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Ch 3 MACROMOLECULES - Vocabulary Flashcards

Overview

  • Typical cell composition (eukaryotic-style example referenced): ~70% water, ~28% macromolecules, ~2% small molecules. The four major macromolecule classes are the same in all cells: lipids, carbohydrates, nucleic acids, and proteins.

  • Macromolecules are built by exergonic reactions that form covalent bonds; carbohydrates, nucleic acids, and proteins are polymers built from monomers (residues). Lipids are not polymers; they are defined by properties (not solely by a repeating monomer unit).

  • Key distinctions between lipids and other macromolecules:

    • Lipids are structurally and functionally diverse and are defined by insolubility in water (hydrophobic). They tend to aggregate in aqueous solutions due to hydrophobic effects.

    • Carbohydrates, nucleic acids, and proteins are polymers with repeating subunits and have broad roles in energy, information storage/transfer, and catalysis.

3.1 Lipids Are Defined by Insolubility in Water (Key Concept 3.1)

  • Lipids are hydrophobic due to many nonpolar C–C and C–H bonds; they are insoluble in water and tend to aggregate in aqueous environments (hydrophobic effect).

  • Structural features of lipids (varied): mostly C and H with nonpolar covalent bonds; include triglycerides, phospholipids, steroids, carotenoids, and waxes (Figure 3.1 in the text).

  • Lipids have high chemical-bond energy in C–C and C–H bonds relative to C=O and O–H bonds; this contributes to high energy density and melting behavior.

  • Lipid melting temperature (Tm) depends on molecule size and packing: larger lipids and greater van der Waals interactions yield higher Tm; unsaturation introduces kinks that reduce packing, lowering Tm.

  • Why class Vitamin A as a lipid: though it contains a polar –OH group, the molecule is largely hydrophobic due to a long hydrocarbon chain; its classification as a lipid reflects overall hydrophobic character.

  • Major lipid categories and roles:

    • Triglycerides (fats and oils): energy storage. Structure: glycerol + 3 fatty acids connected by ester bonds. Chemical formula for triglyceride formation can be summarized as

      \text{Glycerol} + 3 \times \text{Fatty acids} \ \rightarrow \text{Triglyceride} + 3 \, H_2O

      A fatty acid is a long nonpolar hydrocarbon chain with a terminal carboxyl group (–COOH). Condensation forms three ester bonds.

    • Fatty acids: saturated vs unsaturated.

    • Saturated fatty acids: all C–C bonds are single (no C=C). Chain is straight; packs tightly; high melting point; usually solid at body temperature (37°C).

    • Unsaturated fatty acids: contain one or more C=C bonds, causing kinks that prevent tight packing; lower melting temperature; can be fluid at body temperature. Example: linoleic acid (two C=C bonds).

    • Phospholipids: form biological membranes; amphipathic molecules with hydrophilic heads and hydrophobic tails.

    • Structure: glycerol backbone, two fatty acid tails, and a charged phosphate-containing head group.

    • Amphipathic nature causes phospholipids to form bilayers in aqueous environments: tails sequestered interior, heads face water.

    • Biological membranes are composed of phospholipid bilayers with embedded proteins; the bilayer acts as a barrier to many solutes.

    • In association with proteins, phospholipids can form lipoproteins (lipid transport particles) that carry triglycerides and cholesterol in the blood.

    • Waxes: long-chain alcohols bound to fatty acids; hydrophobic, protective coatings (plants, bees, birds/mammals).

    • Carotenoids: lipids capable of absorbing light energy (e.g., \beta-carotene, vitamin A).

    • Steroids: lipid class with fused ring structure; cholesterol is essential in animal membranes and acts as precursor to steroid hormones (e.g., estrogen).

  • Functional diversity: lipids are involved in energy storage, membrane structure, thermoregulation, light absorption (carotenoids, vitamin A), intracellular signaling, and transport (lipoproteins).

Review & Apply – 3.1 (Key Review Questions)

  • Why are fatty acids and triglycerides both classified as lipids while glycerol is not?

  • What is the difference between fats and oils in terms of structure?

  • Why can phospholipids form bilayers but triglycerides cannot?

  • Why is a phospholipid bilayer a barrier to water-soluble molecules?

3.2 Carbohydrates Are Made from Simple Sugars (Key Concept 3.2)

  • General composition and form: carbohydrates are composed of carbon, hydrogen, and oxygen with the general formula

    (CH2O)n

    where n is the number of carbon atoms in the monosaccharide. Many carbohydrates are polymers built from simple sugar units.

  • Simple sugars (monosaccharides) can exist in linear or ring forms; they can be pentoses (five carbons) or hexoses (six carbons).

  • Isomerism: same chemical formula but different structures (structural isomers) or spatial arrangements (stereoisomers). Examples include glucose, mannose, and fructose (all with formula

    \text{C}{6} \text{H}{12} \text{O}_6

    ) but arranged differently; in ring form, orientation at C1 can yield \alpha- or \beta- anomers (\alpha-D-glucose vs \beta-D-glucose).

  • Ring formation and nomenclature: straight-chain form can cyclize to a ring; the ring closure yields \alpha or \beta forms depending on the orientation of the anomeric carbon's substituent.

  • Disaccharides: formed by condensation (glycosidic) bonds between two monosaccharides, releasing water: \text{MonosaccharideA-OH} + \text{MonosaccharideB-OH} \rightarrow \text{Disaccharide} + H_2O Examples:

    • Sucrose: glucose + fructose linked by an \alpha-1,2 glycosidic bond.

    • Maltose: glucose + glucose linked by an \alpha-1,4 glycosidic bond.

    • Cellobiose: glucose + glucose linked by a \beta-1,4 glycosidic bond.

  • Oligosaccharides: 3–10 monosaccharides; often modified with functional groups; can be covalently bonded to proteins or lipids, modifying solubility and function.

    • On cell surfaces, oligosaccharides serve as recognition signals; ABO blood group differences arise from variations in surface oligosaccharide chains.

  • Polysaccharides: polymers of many monosaccharides; two main architectural types are linear (unbranched) and branched.

    • Linear: e.g., cellulose (\beta-1,4 linkages) forms strong, hydrogen-bonded sheets; major structural component of plant cell walls.

    • Branched: starch (\alpha-1,4 with \alpha-1,6 branching) and glycogen (more highly branched) for energy storage in plants and animals respectively.

    • Cellulose vs starch/glycogen: branching in starch and glycogen limits hydrogen bonding and packing density; cellulose forms parallel chains that hydrogen-bond to yield very strong microfibrils; glycogen is highly branched and compact; starch is less compact than cellulose due to branching pattern.

  • Structural and functional implications:

    • Cellulose and chitin provide structural support; starch and glycogen provide energy storage; branching pattern affects solubility and osmotic pressure in cells (insoluble polysaccharides are preferred for energy storage to avoid osmotic pressure of glucose in solution).

  • Osmotic considerations: storing glucose as insoluble polysaccharides reduces osmotic pressure in cells, enabling high glucose storage without drawing in excess water.

Review & Apply – 3.2

  • Why are mono-, di-, and oligosaccharides water-soluble?

  • What are the structural differences between cellulose and starch, and how do they relate to function?

  • Why is cellulose stronger than glycogen or starch?

  • Why are carbohydrates considered macromolecules in part due to their high aggregate presence even if individual units are small?

3.3 Nucleic Acids Are Informational Macromolecules (Key Concept 3.3)

  • Nucleotides: the building blocks of nucleic acids; each nucleotide consists of three components:

    • A five-carbon sugar: ribose (RNA) or deoxyribose (DNA)

    • A nitrogen-containing base: pyrimidine (single ring) or purine (double ring)

    • One to three phosphate groups; in nucleic acids, nucleotides are typically monophosphates within the strand; the triphosphate form is used for the incoming nucleotide during polymerization.

  • Bases: two categories—pyrimidines (C, T, U) and purines (A, G).

  • DNA vs RNA monomers:

    • DNA uses deoxyribose sugar; bases C, T, A, G.

    • RNA uses ribose sugar; bases C, U, A, G.

  • Polymerization and backbone:

    • Nucleotides are joined by phosphodiester bonds: a condensation reaction that links the 3'-OH of the growing chain to the 5'-phosphate of the incoming nucleotide, releasing pyrophosphate (PPi).

    • Result is a sugar–phosphate backbone with bases extending from the sugar moieties.

  • Directionality: nucleic acids are synthesized in the 5' \to 3' direction; the 5' end has a phosphate, the 3' end has a hydroxyl group for chain extension.

  • DNA vs RNA structure and function:

    • DNA is typically double-stranded and highly uniform; strands are antiparallel and complementary: A pairs with T (2 hydrogen bonds), C pairs with G (3 hydrogen bonds).

    • RNA is usually single-stranded but can fold back on itself to create short double-stranded regions; folding is stabilized by complementary base pairing; RNA folding yields distinct three-dimensional shapes that influence function.

  • Replication and expression:

    • DNA replication copies the entire genome, producing two identical DNA molecules.

    • Transcription copies DNA into RNA; translation uses RNA to synthesize proteins.

    • The sequence of bases in DNA encodes information expressed in RNA, which in turn specifies amino acid sequences in proteins.

  • Relationship to genome and information flow:

    • The information in DNA can be reconstructed on the complementary strand due to base-pairing rules.

    • The complete set of DNA in an organism is its genome; not all DNA encodes genes or is expressed.

  • Practical reference: PCR uses synthetic DNA oligonucleotides for amplification.

3.4 Proteins Are Polymers with Variable Structures (Key Concept 3.4)

  • Proteins are the most functionally diverse macromolecules; they perform catalysis, structure, signaling, transport, defense, storage, and more. They are composed of amino acids linked by peptide bonds.

  • Amino acids: 20 standard amino acids; each has:

    • An amino group (-NH2)

    • A carboxyl group (-COOH)

    • A hydrogen atom

    • An R group (side chain) that varies among amino acids and determines chemical properties.

  • Classification of amino acids by R-group properties:

    • Electrically charged (acidic or basic): hydrophilic and interact with water and ions

    • Positive: Arginine (Arg, R), Histidine (His, H), Lysine (Lys, K)

    • Negative: Aspartic acid (Asp, D), Glutamic acid (Glu, E)

    • Polar but uncharged (hydrophilic): Serine (Ser, S), Threonine (Thr, T), Asparagine (Asn, N), Glutamine (Gln, Q), Tyrosine (Tyr, Y)

    • Nonpolar hydrophobic: Alanine (Ala, A), Isoleucine (Ile, I), Leucine (Leu, L), Methionine (Met, M), Phenylalanine (Phe, F), Tryptophan (Trp, W), Valine (Val, V)

    • Special cases: Glycine (Gly, G) is smallest and flexible; Proline (Pro, P) has a ring that limits rotation; Cysteine (Cys, C) contains a thiol (-SH) group capable of forming disulfide bridges.

  • Disulfide bridges: covalent links between cysteine residues (-S-S-) stabilize a protein’s tertiary and quaternary structure.

  • Peptide bonds: formed by condensation reactions between the amino group of one amino acid and the carboxyl group of another, releasing water; peptides range from dipeptides to oligopeptides (short chains) to polypeptides (long chains and the basis of proteins).

  • Levels of protein structure:

    • Primary structure: linear sequence of amino acids (order determined by DNA/RNA sequence).

    • Secondary structure: regular folding patterns stabilized by hydrogen bonds along the backbone; common motifs include \alpha-helix and \beta-pleated sheet.

    • Tertiary structure: three-dimensional folding driven by interactions among R groups (hydrogen bonds, ionic interactions, van der Waals, hydrophobic interactions); disulfide bridges also contribute.

    • Quaternary structure: assembly of two or more polypeptide subunits into a functional protein.

  • Stability and folding considerations:

    • Many proteins require noncovalent interactions for structure; disulfide bonds provide covalent stabilization.

    • Folding is directed by the primary sequence; Anfinsen's experiments showed that a denatured protein can refold to its functional structure under proper conditions, indicating information for folding is in the primary structure.

    • Denaturation disrupts higher-level structure (secondary/tertiary/quaternary) but may not affect the primary sequence; denaturation can be reversible or irreversible depending on conditions.

  • Denaturation factors include pH changes, high concentrations of polar solutes, and nonpolar solvents that disrupt hydrogen bonds, ionic interactions, or hydrophobic core packing.

3.5 Protein Function and Binding (Key Concept 3.5)

  • Proteins display highly specific binding to ligands or substrates at defined sites (active or allosteric sites).

  • Ligand binding can induce conformational changes that affect function; binding affinity measures strength of interaction.

  • Cofactors: nonprotein molecules required for protein function; can be inorganic ions (e.g., Fe, Cu, Zn) or organic molecules (coenzymes). Cofactors vary in binding strength; some are tightly bound (prosthetic groups) while others bind reversibly as cofactors.

  • Proteolysis: some proteins are synthesized in an inactive form and activated by cleavage (proteolysis).

  • Enzymes: biological catalysts that speed up reactions by lowering activation energy, not by changing overall free energy change (\Delta G) of the reaction.

  • Enzyme-substrate interactions occur at the active site; binding can involve hydrogen bonds, ionic interactions, and van der Waals forces; the induced fit model describes how enzymes adapt their active site upon substrate binding to enhance catalysis.

  • Enzyme kinetics: typical rate enhancement ranges from $10^3$ to $10^8$-fold; each enzyme generally catalyzes a specific reaction with specific substrates.

  • Regulation of enzyme activity:

    • Active-site inhibition (competitive inhibition): a regulator binds to the active site and blocks substrate entry; reversible if the inhibitor is not permanently bound.

    • Allosteric regulation: regulators bind to sites other than the active site, altering enzyme conformation and activity; can activate or inhibit.

    • Covalent modification (e.g., phosphorylation) can regulate enzyme activity; often reversible via phosphatases and kinases.

  • Practical examples:

    • Penicillin irreversibly inhibits a bacterial enzyme required for cell wall synthesis (transpeptidase), exemplifying irreversible competitive-like inhibition.

    • Methotrexate acts as a competitive inhibitor of dihydrofolate reductase, reducing DNA/RNA base synthesis and slowing cell division (cancer therapy example).