-dense and used for insulation in many organisms.

  • Parts of a TAG: glycerol + 3 fatty acids.

FATTY ACIDS

  • Saturated fatty acids: no C=C double bonds; linear; typically solid at room temperature.

  • Unsaturated fatty acids: contain one or more C=C double bonds; typically liquid at room temperature.

    • Monounsaturated: one double bond

    • Polyunsaturated: two or more double bonds

PHOSPHOLIPIDS

  • Structure: glycerol backbone + phosphate group + organic molecule (head) + two fatty acid tails.

  • Amphipathic: hydrophilic (polar) head interacts with water; hydrophobic (nonpolar) tails avoid water.

  • Crucial components of biological membranes; form lipid bilayers.

TERPENES

  • Built from five-carbon isoprene units.

  • Found in plants; contribute to aromas, pigments, and hormones.

  • Examples: chlorophyll, carotenoids, retinal; natural rubber; essential oils; some terpene derivatives with four rings include steroids.

PROTEINS

  • Macromolecules that are polymers made from amino acid monomers.

  • Structural diversity = functional diversity; structure determines function.

  • Roles include: enzymes, transport, structural support, motion, regulation, and defense.

AMINO ACIDS (THE BUILDING BLOCKS)

  • General structure: ext{NH}2- ext{CH(R)}- ext{COOH} at the core; at physiological pH typically exists as ext{NH}3^+- ext{CH(R)}- ext{COO}^-.

  • 20 common amino acids; each has a unique side chain (R group) that determines identity and chemical properties.

  • R group determines polarity and hydrophilicity vs hydrophobicity; can render the amino acid polar, nonpolar, or ionic.

  • Most amino acids exist as enantiomers; amino acids found in proteins are almost always in the L- configuration; some amino acids can be D- or L- in other contexts.

  • Sources of amino acids:

    • Plants and bacteria can synthesize their own amino acids.

    • Many animals must obtain essential amino acids from the diet.

PEPTIDE BONDS

  • Condensation reaction joins amino acids via peptide bonds.

  • Bond type: covalent bond between the carboxyl group of one amino acid and the amino group of another.

  • Formed by condensation: removal of a water molecule.

  • Result: dipeptide (two amino acids), tri-/polypeptide (many amino acids).

PROTEIN STRUCTURE LEVELS

1) Primary structure (1°): sequence of amino acids in the polypeptide chain; stabilized by peptide bonds (covalent).
2) Secondary structure (2°): local folding patterns (e.g., α-helix, β-pleated sheet) stabilized by hydrogen bonds within the peptide backbone.

  • Proteins can have both α-helix and β-pleated regions.
    3) Tertiary structure (3°): overall three-dimensional shape of a single polypeptide; stabilized by:

  • Hydrogen bonds, ionic bonds, disulfide bridges, hydrophobic interactions, and van der Waals forces.

  • Determined by the 2° structure and the interactions of side chains (R groups). 4) Quaternary structure (4°): interactions between two or more polypeptide chains; stabilized by hydrogen bonds, ionic bonds, disulfide bridges, hydrophobic interactions, and van der Waals forces.

    • Example: hemoglobin has four polypeptide chains.

    • The final 3D conformation is the protein's functional form.

DENATURATION

  • Unfolding of a protein, disrupting 2°, 3°, and 4° structures.

  • Can occur due to changes in:

    • Temperature

    • pH

    • Exposure to various chemicals

  • Denatured proteins generally cannot perform their normal biological functions and are often irreversibly denatured.

ENZYMES

  • Proteins that regulate the rates of chemical reactions in living organisms.

  • Most enzymes are proteins; many have names ending in the suffix -ase.

NUCLEIC ACIDS

  • Nucleic acids transmit hereditary information by determining which proteins a cell makes.

  • Two main classes:

    • DNA (deoxyribonucleic acid): carries genetic information.

    • RNA (ribonucleic acid): functions in protein synthesis.

NUCLEOTIDES

  • Monomers of nucleic acids.

  • Each nucleotide consists of:

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

    • One or more phosphate groups

    • A nitrogenous base

PURINES AND PYRIMIDINES

  • Purines: double-ringed bases (Adenine A and Guanine G).

  • Pyrimidines: single-ringed bases (Cytosine C, Thymine T, Uracil U).

PHOSPHODIESTER BONDS

  • Nucleotides are linked by phosphodiester bonds.

  • A phosphate group of one nucleotide is bonded to the sugar of the adjacent nucleotide.

  • This linkage creates a polynucleotide with distinct 5' and 3' ends (directionality: 5' → 3').

SUMMARY NOTES

  • Understanding how monomers form polymers via condensation and how polymers can be deconstructed via hydrolysis is foundational for all biomolecules.

  • Carbohydrates provide quick energy (glycogen, starch, glucose) and structural support (cellulose, chitin in fungi/exoskeletons).

  • Lipids are diverse, with triglycerides for energy storage, phospholipids for membranes, and terpenes for signaling and pigments.

  • Proteins derive from 20 amino acids; their sequence determines structure and function; higher-order structures (2°, 3°, 4°) enable complex biological roles; denaturation disrupts function.

  • Nucleic acids store and express genetic information through DNA and RNA, with nucleotides connected by phosphodiester bonds and directionality from 5' to 3'.

ext{Glucose: } C6H{12}O6 ext{Glycerol: } C3H8O3
ext{Amino acid general: } ext{NH}2- ext{CH(R)}- ext{COOH} ext{Peptide bond formation: } ext{AA}1- ext{CO}- ext{NH}- ext{AA}_2
ext{Phosphodiester bond: } ext{5'}- ext{O}- ext{P}(=O)(-O-)- ext{O}- ext{3'}
ext{5' and 3' ends: } 5' o 3'