The Structure and Function of Large Biological Molecules — Vocabulary Flashcards (Carbohydrates, Lipids, Proteins, Nucleic Acids)

Part 1: Overview & Carbohydrates

• Focus: structure and function of large biological molecules; emphasis on carbohydrates as one of the four major macromolecule classes.
• Carbohydrates general role:
  • Primary energy source for many organisms; also contribute to structure (e.g., cellulose in plant cell walls).
  • Carbohydrates are built from monosaccharide units and can form disaccharides and polysaccharides.
• General formula:
  • Carbohydrates are often represented by the empirical formula Cn(H2O)n or CxH{2x}Ox, reflecting their basic composition.
• Monomers, linkages, and reactions:
  • Monosaccharides: simple sugars (e.g., glucose, galactose, fructose).
  • Disaccharides: formed by a dehydration (condensation) reaction that links two monosaccharides via a glycosidic bond. Common examples:
  • Maltose (glucose–glucose)
  • Sucrose (glucose–fructose)
  • Lactose (glucose–galactose)
  • Polysaccharides: long chains of monosaccharides formed by repeated glycosidic linkages; may be branched or unbranched.
• Glycosidic bonds and ring forms:
  • Glycosidic bonds connect monosaccharides; linkage position denoted as e.g., 1–4, 1–6 glycosidic linkages.
  • Monosaccharides can exist in ring forms; two anomeric configurations:
  • Alpha (α): OH on C1 is down (below the plane in the common Haworth projection).
  • Beta (β): OH on C1 is up (above the plane).
  • Graphically: ring closure creates stereoisomers (anomers) that differ at the anomeric carbon.
• Common polysaccharides and their roles:
  • Starch (plants): storage polysaccharide of glucose; consists of:
  • Amylose: unbranched
  • Amylopectin: branched
  • Linkages: predominantly \alpha-glycosidic bonds
  • Glycogen (animals): highly branched glucose storage polymer located in liver and muscle.
  • Cellulose (plants): structural polysaccharide; glucose monomers linked by \beta-glycosidic bonds; humans cannot digest cellulose.
  • Chitin: structural polysaccharide in fungal cell walls and arthropod exoskeletons; contains amino sugar monomers linked by \beta-glycosidic bonds.
• Dietary and health context:
  • Carbohydrates in foods include labeled carbohydrates, sugar sources, starches, fibers.
  • Lactose intolerance relates to the inability to properly digest lactose (glucose–galactose disaccharide).
  • High-fructose corn syrup (HFCS) and sugar substitutes (e.g., Splenda) are common topics in discussions of diet and health.
• Abbreviated carb concepts (from slide prompts):
  • Abbreviated carbohydrate illustrations often show monosaccharides entering a condensation reaction to form disaccharides and polysaccharides via glycosidic bonds.
• Connections and relevance:
  • Carbohydrates provide quick energy (e.g., glucose) and longer-term storage (starch and glycogen).
  • Structural polysaccharides (cellulose, chitin) illustrate diversity of carbohydrate function beyond energy storage.
• Quick recap of key terms:
  • Monosaccharide, disaccharide, polysaccharide; glycosidic linkage; α- vs β- linkage; ring forms; glycogen; starch; amylose; amylopectin; cellulose; chitin.

Part 2: Lipids

• Major categories and roles:
  • Lipids are nonpolar, hydrophobic molecules that do not mix well with water.
  • Main classes discussed: fats (fats/triglycerides), phospholipids, steroids (including cholesterol).
• Fatty acids:
  • Carboxylic acids with long hydrocarbon chains.
  • Saturated fatty acids: all carbons connected by single bonds; typically solid at room temperature.
  • Unsaturated fatty acids: contain one or more double bonds; typically liquid at room temperature.
  • Trans fats: unsaturated fats with trans double bonds (often artificially produced by hydrogenation).
• Triglycerides (fats):
  • Consist of glycerol bound to three fatty acids via ester bonds.
  • Primary energy storage form in animals; high energy density.
• Phospholipids:
  • Glycerol bound to two fatty acids and a phosphate group.
  • Amphipathic: hydrophobic tails, hydrophilic head; major component of cell membranes forming bilayers.
• Steroids:
  • Carbon skeleton of four fused rings with various functional groups.
  • Cholesterol is a steroid essential for membranes and a precursor to other steroids.
• Key structural notes:
  • Ester bonds join fatty acids to glycerol in triglycerides and phospholipids.
  • Lipids are nonpolar and rely on hydrophobic interactions in membranes and storage.
• Health and dietary context:
  • Understanding saturated vs unsaturated fats helps interpret dietary fats and cardiovascular risk.
• Quick recap of concepts and terms:
  • Fatty acids; triglycerides; phospholipids; steroids; cholesterol; hydrogenation; ester bond.

Part 3: Amino Acids & Proteins

• Amino acids:
  • Building blocks of proteins; each amino acid has an amino group, a carboxyl group, a hydrogen atom, and a variable side chain (R group).
  • 20 standard amino acids; categorized by the properties of their R groups:
  • Nonpolar (mostly hydrophobic)
  • Polar (uncharged)
  • Charged (acidic negative or basic positive)
  • Examples (representative): Gly (G), Ser (S), Asp (D), Ala (A), Thr (T), Glu (E), Val (V), Cys (C), Lys (K), Leu (L), Tyr (Y), Arg (R), Ile (I), Asn (N), His (H), Met (M), Gln (Q), Phe (F), Trp (W), Pro (P).
• Peptide bonds:
  • Covalent bond between the carboxyl group of one amino acid and the amino group of another.
  • Formed by a dehydration (condensation) reaction.
  • Polypeptide backbone: N–Cα–C–N–Cα–C–N–Cα–C …
• Protein structure levels:
  • 1° Primary structure: unique linear sequence of amino acids (peptide bonds).
  • 2° Secondary structure: regular local folding due to backbone hydrogen bonds; includes α-helix and β-sheet.
  • 3° Tertiary structure: overall 3-D shape of a single polypeptide, driven by interactions among R groups, including:
  • Hydrophobic interactions; ionic bonds; hydrogen bonds; disulfide bridges (covalent bonds between cysteine residues).
  • 4° Quaternary structure: association of two or more polypeptide chains (subunits) into a functional protein.
• Determinants and stability:
  • R-group chemistry drives folding and final shape.
  • Factors that affect protein structure: pH, salt concentration, temperature, solvent polarity, and environment.
  • Denaturation: loss of native shape due to disruption of weak bonds/interactions (extreme pH, salt, or temperature).
• Sickle-cell anemia (an example of structure–function relationship):
  • A single amino acid substitution in the beta chain of hemoglobin (valine replacing glutamic acid at position 6) creates a hydrophobic patch that causes polymerization of Hb under low oxygen, deforming red blood cells and impairing oxygen transport.
• Folding and helpers:
  • Chaperonins and other folding aids help proteins reach their functional conformations, especially under heat stress.
• Protein data and methods:
  • X-ray crystallography used to study 3-D structures by diffracting X-rays through crystallized proteins.
• Quick recap of concepts and terms:
  • Primary, secondary, tertiary, quaternary structures; peptide bond; dehydration synthesis; disulfide bridge; hydrophobic interactions; cooperativity; allosteric regulation; feedback inhibition.

Part 4: Nucleic Acids

• Nucleic acids overview:
  • Polymers built from nucleotide monomers; store and transmit genetic information; some RNA molecules have catalytic roles.
• Nucleotides and nucleosides:
  • Nucleoside: sugar + nitrogenous base.
  • Nucleotide: sugar + nitrogenous base + one or more phosphate groups.
  • Nitrogenous bases: Purines (Adenine A, Guanine G) and Pyrimidines (Cytosine C, Thymine T, Uracil U).
• Types of sugars:
  • Deoxyribose in DNA; Ribose in RNA.
• Backbone and directionality:
  • Nucleic acids have a sugar–phosphate backbone linked by phosphodiester bonds.
  • Directionality is 5' to 3' in the strand.
• Base pairing and structure:
  • DNA typically forms a double helix consisting of two antiparallel polynucleotide strands.
  • A pairs with T via two hydrogen bonds; C pairs with G via three hydrogen bonds.
  • In RNA, A pairs with U (and C with G) and RNA is usually single-stranded but can fold into complex structures.
• Genome-scale concepts:
  • Human Genome Project (1990–2003): sequence the entire human genome (~3.0 × 10^9 bases).
  • Bioinformatics: use of computational tools to analyze large data sets; Genomics (gene-level), Proteomics (proteins).
• Central dogma and sequencing relevance:
  • The order of nucleotides (sequence) determines amino acid sequences in proteins (via the genetic code).
  • Nucleic acids can be used as markers to compare relatedness among organisms (e.g., globin gene/protein alignments).
• Common practical notes:
  • DNA in foods and organisms is present; non-GMO discussions; CRISPR and genetic engineering topics relate to modifying nucleic acids.
• Key terms and concepts:
  • Nucleotide, nucleoside, phosphodiester bond, 5'–3' directionality, antiparallel strands, base pairing (A–T/U, C–G), DNA vs RNA, genome projects, proteomics, bioinformatics.

Common foundational concepts across macromolecules

• Macromolecule formation and breakdown:
  • Condensation (dehydration) reactions join monomers to form polymers; water is released.
  • Hydrolysis reactions break polymers into monomers by adding water.
• Energetics and catalysis:
  • Activation energy (EA) is the energy required to start a reaction; enzymes lower EA and accelerate reactions without being consumed.
  • Enzymes are highly specific to substrates; active sites bind substrates and stabilize transition states (often via induced fit).
  • Enzyme kinetics: saturation occurs when all active sites are occupied; increasing substrate concentration no longer increases rate.
• Temperature and pH effects on enzymes:
  • Enzymes have an optimum temperature (often around 35–40 °C for many human enzymes) and an optimum pH (environment-specific; often near neutral for cytosolic enzymes).
  • Deviations from optimum can denature enzymes or reduce activity.
• Cofactors and inhibitors:
  • Cofactors and sometimes coenzymes are required for proper enzyme function.
  • Competitive inhibitors compete with substrate for the active site; noncompetitive inhibitors bind elsewhere and change enzyme shape.
  • Reversible inhibitors interact weakly; irreversible inhibitors form covalent bonds.
  • Allosteric regulation: regulatory molecule binds at a site other than the active site to alter enzyme activity; activators stabilize the active form; inhibitors stabilize the inactive form.
  • Cooperativity: binding of substrate to one subunit increases the activity of other subunits in multimeric enzymes.
• Energy coupling in cells:
  • ATP is the primary energy currency: hydrolysis of ATP drives endergonic reactions, enabling cellular work (chemical, transport, mechanical).
  • The ATP cycle involves phosphorylation of ADP to ATP in catabolic pathways and hydrolysis of ATP to drive anabolic pathways; typically, millions of ATP molecules are cycled per cell per second.
• Water as a universal solvent and its properties:
  • Water’s polarity, hydrogen bonding, cohesion, adhesion, high specific heat, and heat of vaporization underlie many biological processes and temperature regulation in organisms.
• Nucleic acid information and evolution:
  • Sequence data from DNA and proteins serve as measurement tools for evolutionary relatedness (genomics, proteomics, bioinformatics).
• Notable numerical references (for quick recall):
  • Carbohydrate formula: Cn(H2O)n and CxH{2x}Ox
  • Carbon forms four covalent bonds with bond angles of about 109.5^ ext{o} in a tetrahedral geometry.
  • Avogadro’s number: N_A = 6.022 \times 10^{23}
  • Activation energy and enzyme catalysis: typically lowers EA; typical enzymes can act on ~10^3 substrate molecules per second.
  • Thermodynamics clarity: thermodynamics tells whether a process is favorable, not the rate; spontaneous reactions can be slow.
• Key quantitative references you should remember:
  • [H^+][OH^-] = 10^{-14} at 25 °C (pH scale relationship).
  • 1 Calorie (cal) = 4.184\ \text{J}; 1 kilocalorie (kcal) = 4184\ \text{J}; 1 kcal raises 1 kg of water by 1 °C.
  • 1 Molar (1 M) = 1 mole solute per liter of solution: M = \frac{n}{V}\,.
• Practical connections:
  • Food labels illustrate macromolecule concepts (carbohydrates, fats, proteins) and daily dietary choices impact energy balance and health.
  • Modern technologies (genomics, proteomics, bioinformatics) connect molecular biology to medicine, agriculture, and evolution.