Unit 1 Lec 3

Organic vs. Inorganic and essential context

• Organic chemistry in biology focuses on molecules that contain carbon-hydrogen (C–H) bonds.
• Living things predominantly use elements such as hydrogen (H), carbon (C), oxygen (O), and nitrogen (N). Other smaller elements exist but the key feature is carbon_backbone with hydrogen attached.
• Definition distinction:
  • Organic molecules: contain carbon and hydrogen (C–H bonds) and typically form a carbon backbone with various atoms bonded to it.
  • Inorganic molecules: lack the carbon–hydrogen framework or are carbon-containing but without C–H bonds; for example, water is H₂O (inorganic).
• Water (H₂O) is essential for all metabolic processes; life depends on water as a solvent and medium for reactions.
• In living systems, molecules bond via covalent bonds to form larger macromolecules; common elements in biological macromolecules include O, H, N, C.
• When biological molecules bond to proteins, you can get glycoproteins: glyco- means carbohydrate; a carbohydrate is attached to a protein to form a single molecule with both protein and carbohydrate components.
• Four major biomolecule categories (structure and function are tied to monomer length/arrangement):
  • Carbohydrates
  • Nucleic acids
  • Lipids
  • Proteins

The four major biomolecule groups and their overarching principle

• For each category, the length and arrangement of monomers determine the type of polymer produced and, consequently, function.
• Shape determines function: monomers link to form polymers; the resulting three-dimensional structure dictates activity.
• Monomer/polymer concepts recur across categories; breaking and forming bonds involves water in hydrolysis and dehydration synthesis, respectively.

Carbohydrates

• Monomer units: monosaccharides (the smallest carbohydrate unit).
  • Examples include:
  • Glucose, fructose, galactose (common monosaccharides in biology). ext{C}6 ext{H}{12} ext{O}_6 (general formula for a simple monosaccharide is illustrative; specific monosaccharide formulas vary).
  • Ribose (in RNA) and deoxyribose (in DNA) as sugar components of nucleic acids.
• Linkage of monosaccharides forms disaccharides via covalent bonds; breaking these bonds with water is hydrolysis. The reverse process (joining monomers) is dehydration synthesis.
  • Disaccharides example: sucrose (table sugar), lactose (milk sugar).
  • Hydrolysis reaction:
    ext{Disaccharide} + ext{H}2 ext{O} ightarrow ext{Monosaccharide}1 + ext{Monosaccharide}_2
• Polysaccharides: long chains of monosaccharides; multiple units linked by glycosidic bonds.
  • Examples: starch, glycogen, cellulose.
  • Functions:
  • Energy storage (glycogen in animals; starch in plants).
  • Structural support (cellulose in plant cell walls).
  • Quick energy sources when polysaccharides are broken down into monosaccharides.
• Metabolic role and energy flow:
  • In digestion, polysaccharides are hydrolyzed into monosaccharides, providing quick energy after meals.
  • The liver and muscles store excess glucose as glycogen; in the absence of immediate energy demand, glycogen is mobilized for later use.
• Physical chemistry note:
  • Carbohydrates are polar and tend to dissolve well in polar solvents like water; water is the universal solvent for polar substances. This supports transport of sugars in bodily fluids.
• Context on diet and energy:
  • For athletic performance, high-carbohydrate meals before activity supply glycogen stores for sustained energy.
  • Quick energy snacks (e.g., candy or soda) supply monosaccharides that rapidly raise blood glucose.
• Structural note:
  • In plant cells, cellulose provides structural integrity (cell wall) and is not digestible by humans.
• Quick mnemonic:
  • Monosaccharides → Disaccharides → Polysaccharides; energy storage vs. structure.

Lipids

• General properties:
  • Lipids include fats and oils (triglycerides), phospholipids, cholesterol, and more.
  • They are nonpolar (hydrophobic) and do not dissolve well in water; they are not soluble in polar solvents.
• Triglycerides (fats/oils): main energy storage lipids.
  • Structure: glycerol backbone with three fatty acids attached (via ester bonds). They are a major energy source and insulator.
  • Saturated vs. unsaturated fatty acids:
  • Saturated fats: no double bonds between carbon atoms; straight chains; tend to be solid at room temperature (e.g., animal fats, butter).
  • Unsaturated fats: contain one or more double bonds; kinked chains due to double bonds; typically liquid at room temperature (oils).
  • Shape and function example: a double bond creates a kink, which prevents tight packing; “shape determines function.”
• Phospholipids: key structural components of cell membranes.
  • Structure: glycerol backbone with two fatty acid tails (nonpolar, hydrophobic) and a phosphate-containing head (polar, hydrophilic).
  • Amphipathic nature: two lives—polar head interacts with water, nonpolar tails avoid water.
  • Membrane formation: spontaneously form a phospholipid bilayer in aqueous environments, with hydrophilic heads facing outward and hydrophobic tails packed inside.
  • Cell membrane relevance: this bilayer forms the boundary of cells; contains various proteins and other molecules that regulate transport and signaling.
• Cholesterol:
  • Essential component of membranes; stabilizes and modulates fluidity.
  • Synthesized in the liver and obtained from diet; excessive cholesterol in blood is a risk factor for cardiovascular disease.
  • Cholesterol also serves as a precursor for steroid hormones.
• Lipids in signaling:
  • Some hormones are lipid-derived and can diffuse through lipid membranes to act quickly on target cells.
• Absorption and digestion note:
  • Not all dietary fats are absorbed; some pass through the digestive tract; efficiency of absorption depends on digestion and transport mechanisms.
• Real-world context:
  • The balance of saturated and unsaturated fats influences health outcomes; dietary patterns can affect membrane properties and signaling processes.

Nucleotides and Nucleic Acids

• Monomer: nucleotide (the building block for nucleic acids).
  • Required components of a nucleotide:
  • A sugar (ribose in RNA or deoxyribose in DNA),
  • A nitrogenous base, and
  • A phosphate group.
  • At least one sugar, one nitrogen base, and one phosphate must be present in each nucleotide.
  • Example: ATP (adenosine triphosphate) contains adenosine (adenine + ribose) and three phosphate groups; it functions as an energy carrier.
  • ATP hydrolysis provides energy for biological processes: ext{ATP}
    ightarrow ext{ADP} + ext{P}_i + ext{energy}
• Nucleic acids:
  • DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) store and transmit genetic information.
  • ATP and other nucleotides also play roles as energy carriers and cofactors in metabolism.
• Sugar components:
  • DNA uses deoxyribose; RNA uses ribose; these sugars are part of the nucleotide backbone.
• Functional implication:
  • The sequence of nucleotides encodes information that directs protein synthesis and cellular function.

Proteins

• Major roles:
  • Growth, repair, and maintenance of body tissues; enzymes as catalysts; antibodies as part of the immune system; structural and transport roles, etc.
• Monomers: amino acids (20 standard amino acids).
  • General structure of an amino acid:
  • A central carbon (alpha carbon) attached to a hydrogen atom, an amino group (–NH₂), a carboxyl group (–COOH), and a side chain (R group).
  • The R group (side chain) differentiates amino acids and determines chemical properties and function.
  • The 20 amino acids differ only in their R groups, which include hydrophobic, hydrophilic, acidic, and basic residues.
• Protein synthesis and variety:
  • The sequence of amino acids (primary structure) determines the protein’s final shape and function.
  • A protein can be thousands of amino acids long; even a single amino acid change can produce a different protein.
  • The arrangement of amino acids is like letters that form a vast set of words (proteins) with diverse functions.
• Protein structure levels:
  • Primary structure: linear sequence of amino acids.
  • Secondary structure: local folding patterns, mainly alpha helices and beta pleated sheets, stabilized by hydrogen bonds.
  • Tertiary structure: overall three-dimensional shape formed by further folding, culled by interactions among R groups (hydrophobic interactions, disulfide bonds, ionic bonds, hydrogen bonds).
  • Quaternary structure: assembly of multiple polypeptide subunits into a functional protein (e.g., hemoglobin).
• Factors and helpers:
  • Chaperone proteins assist in proper folding of polypeptides.
  • The correct folding is essential for function; misfolding can lead to loss of function or diseases.
• Enzymes and specificity:
  • Enzymes are proteins that act as catalysts, speeding up reactions by lowering activation energy without being consumed.
  • Activation energy is the energy required to start a reaction; enzymes reduce this barrier to initiate reactions efficiently.
• Protein diversity and function:
  • The shape and charge distribution of a protein determine its function (e.g., enzymes, antibodies, structural proteins).
• Glycoproteins:
  • Some proteins are glycosylated; they have carbohydrate (glycan) moieties attached, affecting stability, localization, and function.

Connections to metabolism, health, and real-world relevance

• The four biomolecule classes work together to sustain life: energy production (carbohydrates, lipids), information storage and transfer (nucleic acids), structure and function of cells (proteins, lipids), and signaling (hormones, enzymes).
• Diet and energy balance illustrate practical outcomes of these biomolecules: carbohydrates provide quick energy; lipids provide long-term energy and membrane structure; proteins supply amino acids for repair and enzymes; nucleotides underpin genetic information and energy transactions (ATP).
• Health implications:
  • Membrane composition (phospholipids, cholesterol) affects fluidity, signaling, and transport.
  • Excess saturated fats can impact membranes and cardiovascular health; unsaturated fats tend to be healthier for many diets.
  • Cholesterol is essential but needs to be regulated; statins and dietary choices influence blood cholesterol levels and overall health risk.
• Ethical/practical considerations:
  • Dietary guidelines and lifestyle choices can influence membrane function, enzyme activity, and disease risk; understanding these biomolecules informs healthcare choices.