Fundamental Chemical Reactions in Biology

Why This Matters

Every biological process you'll encounter in this course—from how your cells extract energy from glucose to how your body builds the proteins that make you you—comes down to a handful of core reaction types. You're not just memorizing reactions here; you're learning the chemical logic that explains metabolism, energy transfer, homeostasis, and genetic continuity. When you understand why hydrolysis breaks bonds while condensation builds them, or why electrons flowing through redox reactions power your mitochondria, you're thinking like a biochemist.

The exam will test whether you can connect specific reactions to their biological functions and compare mechanisms across different contexts. Don't just memorize that ATP hydrolysis releases energy—know why breaking that phosphate bond matters and how it relates to the broader theme of energy coupling in cells. Master the underlying principles, and you'll be ready for anything from multiple choice to FRQ-style applications.

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Bond-Breaking and Bond-Making Reactions

These complementary reactions control how biological macromolecules are assembled and disassembled. The key mechanism is water—either added to break bonds or removed to form them.

Hydrolysis Reactions

• Water addition breaks covalent bonds—the $\text{H}$ and $\text{OH}$ from water attach to the fragments, cleaving the original molecule
• Essential for digestion of all macromolecules: proteins → amino acids, polysaccharides → monosaccharides, lipids → fatty acids and glycerol
• ATP hydrolysis ($\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{P}_i$) releases approximately $30.5 \text{ kJ/mol}$, powering cellular work

Condensation Reactions

• Dehydration synthesis joins monomers by removing water—one molecule donates $\text{OH}$, the other donates $\text{H}$
• Builds all biological polymers: peptide bonds link amino acids, glycosidic bonds link sugars, phosphodiester bonds link nucleotides
• Energetically unfavorable on its own—requires coupling to ATP hydrolysis to proceed in cells

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Electron Transfer Reactions

Redox reactions are the engine of cellular energy production. Electrons carry energy, and controlling their flow allows cells to capture that energy in usable forms.

Oxidation-Reduction (Redox) Reactions

• Electron transfer changes oxidation states—the molecule losing electrons is oxidized (OIL: Oxidation Is Loss), the one gaining is reduced (RIG: Reduction Is Gain)
• Powers both cellular respiration and photosynthesis—electron carriers like $\text{NAD}^+/\text{NADH}$ and $\text{FAD}/\text{FADH}_2$ shuttle electrons between reactions
• Drives the electron transport chain—stepwise electron transfer creates the proton gradient that produces most cellular ATP

Krebs Cycle (Citric Acid Cycle)

• Oxidizes acetyl-CoA ($\text{C}_2$) completely to $\text{CO}_2$ through eight enzymatic steps in the mitochondrial matrix
• Generates electron carriers: each turn produces $3 \text{ NADH}$, $1 \text{ FADH}_2$, and $1 \text{ GTP}$ (equivalent to ATP)
• Metabolic hub connecting carbohydrate, lipid, and protein catabolism—intermediates enter and exit for biosynthesis

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Proton Transfer and Phosphate Group Reactions

These reactions regulate cellular activity through chemical signaling and pH control. Protons and phosphate groups act as molecular switches.

Acid-Base Reactions

• Proton ($\text{H}^+$) transfer between molecules—acids donate protons, bases accept them (Brønsted-Lowry definition)
• Buffer systems maintain homeostasis—the bicarbonate buffer ($\text{H}_2\text{CO}_3/\text{HCO}_3^-$) keeps blood pH near 7.4
• Enzyme activity depends on pH—protonation states of amino acid side chains determine protein shape and function

Phosphorylation Reactions

• Addition of phosphate group ($\text{PO}_4^{3-}$) changes a molecule's charge, shape, and activity—often acts as an on/off switch
• ATP is the universal phosphate donor—kinases transfer phosphate to substrates, phosphatases remove it
• Signal transduction cascades rely on sequential phosphorylation to amplify and transmit cellular signals

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Energy Conversion Pathways

These multi-step processes transform energy between different chemical forms. They represent the integration of multiple reaction types working together.

Glycolysis

• Ten-step pathway converts one glucose ($\text{C}_6\text{H}_{12}\text{O}_6$) into two pyruvate ($\text{C}_3\text{H}_4\text{O}_3$) molecules in the cytoplasm
• Net yield: $2 \text{ ATP}$ (substrate-level phosphorylation) and $2 \text{ NADH}$—occurs with or without oxygen
• Investment phase uses 2 ATP; payoff phase generates 4 ATP—understanding this split is frequently tested

Photosynthesis

• Light-dependent reactions in thylakoid membranes split water, release $\text{O}_2$, and generate ATP + NADPH via electron transport
• Calvin cycle (light-independent) in the stroma uses ATP and NADPH to fix $\text{CO}_2$ into glucose: $6\text{CO}_2 + 6\text{H}_2\text{O} \xrightarrow{\text{light}} \text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2$
• Reverses cellular respiration energetically—stores light energy in chemical bonds rather than releasing it

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Information Transfer Reactions

These reactions ensure genetic information is accurately copied and expressed. The chemistry of nucleic acids underlies heredity and protein production.

DNA Replication

• Semi-conservative mechanism—each new double helix contains one original strand and one newly synthesized strand
• DNA polymerase adds nucleotides to the $3'$ end, forming phosphodiester bonds via condensation reactions
• High fidelity maintained through complementary base pairing (A-T, G-C) and proofreading—error rate approximately $10^{-9}$

Protein Synthesis

• Transcription in the nucleus: RNA polymerase builds mRNA from DNA template using condensation reactions
• Translation at ribosomes: tRNA delivers amino acids, peptide bonds form between them (also condensation)
• Central dogma (DNA → RNA → Protein) represents the flow of genetic information in all cells

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Quick Reference Table

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Self-Check Questions

1. Which two reaction types are exact opposites involving water, and how do they relate to building versus breaking macromolecules?

2. Both glycolysis and the Krebs cycle are central metabolic pathways—compare their locations, oxygen requirements, and primary products.

3. If a cell needs to activate an enzyme quickly without synthesizing new protein, which reaction type would most likely be involved, and why?

4. Explain how redox reactions connect photosynthesis and cellular respiration. Which process oxidizes water, and which reduces oxygen?

5. FRQ-style: A mutation prevents a cell from performing condensation reactions. Predict the effects on (a) protein synthesis, (b) DNA replication, and (c) ATP production. Justify each prediction with specific reaction mechanisms.