Biochemistry: Amino Acids and Proteins

Amino acids are the small, versatile building blocks that give proteins their structure, charge, chemistry, and ultimately their function. In biochemistry courses, the expectation is not only to recognize all 20 standard amino acids, but also to understand how their side chains behave at different pH values, how peptide bonds connect them, and how proteins fold into functional shapes. Mastery comes from linking structure to property to biological consequence.

The 20 Standard Amino Acids: Shared Backbone, Diverse Side Chains

All standard amino acids share the same core: an $\alpha$-carbon bonded to an amino group, a carboxyl group, a hydrogen, and a variable side chain (R group). At physiological pH, most amino acids exist as zwitterions, with a deprotonated carboxylate ($-\mathrm{CO}{\mathrm{O}}^{-}$) and a protonated amino group ($-\mathrm{N}{\mathrm{H}}_3^{+}$).

The side chain is where the chemistry lives. It determines whether an amino acid is hydrophobic, polar, acidic, basic, aromatic, or uniquely reactive. When you memorize amino acids, focus on patterns: side-chain functional groups tell you what the amino acid “wants” to do in water, in a membrane, in an active site, or in a folded core.

Classification by Side-Chain Properties

Nonpolar (Hydrophobic)

These side chains prefer the protein interior and drive folding by the hydrophobic effect.

• Glycine (Gly, G): smallest, no chiral center, flexible
• Alanine (Ala, A)
• Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I): branched aliphatic
• Methionine (Met, M): thioether, often internal
• Proline (Pro, P): cyclic, restricts backbone rotation, common in turns and helices breakers

Polar, Uncharged

These form hydrogen bonds and often sit on protein surfaces or in binding pockets.

• Serine (Ser, S), Threonine (Thr, T): hydroxyl groups; common phosphorylation sites
• Asparagine (Asn, N), Glutamine (Gln, Q): amide side chains; strong H-bonding
• Cysteine (Cys, C): thiol; can form disulfide bonds
• Tyrosine (Tyr, Y): phenolic OH; aromatic but can H-bond and be phosphorylated

Acidic (Negatively Charged at Physiological pH)

• Aspartate (Asp, D)
• Glutamate (Glu, E)

These contribute negative charge, participate in salt bridges, and often act as catalytic acids or bases depending on microenvironment.

Basic (Positively Charged at Physiological pH)

• Lysine (Lys, K): primary amine
• Arginine (Arg, R): guanidinium; strong positive charge
• Histidine (His, H): imidazole; special because it can be protonated or neutral near physiological pH

Aromatic

• Phenylalanine (Phe, F)
• Tyrosine (Tyr, Y)
• Tryptophan (Trp, W)

Aromatics contribute to hydrophobic cores, stacking interactions, and optical absorbance (notably Trp and Tyr).

pKa Values and Ionization: Predicting Charge with pH

pKa values matter because charge controls solubility, folding, binding, and catalysis. The rule to keep in mind: when $\mathrm{pH}<\mathrm{p}{K}_a$, the group tends to be protonated; when $\mathrm{pH}>\mathrm{p}{K}_a$, it tends to be deprotonated.

Typical values to memorize (approximate, environment-dependent):

• $\alpha$-carboxyl: pKa $\sim 2$
• $\alpha$-amino: pKa $\sim 9$ to 10
• Asp (D) side chain: pKa $\sim 4$
• Glu (E) side chain: pKa $\sim 4$ to 4.5
• His (H) side chain: pKa $\sim 6$
• Cys (C) side chain: pKa $\sim 8$ to 8.5
• Tyr (Y) side chain: pKa $\sim 10$
• Lys (K) side chain: pKa $\sim 10.5$
• Arg (R) side chain: pKa $\sim 12.5$

Histidine deserves special attention. Because its pKa is close to physiological pH, small shifts in local environment can flip it between charged and uncharged forms. That property is why histidine is so common in enzyme active sites and metal-binding motifs.

Isoelectric Point (pI): Where Net Charge is Zero

The isoelectric point is the pH at which an amino acid (or protein) has no net charge. For simple amino acids without ionizable side chains, pI is roughly the average of the $\alpha$-carboxyl and $\alpha$-amino pKa values. For acidic or basic side chains, you average the two pKa values that flank the neutral (zwitterionic) species. pI explains electrophoresis behavior and helps predict solubility: proteins are often least soluble near their pI.

Peptide Bonds and Protein Backbone Chemistry

A peptide bond forms when the carboxyl group of one amino acid reacts with the amino group of another, releasing water. The resulting amide linkage has partial double-bond character, making it planar and restricting rotation. Protein backbone flexibility comes mainly from rotations around the $\varphi$ (N–C$\alpha$) and $\psi$ (C$\alpha$–C) bonds, which is why conformational constraints like proline can dramatically affect structure.

Direction matters: proteins are synthesized and written from N-terminus to C-terminus. That convention becomes critical when discussing motifs, signal peptides, and active-site residues.

Levels of Protein Structure: From Sequence to Function

Protein structure is described at four levels. Knowing definitions is not enough; the value is in understanding how each level arises from chemistry.

Primary Structure

The amino acid sequence. A single substitution can be minor or catastrophic depending on context. Replacing a buried hydrophobic residue with a charged one, for example, can destabilize folding. Conversely, swapping similar residues on a surface might have little effect.

Secondary Structure

Local backbone folding stabilized primarily by hydrogen bonding:

• __MATH_INLINE_22__-helix: hydrogen bonds between residue $i$ and $i+4$, side chains point outward
• __MATH_INLINE_25__-sheet: strands aligned with inter-strand hydrogen bonds; can be parallel or antiparallel
• Turns and loops: often enriched in glycine (flexible) and proline (structural constraint)

Secondary structures are limited by sterics and backbone geometry, which is why not all $\varphi /\psi$ angles are allowed.

Tertiary Structure

The overall 3D fold of a single polypeptide chain, shaped by:

• Hydrophobic effect (major driver)
• Hydrogen bonds
• Ionic interactions (salt bridges)
• van der Waals packing
• Disulfide bonds (especially in extracellular proteins)

A key practical insight is that a residue’s behavior depends on its environment. An aspartate buried in a hydrophobic pocket may have an unusually shifted pKa, changing its charge state and catalytic role.

Quaternary Structure

Assembly of multiple polypeptide chains (subunits) into a functional complex. Quaternary structure enables cooperativity, regulation, and division of labor across subunits. The interfaces often feature complementary hydrophobic patches, hydrogen bonding networks, and sometimes salt bridges tuned for stability.

Protein Folding: Why Sequence Encodes Structure

Protein folding is not random trial and error. The sequence biases the chain toward conformations that minimize free energy in a given environment. Hydrophobic residues tend to cluster away from water, polar and charged residues tend to remain solvent-exposed, and certain side chains favor particular secondary structures.

Folding is also a kinetic process. Some proteins fold quickly and reliably; others require assistance from molecular chaperones to avoid misfolded states and aggregation. Misfolding can be biologically costly because exposed hydrophobic regions promote clumping, which can impair cellular function.

Connecting Amino Acid Properties to Protein Function

Many exam questions and real-world biochemical problems reduce to a few repeatable links between residue chemistry and function:

• Catalysis: Histidine, aspartate, glutamate, lysine, and cysteine often act as acid-base catalysts or nucleophiles depending on pH and local environment.
• Binding: Charged residues mediate electrostatic recognition; aromatics can stack with ligands; polar residues provide specificity through hydrogen bonds.
• Stability: Hydrophobic packing and disulfide bonds stabilize structure; disrupting the core is usually more damaging than altering a surface residue.
• Regulation: Serine, threonine, and tyrosine are common phosphorylation sites; lysine can be modified in many contexts, affecting interactions and localization.

Practical Memorization Strategy: Learn Chemistry, Not Just Names

To memorize the 20 amino acids with pKa values and classifications, anchor each one to a chemical feature: “amide,” “thiol,” “phenol,” “guanidinium,” “imidazole,” “bran