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Chapter 4 Notes: Carbon and the Molecular Diversity of Life

CONCEPT 4.1 Organic chemistry is key to the origin of life

  • Definition and scope
    • Compounds that contain carbon are called organic; study is organic chemistry.
    • Range of organic compounds: from simple molecules like CH_4 to colossal macromolecules (proteins, nucleic acids, etc.).
  • Origin of life and abiotic synthesis (Miller–Urey type work)
    • In 1953, Stanley Miller designed an experiment to test abiotic synthesis of organic compounds under presumed early-Earth conditions.
    • Setup (Figure 4.2): closed system with a primeval-sea analog, a gas mixture (the “atmosphere”), electrical sparks to simulate lightning, and a condenser that returns water and dissolved organics to the sea.
    • Atmosphere mixture: H2, CH4, NH_3, and water vapor; water heated to form vapor that enters the atmosphere flask; sparks discharged to mimic lightning; condenser cools the atmosphere and rain carries dissolved molecules back to the sea.
    • Over cycles, Miller collected samples and analyzed them for organic products.
    • Results: formation of several organic molecules common in organisms, including simple molecules such as formaldehyde CH_2O and hydrogen cyanide HCN, as well as more complex molecules like amino acids and long hydrocarbon chains.
    • Conclusion: organic molecules could be synthesized abiotically under plausible prebiotic conditions; later work refined atmospheric compositions but still produced organics under revised scenarios.
  • Relevance to life and planetary missions
    • The uniformity of major bioelements across life (C, H, O, N, S, P) supports a common origin, with carbon’s ability to form four bonds enabling vast molecular diversity.
    • Mars connection: 2018 NASA Curiosity findings of carbon-based compounds in a former lake crater raise questions about past life or prebiotic chemistry elsewhere; the presence of such compounds could reflect abiotic synthesis or relics of life.
  • Key quantitative concept
    • Avogadro’s number: N_A = 6.02 \times 10^{23} molecules (or atoms) per mole.
  • Mastering Biology: Interview context
    • Interview with Stanley Miller discusses how life’s chemistry could be governed by physical and chemical laws at origin.
  • Concept Check 4.1 (quick assessment)
    • Visual Skills: Figure 4.2 interpretation about controls lacking sparks versus those with sparks.
    • Inquiry: Can organic molecules form under early-Earth simulations?
  • Additional historical data and insights
    • Miller’s classic 1953 data inspired further experiments; later analyses used revised starting chemistries but also yielded organic products.
  • Summary of implications
    • Organic chemistry is central to life: carbon’s tetravalence and versatility enable immense molecular diversity; life’s building blocks may have arisen through straightforward abiotic processes under plausible early-Earth conditions.
    • This underpins the view that biology is constrained and explained by chemistry and physics.

CONCEPT 4.2 Carbon atoms can form diverse molecules by bonding to four other atoms

  • Core idea: carbon’s chemical characteristics arise from its electron configuration
    • Valence electrons (outer shell) govern bonding possibilities.
    • Carbon has 6 electrons: 2 in the first shell, 4 in the second shell; thus, 4 valence electrons available for bonding.
    • Carbon often completes its valence shell by sharing electrons, forming covalent bonds.
    • In organic molecules, carbon typically forms single or double covalent bonds and can act as an intersection point with up to four directions for branching.
  • Bonding and shapes
    • Single bonds: tetrahedral geometry around a carbon with four single bonds; bond angles ~109.5° (e.g., in CH_4).
    • Double bonds: when two carbons are joined by a double bond (as in C2H4), the attached substituents lie in the same plane (flat geometry).
    • Graphical depictions include structural formulas, ball-and-stick models, and space-filling models; note that molecules are three-dimensional and shape affects function.
  • Valence and major partners
    • The valence (number of covalent bonds) generally equals the number of electrons needed to fill the valence shell.
    • Common partners: hydrogen (H), oxygen (O), nitrogen (N), and carbon–carbon bonds; other partners expand diversity.
  • Examples: CO₂ and urea
    • Carbon dioxide: a carbon atom double-bonded to two oxygens, written as O=C=O. Each bond represents a double covalent bond; valence shells are satisfied for C and O. Although simple, CO₂ is inorganic in common usage, yet it is central for carbon supply to organic molecules via photosynthesis.
    • Urea: chemical formula CO(NH2)2; features one carbon atom with both single and double bonds; illustrates how carbon can participate in varied bonding patterns.
  • Carbon skeleton variation (how diversity arises)
    • Carbon skeletons: vary in length, branching, presence of rings, and double-bond position.
    • Examples: unbranched alkanes (ethane), branched alkanes (2-methylpropane, isobutane), and longer chains (propane, butane).
  • Carbon skeleton variation visualized
    • (a) Length: examples include ethane, propane, butane; skeletons vary in chain length.
    • (b) Branching: skeletons may be unbranched or branched (e.g., butane vs. 2-methylpropane).
    • (c) Double-bond position: presence of one or more double bonds changes geometry and reactivity.
    • (d) Rings: cyclic structures such as cyclohexane and benzene demonstrate ring formation.
  • Hydrocarbons
    • Hydrocarbons: molecules consisting only of carbon and hydrogen; serve as major energy sources and backbones for larger molecules.
    • Hydrogens are attached wherever electrons are available; hydrocarbons are hydrophobic due to predominantly nonpolar C–H bonds.
    • Hydrocarbons can release substantial energy upon reaction, making them important as fuels (e.g., in gasoline) and fat storage in organisms.
  • Role of carbon skeletons in biology
    • Fats: long hydrocarbon tails attached to a nonhydrocarbon component; tails store energy for seeds and animals; fats are hydrophobic due to nonpolar bonds.
  • Rings and aromaticity
    • Some carbon skeletons form rings; examples include cyclohexane and benzene, illustrating combo of ring geometry with hydrogens.
  • Isomerism (the diversity beyond formula)
    • Isomers have the same molecular formula but different structures, leading to different properties.
    • Types covered: structural isomers, cis-trans (geometric) isomers, and enantiomers.
  • Structural isomers
    • Different covalent arrangements of atoms; e.g., two C₅H₁₂ isomers with the same formula but different skeletons (linear vs. branched).
    • The number of isomers increases rapidly with molecular size (e.g., C₈H₁₈ has 18 structural isomers; C₂₀H₄₂ has 366,319).
  • Cis-trans (geometric) isomers
    • Double bonds prevent rotation; if each double-bonded carbon has two different substituents, cis/trans isomers arise.
    • Example: a double bond with two different groups (X) can yield cis isomer (X on same side) or trans isomer (X on opposite sides).
    • Biological relevance: geometry can dramatically affect activity (e.g., vision and trans fats).
  • Enantiomers
    • Enantiomers are mirror-image isomers around an asymmetric carbon (a carbon attached to four different groups).
    • Often only one enantiomer is biologically active because only that form binds specific targets.
    • Pharmaceutical relevance: different enantiomers can have very different effects (e.g., ibuprofen, albuterol; methamphetamine has distinct effects by enantiomer).
  • Visual and conceptual checks
    • Enantiomers behave differently in biology even though they share formula and connectivity.
    • The presence of an asymmetric carbon creates non-superimposable mirror images (R vs S forms).
  • Concept Check 4.2 (quick assessment)
    • Draw structural formula for C2H4; draw the trans isomer of C2H2Cl_2.
    • Identify isomer pairs in the shown hydrocarbons; classify each.
    • How are gasoline and fat chemically similar?
    • Can propane C3H8 form isomers? Explain.
  • Summary takeaway
    • Carbon’s tetravalence and ability to form diverse skeletons underlie the vast molecular diversity of life, including hydrocarbons, functional groups, and complex biomolecules.

CONCEPT 4.3 A few chemical groups are key to molecular function

  • Core idea
    • The properties of an organic molecule depend not only on the carbon skeleton but also on chemical groups attached to it.
    • These groups can participate in chemical reactions (functional groups) or influence molecular shape, thereby affecting function.
  • Functional groups and their roles
    • Seven key groups frequently seen in biology: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl.
    • The first six groups are chemically reactive; all except the sulfhydryl group are hydrophilic and generally increase solubility in water.
    • The methyl group is not highly reactive but can serve as a recognizable tag that influences molecule behavior and gene expression.
  • Highlights of each group (from Figure 4.9)
    • Hydroxyl group (-OH)
    • Polar due to electronegative oxygen; forms hydrogen bonds with water; increases solubility of sugars; common in alcohols (e.g., CH3CH2OH).
    • Example: Ethanol (an alcohol).
    • Carbonyl group (C=O)
    • Within a carbon skeleton (ketone) or at the end (aldehyde).
    • Examples: Acetone (ketone) and Propanal (aldehyde).
    • Carboxyl group (-COOH)
    • Acts as an acid (donates H+) because the O–H bond is highly polar.
    • Ionized form at cellular pH: carboxylate (-COO⁻).
    • Examples: Acetic acid (in vinegar).
    • Amino group (-NH₂)
    • Acts as a base; can pick up an H⁺ from solution.
    • Examples: Propanal (aldehyde includes amino in amino acids? Note: the amino group is present in amino acids like glycine but shown here in abstract form).
    • Sulfhydryl group (-SH)
    • Thiol; Can form disulfide bridges that help stabilize protein structure (cross-links).
    • Example: Cysteine (a sulfur-containing amino acid).
    • Phosphate group (-OPO₃²⁻)
    • Contributes negative charge; attached to molecules confers reactivity with water and release of energy when hydrolyzed.
    • Example: Glycerol phosphate.
    • Methyl group (-CH₃)
    • Nonreactive; a tag that can affect gene expression and hormone shape when attached to DNA or proteins; modulates activity and recognition.
  • ATP as a special case of a phosphate-containing molecule
    • ATP structure: adenosine attached to a chain of three phosphate groups.
    • Reaction (hydrolysis): ATP reacts with water to yield ADP and inorganic phosphate (P_i) plus energy.
    • Overall representation: ext{ATP} + ext{H}2 ext{O} ightarrow ext{ADP} + ext{P}i + ext{Energy}
    • ADP is adenosine diphosphate after losing one phosphate; ATP stores the potential to react with water or other molecules, releasing usable energy when hydrolyzed.
  • The chemical elements of life: a quick synthesis
    • Living matter is built mainly from carbon, oxygen, hydrogen, and nitrogen, with sulfur and phosphorus in smaller amounts.
    • These elements form strong covalent bonds that build complex organic molecules whose properties emerge from their carbon skeletons and attached groups.
    • Carbon remains the central element enabling the vast diversity of life.
  • Concept Check 4.3 (quick assessment)
    • Visual Skills: definition of an amino acid in the context of Figure 4.9.
    • What chemical change occurs to ATP when it reacts with water and releases energy?
    • Draw cysteine with -NH₂ replaced by -COOH; discuss how this alters properties and whether the central carbon remains asymmetric before/after.
  • Summary of the chapter’s key themes
    • Organic chemistry enables the origin and diversity of life through carbon’s tetravalence and the variety of functional groups.
    • Isomerism (structural, cis-trans, enantiomers) adds richness to molecular diversity and biological activity.
    • Functional groups determine reactivity, solubility, and biological function; small changes in groups can dramatically alter outcomes (drug activity, metabolism, structure-function relationships).
    • ATP and phosphates illustrate how chemistry directly fuels cellular processes.

Concept Check 4.3: Quick review prompts (from the chapter)

  • 1) Visual Skills: What does the term amino acid signify about the structure of such a molecule? See Figure 4.9.
  • 2) What chemical change occurs to ATP when it reacts with water?
  • 3) Draw cysteine with the -NH₂ group replaced by -COOH. How would this change affect chemical properties and the symmetry of the central carbon before/after?

Test Your Understanding (selected items from the chapter)

  • Levels 1–2: Remembering/Understanding
    1. Organic chemistry is currently defined as
    • (A) the study of compounds made only by living cells.
    • (B) the study of carbon compounds.
    • (C) the study of natural (as opposed to synthetic) compounds.
    • (D) the study of hydrocarbons.
    1. Visual Skills: Which functional group is present in this molecule?
    • (A) sulfhydryl
    • (B) carboxyl
    • (C) methyl
    • (D) phosphate
      [Molecule shown: HO-CH-–O–H, etc.]
    1. MAKE CONNECTIONS: Which chemical group is most likely responsible for an organic molecule behaving as a base (see Concept 3.3)?
    • (A) hydroxyl
    • (B) carbonyl
    • (C) amino
    • (D) phosphate
  • Levels 3–4: Applying/Analyzing
    1. Visual Skills: Visualize the structural formula of each of the following hydrocarbons. Which hydrocarbon has a double bond in its carbon skeleton?
    • (A) C3H8
    • (B) C2H6
    • (C) C2H4
    • (D) C2H2
    1. Visual Skills: Which of the molecules shown in question 5 has an asymmetric carbon? Which carbon is asymmetric?
    2. Visual Skills: Could propane C3H8 form isomers? Explain.
  • Levels 5–6: Evaluating/Creating
    1. Evolution connection – Draw it: Consider life elsewhere potentially silicon-based. Draw the Lewis dot structure for silicon and compare properties with carbon that would influence silicon-based life vs. neon/aluminum-based life.
    2. Scientific Inquiry: Thalidomide enantiomers – propose a reason for the persistent harmful enantiomer in the body despite presence of the beneficial enantiomer.
    3. Write about a theme: Organization – L-dopa vs. D-dopa in treating Parkinson-like symptoms and how enantiomerism illustrates structure–function relationships.
    4. Synthesize your knowledge: Provide insight on how the two sugar diagrams relate (structural isomers, cis-trans, enantiomers, etc.).
  • Other selected prompts from the end-of-chapter materials
    • Visual Skill and synthesis prompts about isomers, asymmetric carbons, and the relationship between structure and function in biochemistry.

Key definitions and formulas (quick reference)

  • Major organic compounds and formulas

    • Methane: CH_4
    • Ethane: C2H6
    • Ethene (ethylene): C2H4
    • Carbon dioxide: O=C=O
    • Glycine: C2H5NO_2
    • Serine: C3H7NO_3
    • Methionine: C5H{11}NO_2S
    • Alanine: C3H7NO_2

  • Important matrices and constants

    • Avogadro’s number: N_A = 6.02 \times 10^{23} (molecules per mole)

  • Functional groups (as a quick map)

    • Hydroxyl: -OH
    • Carbonyl: C=O
    • Carboxyl: -COOH
    • Amino: -NH₂
    • Sulfhydryl: -SH
    • Phosphate: -OPO_3^{2-}
    • Methyl: -CH_3

  • ATP hydrolysis (energy release)

    • ext{ATP} + ext{H}2 ext{O} ightarrow ext{ADP} + ext{P}i + ext{Energy}

  • Note: Throughout these notes, numbers and chemical formulas use LaTeX formatting as shown, e.g., CH4, O=C=O, C2H_4, etc.