Key Biochemical Molecules

Why This Matters

In General Chemistry with a Biological Focus, you're not just learning abstract chemical principles—you're discovering how chemistry makes life possible. The molecules covered here represent the core players in every biological system, from the water that makes reactions possible to the ATP that powers them. Understanding these molecules means understanding structure-function relationships, intermolecular forces, thermodynamics, and chemical equilibrium in their most relevant context.

When you encounter these molecules on exams, you're being tested on your ability to connect their chemical properties to their biological roles. Why does water's polarity matter? How do hydrogen bonds determine protein shape? What makes ATP an effective energy carrier? Don't just memorize names and functions—know what chemical principle each molecule illustrates and why its structure enables its function.

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Molecules That Enable Life's Chemistry

Water isn't just a backdrop for biochemistry—it's an active participant. Its unique chemical properties create the environment where all other biochemical reactions occur.

Water

• Polar covalent bonds create a bent molecular geometry—the oxygen atom's partial negative charge and hydrogen atoms' partial positive charges enable extensive hydrogen bonding
• High specific heat capacity ($4.18 \, \text{J/g·°C}$) results from hydrogen bonds absorbing energy before temperature rises, stabilizing biological temperatures
• Cohesion and adhesion drive capillary action and surface tension, critical for nutrient transport in organisms

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Energy Storage and Transfer Molecules

Living systems need to capture, store, and deploy energy efficiently. These molecules solve that problem through different chemical strategies—some for quick access, others for long-term reserves.

Carbohydrates

• Primary rapid energy source—glucose ($\text{C}_6\text{H}_{12}\text{O}_6$) releases approximately $4 \, \text{kcal/g}$ through cellular respiration
• Classified by complexity: monosaccharides (glucose, fructose), disaccharides (sucrose, lactose), and polysaccharides (starch, glycogen, cellulose)
• Structural roles include cellulose in plant cell walls and chitin in arthropod exoskeletons, both utilizing $\beta$-glycosidic linkages for rigidity

Lipids

• Energy-dense storage molecules—yield approximately $9 \, \text{kcal/g}$, more than double that of carbohydrates due to their highly reduced carbon chains
• Hydrophobic character arises from long nonpolar hydrocarbon tails, making them ideal for membrane formation and water-insoluble storage
• Diverse classes include triglycerides (energy storage), phospholipids (membrane structure), and steroids (signaling molecules like hormones)

ATP (Adenosine Triphosphate)

• Universal energy currency—the hydrolysis reaction $\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{P}_i$ releases approximately $-30.5 \, \text{kJ/mol}$ under standard conditions
• High-energy phosphoanhydride bonds store energy due to electrostatic repulsion between negatively charged phosphate groups
• Couples exergonic to endergonic reactions—energy released from ATP hydrolysis drives otherwise unfavorable cellular processes

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Information-Carrying Molecules

Life requires a system for storing, copying, and expressing genetic information. Nucleic acids solve this problem through complementary base pairing and a sugar-phosphate backbone.

Nucleic Acids (DNA and RNA)

• Nucleotide structure: each monomer contains a pentose sugar (deoxyribose in DNA, ribose in RNA), a phosphate group, and a nitrogenous base
• DNA's double helix is stabilized by hydrogen bonds between complementary bases (A-T with 2 bonds, G-C with 3 bonds) and hydrophobic base stacking
• RNA's single-stranded structure allows it to fold into functional shapes, enabling roles in transcription, translation, and catalysis (ribozymes)

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Catalysis and Reaction Control

Biological systems operate at mild temperatures and pressures, yet they run thousands of reactions simultaneously. Enzymes make this possible by dramatically lowering activation energy barriers.

Proteins

• Amino acid polymers linked by peptide bonds ($-\text{CO-NH}-$), with 20 standard amino acids providing diverse R-group chemistry
• Four structural levels: primary (sequence), secondary ($\alpha$-helices, $\beta$-sheets from hydrogen bonding), tertiary (3D folding), and quaternary (multi-subunit assembly)
• Structure determines function—denaturation disrupts non-covalent interactions, destroying biological activity while leaving peptide bonds intact

Enzymes

• Biological catalysts that lower activation energy ($E_a$) without altering reaction thermodynamics—they speed up reactions but don't change $\Delta G$
• Substrate specificity arises from the active site's complementary shape and chemical environment, often described by the induced fit model
• Sensitive to conditions—optimal pH and temperature reflect the non-covalent interactions maintaining active site geometry

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Signaling and Communication Molecules

Multicellular organisms require coordination between cells and tissues. Chemical messengers enable this communication through specific receptor interactions.

Hormones

• Long-distance chemical messengers transported through the bloodstream to target cells with specific receptors
• Two major classes: steroid hormones (lipid-soluble, cross membranes, bind intracellular receptors) and peptide hormones (water-soluble, bind surface receptors)
• Regulate homeostasis by controlling metabolism, growth, reproduction, and stress responses through signal transduction cascades

Neurotransmitters

• Short-range signaling molecules released at synapses, enabling rapid communication between neurons and target cells
• Mechanism: released from presynaptic vesicles, diffuse across the synaptic cleft, bind postsynaptic receptors, then are rapidly cleared
• Examples with distinct functions: dopamine (reward, movement), serotonin (mood regulation), acetylcholine (muscle contraction, memory)

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Cofactors and Essential Nutrients

Many enzymes require helper molecules to function. Vitamins often serve this role, acting as coenzymes that participate directly in catalytic mechanisms.

Vitamins

• Organic micronutrients required in small amounts because the body cannot synthesize them in sufficient quantities
• Function as coenzymes—for example, B vitamins assist in energy metabolism, while vitamin C serves as an electron donor in hydroxylation reactions
• Classified by solubility: water-soluble vitamins (B complex, C) are not stored and require regular intake; fat-soluble vitamins (A, D, E, K) accumulate in tissues

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Quick Reference Table

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Self-Check Questions

1. Both DNA and proteins rely on hydrogen bonding for their structure. How does the role of hydrogen bonding differ between maintaining DNA's double helix versus stabilizing protein secondary structure?

2. ATP and glucose both provide energy to cells. Compare their chemical mechanisms of energy release and explain why cells use ATP as an energy currency rather than directly using glucose for every reaction.

3. Which two molecule types discussed are classified primarily by their solubility properties, and how does this classification affect their biological function?

4. An enzyme loses its catalytic activity when heated to $80°C$ but regains some function when cooled. Using your knowledge of protein structure, explain what likely happened at the molecular level.

5. FRQ-style prompt: A patient has a deficiency in a water-soluble B vitamin that serves as a coenzyme. Predict and explain the metabolic consequences, and contrast this with what would happen if they were deficient in a fat-soluble vitamin instead.