Biochemistry Basics

Definition: Biochemistry is the study of the chemical processes and molecules, proteins, carbohydrates, lipids, and nucleic acids, that occur within living organisms.

How It Works

Living systems build almost everything from four classes of biomolecules, each assembled from repeating monomers linked by specific bonds:

Proteins: chains of amino acids joined by peptide bonds, a condensation reaction between an amino group and a carboxyl group, releasing water.
Amino acid sequence determines 3D folding, which determines function.
Carbohydrates: built from monosaccharides (glucose, fructose) linked by glycosidic bonds.
Starch and glycogen store energy; cellulose and chitin provide structure.
These differ from starch only in bond geometry, beta- versus alpha-linkages.
Lipids: fats (glycerol plus three fatty acids joined by ester bonds), phospholipids (form cell membranes), and steroids.
Saturated fatty acids have no C=C double bonds and pack tightly; unsaturated ones have kinks that keep them liquid at room temperature.
Nucleic acids (DNA, RNA): chains of nucleotides linked by phosphodiester bonds.
Each nucleotide has a sugar, a phosphate, and a nitrogenous base.
Base pairing (A-T, G-C via hydrogen bonds) lets DNA template its own replication and direct protein synthesis.

Enzymes and information flow:

Enzymes, almost always proteins, catalyze nearly every reaction in this system by lowering activation energy.
This lets reactions that would otherwise take years happen in milliseconds.
The central dogma summarizes the information flow: DNA is transcribed into messenger RNA, which is translated into protein.
Each amino acid is specified by a three-nucleotide codon read off the mRNA sequence.

Metabolism:

Catabolism breaks molecules down to release energy: glycolysis, the citric acid cycle.
Anabolism builds larger molecules from smaller ones, consuming energy: protein synthesis, fatty acid synthesis.
Cells constantly balance both directions depending on whether energy or building blocks are needed.

Protein structure, four levels, each building on the last:

Primary: the linear amino acid sequence, held together by peptide bonds.
Secondary: local folding patterns (alpha helices, beta sheets) stabilized by hydrogen bonds between backbone atoms.
Tertiary: the overall 3D shape of a single chain, driven by side-chain interactions, hydrophobic clustering, disulfide bridges, and ionic bonds.
Quaternary: how multiple folded chains assemble into a functional complex, as in hemoglobin’s four subunits.

Under the Hood

Peptide bond formation is a condensation (dehydration synthesis) reaction:

H2N-CHR1-COOH + H2N-CHR2-COOH → H2N-CHR1-CO-NH-CHR2-COOH + H2O

Each bond formed releases one water molecule.
An n-amino-acid polypeptide has released (n-1) waters relative to its free amino acids.

Worked example: enzyme kinetics.

v = Vmax[S] / (Km + [S])

Km is the substrate concentration at half-maximal velocity, lower Km means higher affinity.
Given: Vmax = 100 μmol/min, Km = 2.0 mM
Step 1: rate at [S] = 2.0 mM

v = (100 × 2.0)/(2.0 + 2.0) = 200/4.0

Answer: v = 50 μmol/min, exactly half of Vmax, as expected when [S] = Km
Step 2: rate at [S] = 20 mM (ten times Km)

v = (100 × 20)/(2.0 + 20) = 2000/22

Answer: v = 90.9 μmol/min, showing the curve flattening as it approaches Vmax

Worked example: energy yield.

Given: complete oxidation of one glucose molecule

C6H12O6 + 6O2 → 6CO2 + 6H2O
ΔG° ≈ -2,870 kJ/mol

Step 1: theoretical ATP yield is about 30-32 ATP (older textbooks cite 36-38; the lower figure accounts for the real cost of shuttling NADH across the mitochondrial membrane)
Step 2: each ATP captures roughly 30.5 kJ/mol

(30 × 30.5)/2870 × 100 ≈ 32%

Answer: about 32% of the reaction’s free energy is captured as ATP, the rest released as heat

Why It Matters

Biochemistry underlies medicine, nutrition, agriculture, and biotechnology.
Drug design depends on understanding how small molecules bind enzyme active sites or receptors.
Diagnosing metabolic disease often means tracing a broken step in a biochemical pathway.
PCR, CRISPR, and recombinant insulin production are direct applications of nucleic acid and protein chemistry.
Nutrition labels trace back to the different oxidation states of carbon in lipids versus sugars.
Fats are more reduced, more C-H bonds relative to C-O, so oxidizing them releases more energy per gram.
Per-gram energy counts: 4 kcal/g for carbohydrates, 4 kcal/g for protein, 9 kcal/g for fat.
These differences come directly from how reduced, hydrogen-rich, oxygen-poor, each molecule class is before oxidation.

Common Pitfalls

Assuming DNA and RNA are interchangeable: RNA uses ribose (has a 2’-OH) and uracil instead of thymine, and is typically single-stranded.
These structural differences make RNA chemically less stable than DNA.
Thinking enzymes are consumed in the reactions they catalyze; like all catalysts, they’re regenerated and reused.
Enzymes can still be inhibited or denatured over time, even though they aren’t consumed.
Confusing saturated and unsaturated fats by structure: “saturated” refers to being saturated with hydrogen, not solution saturation.
Forgetting protein function depends on 3D folding, not just amino acid sequence.
Denaturation (heat, pH, agitation) can destroy function without breaking a single peptide bond.
Treating “organic” (contains carbon) and “biological” as synonyms; many organic compounds are entirely synthetic.
Assuming a low Km always means a “better” enzyme; it means higher substrate affinity, not higher maximum speed (Vmax).

Comparison

Biomolecule	Monomer	Bond Type	Primary Role
Protein	Amino acid	Peptide bond	Catalysis, structure, transport, signaling
Carbohydrate	Monosaccharide	Glycosidic bond	Energy storage, structure
Triglyceride (fat)	Glycerol + fatty acids	Ester bond	Energy storage
Phospholipid	Glycerol + fatty acids + phosphate	Ester bond	Cell membrane structure
DNA	Nucleotide (deoxyribose)	Phosphodiester bond	Genetic storage, replication
RNA	Nucleotide (ribose)	Phosphodiester bond	Genetic expression, protein synthesis

Feature	DNA	RNA
Sugar	Deoxyribose (no 2’-OH)	Ribose (has 2’-OH)
Unique base	Thymine	Uracil
Strandedness	Typically double-stranded	Typically single-stranded
Stability	More chemically stable	Less chemically stable
Primary role	Long-term genetic storage	Transcription, translation

Real-World Application

Lactose intolerance is a direct biochemical enzyme deficiency.

Lactase hydrolyzes the glycosidic bond in lactose, a disaccharide of glucose and galactose, into its two absorbable monosaccharides:

Lactose + H2O → Glucose + Galactose

Without enough lactase, undigested lactose reaches the colon.
Gut bacteria ferment it there, producing gas and drawing water into the intestine by osmosis.
That’s the direct cause of the bloating and discomfort associated with the condition.
Lactase supplements or lactose-free dairy, pre-treated with the enzyme, work by supplying the missing catalytic step directly.

Example

Digestive enzymes like amylase break the alpha-glycosidic bonds in starch, converting it into glucose molecules the small intestine can absorb. Insulin, a small protein hormone, then signals cells to take up that glucose from the bloodstream, an entire physiological response driven by molecules built from the same handful of monomer classes.

FAQ

Why does DNA use thymine while RNA uses uracil?

Uracil is a slightly cheaper molecule to make.
DNA needs thymine because cytosine spontaneously degrades into uracil over time.
Using thymine as DNA’s normal base lets repair enzymes recognize any uracil they find as damage and excise it.
That check wouldn’t work if uracil were also the normal base.

Are all proteins enzymes?

No. Enzymes are one functional category of protein.
Others include structural proteins (collagen, keratin), transport proteins (hemoglobin), antibodies, and signaling hormones (insulin).

Why do proteins denature when heated but DNA doesn’t cook the same way?

Both lose their folded structure under heat.
DNA’s structure is far more resistant, stabilized by many stacked, mutually reinforcing hydrogen bonds and base-stacking interactions.
DNA can renature (re-anneal) once cooled, which most proteins cannot reliably do.

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