Chapter 3: Organic Molecules Review

Organic Molecules and Life

• We're extending chemistry into living things by studying molecules that build organisms and will appear in upcoming chapters.

• Organic vs inorganic (in everyday context): organic often labeled in grocery stores; inorganic is natural or unprocessed; biology-specific: organic molecule must contain carbon and hydrogen (C–H bonds) and may include other elements.

• Autotrophs vs heterotrophs

  • Autotrophs: can produce organic molecules (e.g., via photosynthesis) to transform or store energy.
  • Heterotrophs: consume organic molecules produced by autotrophs; may make some molecules from pieces of autotrophs but cannot synthesize everything from scratch.

• Four major classes of organic molecules in biology: carbohydrates, nucleic acids, lipids, and proteins.

• Polymers and monomers

  • Organic molecules are polymers (poly = many).
  • Monomers: the small subunits that join to form polymers (mono = one).
  • The typical way to build polymers: dehydration synthesis (condensation)
  • Monomer + Monomer → Polymer + H2O
  • Water is produced during polymer formation.
  • The reverse reaction is hydrolysis
  • Polymer + H2O → Monomer(s)

• The four classes and their general polymers

  • Carbohydrates: polymers built from sugar monomers; function includes energy storage and structural roles.
  • Nucleic acids: polymers of nucleotides that store and transmit genetic information.
  • Proteins: polymers of amino acids that perform a huge range of cellular functions.
  • Lipids: not true polymers in the same way as the others; built from various blocks and include fats, sterols, waxes, phospholipids; important in storage and membranes.

• Quick visuals and analogies used in class

  • Train car analogy for polymers and monomers: polymer = train; monomers = train cars; dehydration synthesis = attaching cars with water produced; hydrolysis = breaking the train apart with water.
  • Simple vs complex carbohydrates depend on how many sugar monomers are linked:
  • Monosaccharides: single sugar units.
  • Disaccharides: two linked sugars.
  • Oligosaccharides: roughly 3–100 sugar units.
  • Polysaccharides: more than about 100 sugar units (e.g., cellulose, starch, glycogen).

• Carbohydrates overview

  • Carbohydrates are the simplest organic molecules among the four classes, carrying C, H, and O.
  • General ratio and formula:
  • Empirical ratio: 1 carbon : 2 hydrogens : 1 oxygen (1:2:1).
  • General formula:
  • (CH2O)n
  • An example formula for sugars: C6H{12}O_6
  • Monomers (sugars): monosaccharides (e.g., glucose).
  • When two monosaccharides join, they form a disaccharide (e.g., sucrose, formed from glucose and fructose).
  • The dehydration synthesis that makes sucrose from glucose + fructose is also called condensation.
  • When disaccharides or polysaccharides are broken down, hydrolysis occurs, adding water to split them into monosaccharides.
  • If you have 3–100 sugar units: oligosaccharide; >100 units: polysaccharide.
  • Notable polysaccharides and related topics:
  • Cellulose: major component of plant cell walls (structural).
  • Starch: energy storage in plants (e.g., potatoes).
  • Glycogen: energy storage in animals (liver).
  • Monomers of carbohydrates are sugars; polymer is the carbohydrate; the building blocks are sugars.

• Nucleic acids

  • Monomer units: nucleotides.
  • A nucleotide consists of three parts: a sugar, a phosphate group, and a nitrogenous base.
  • Two types of nucleic acids: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).
  • Differences between DNA and RNA (at the level of this chapter):
  • The sugar component differs (deoxyribose in DNA vs ribose in RNA).
  • The nitrogenous bases differ; DNA and RNA share three bases but have different others; crucially, thymine in DNA vs uracil in RNA (in RNA, uracil pairs with adenine).
  • Visuals/types: single-stranded RNA and the double-helix form of DNA; nucleotide units are repeated along a strand to form DNA or RNA.
  • Polymerization of nucleotides occurs via dehydration synthesis to form nucleic acids.
  • Key reconnaissance: nucleic acids store and transmit genetic information; structure and sequence dictate function.

• Proteins

  • Monomer: amino acids (20 standard amino acids).
  • Basic amino acid structure: a central carbon atom attached to an amino group (–NH2), a carboxyl group (–COOH), a hydrogen, and a variable side chain (R group).
  • The R group determines identity and properties of each amino acid.
  • Peptide bonds connect amino acids; the resulting chain is called a polypeptide, and a protein is one or more polypeptides folded into a functional form.
  • Protein structure levels:
  • Primary structure: linear sequence of amino acids.
  • Secondary structure: folding due to hydrogen bonds forming alpha helices and beta-pleated sheets.
  • Tertiary structure: 3D folding and interactions among R groups, producing a single protein’s overall shape.
  • Quaternary structure: multiple polypeptide chains interacting to form a functional protein complex.
  • Shape dictates function; changes in sequence or folding can change function.
  • Denaturation: extreme conditions (heat, pH, salt) can unfold proteins, destroying function.
  • Practical example and visual cue: cooking an egg demonstrates denaturation—the clear liquid egg white becomes solid as proteins unfold and refold differently under heat.
  • Functional versatility: proteins perform catalysis (enzymes), defense, transport, structural support, motion, regulation, and storage, among other roles.
  • Important note on diversity: although there are only 20 amino acids, countless proteins arise from different orderings and foldings.
  • Prions: misfolded proteins that can cause brain diseases (e.g., Creutzfeldt–Jakob disease); prion diseases highlight how misplaced protein folding can be harmful and have serious consequences.

• Lipids

  • Lipids are not true polymers like carbohydrates, nucleic acids, and proteins, but they form larger structures by combining distinct building blocks into polymer-like assemblies.
  • Four main lipid types discussed: 1) Triglycerides (fats): glycerol backbone + three fatty acid tails.
    • Saturated fats: tails are straight, fully hydrogen-saturated; solid at room temperature; commonly from animal sources (but not exclusively).
    • Unsaturated fats: tails have one or more double bonds causing kinks; typically liquids at room temp; commonly from plant sources.
    • Trans fats (partially hydrogenated fats): artificial fats with altered structure; often solid at room temperature; less healthy; increasingly labeled to avoid.
    • Practical implication: dietary recommendations favor unsaturated fats over saturated fats due to energy yield and health effects.
      2) Sterols: four-ring carbon structures; many hormones and vitamins are sterols (e.g., cholesterol is a sterol constituent of membranes and precursor to steroid hormones).
      3) Waxes: long-chain fatty acids esterified with long-chain alcohols; highly water-repellent; used by organisms to waterproof surfaces (e.g., on fur, feathers).
      4) Phospholipids: glycerol backbone with a phosphate-containing head group and two fatty acid tails.
    • Head is hydrophilic (water-loving); tails are hydrophobic (water-fearing).
    • In aqueous environments, phospholipids arrange into bilayers with tails pointing inward and heads facing water, forming cell membranes (phospholipid bilayer).
  • Phospholipid bilayers are central to membranes in eukaryotic cells; membranes create a barrier and provide a controlled environment inside cells.

• Cross-cutting implications and context

  • The physical properties of each class (e.g., carbohydrate ratios, lipid hydrophobic/hydrophilic nature, protein folding) influence their biological roles and how organisms store energy, build structures, and regulate internal environments.
  • Homeostasis and proteins: maintaining stable internal conditions preserves protein structure and function; deviations (e.g., extreme pH or temperature) can lead to denaturation and loss of function.
  • Real-world relevance and ethics: understanding lipids informs nutrition and health (e.g., dietary fats) and recognizing prion diseases underscores importance of protein folding in health.
  • Foundational connections: the idea of polymers and monomers ties into chemistry, biology, and physiology, linking Chapter 1 concepts (energy, metabolism) to Chapter 3 topics (molecular basis of life).

• Quick recap of key equations and numerical notes

  • Carbohydrate general formula and ratio: (CH2O)n \text{ with } 1:2:1 ext{ ratio (C:H:O)}
  • Monomer to polymer concept: ext{Monomer} + ext{Monomer}
    ightarrow ext{Polymer} + H_2O ag{dehydration synthesis/condensation}
  • Polymer to monomers (hydrolysis): ext{Polymer} + H_2O
    ightarrow ext{Monomer} + ext{Monomer} +
    abla ext{(additional units as needed)}

• Nucleic acids and proteins rely on dehydration synthesis to join monomers: nucleotides; amino acids; and the formation of peptide bonds between amino acids.

• Amino acid general structure (concise): NH2-CHR-COOH, where R varies among the 20 standard amino acids.

• Protein structure and terminology: primary, secondary, tertiary, quaternary; peptide bonds connect amino acids; denaturation and prions illustrate the importance of correct folding for function.

• Lipids structural notes: triglycerides (backbone + 3 fatty acids), phospholipids (glycerol + phosphate head + 2 fatty acids) forming membranes; saturated vs unsaturated vs trans fats; sterols and waxes provide other roles in organisms.

• Examples mentioned in class: glucose (monosaccharide; C6H12O6), sucrose (disaccharide), cellulose (plant cell wall), starch (plant energy storage), glycogen (animal energy storage, e.g., liver), DNA/RNA structures, ATP synthase as an important protein example, collagen/keratin as protein examples (not exhaustively required for this chapter).

• Prions and related diseases highlighted the real-world implications of protein misfolding (e.g., Mad Cow disease, Creutzfeldt–Jakob disease).

• Organismal relevance to lifestyle: carbohydrates as dietary energy sources; fats as dense energy storage; proteins as structural and functional workhorses in cells; lipids forming membranes essential for cellular integrity and selective permeability.

• Questions to check understanding (example prompts):

  • How does dehydration synthesis differ from hydrolysis in terms of water involvement and bonds formed/broken?
  • What are the monomers and polymers for each of the four organic molecule classes?
  • How does protein folding affect function, and what can denaturation do to a protein?
  • Describe the phospholipid bilayer and why it forms a barrier for aqueous environments.
  • Outline the differences between saturated, unsaturated, and trans fats in terms of structure and health implications.