Peptide Bonds and Protein Primary Structure (1A) - MCAT Biological and Biochemical Foundations of Living Systems

$N$-terminus (typically $NH_3^+$). Represents the starting point of the chain where the first amino acid's amino group remains unlinked and protonated at physiological pH.

$C$-terminus (typically $COO^-$). Marks the end of the chain where the last amino acid's carboxyl group remains unlinked and deprotonated at physiological pH.

Linear amino acid sequence linked by peptide bonds. Determines the unique identity and function of the protein, as it specifies the order of residues that dictates higher-order folding.

...$N$$C_$$C$... or ...$N$-$C_$-$C$... pattern. Reflects the polypeptide backbone's repeating motif where nitrogen bonds to alpha carbon, which bonds to carbonyl carbon.

$N$-terminus = Ala end; $C$-terminus = Ser end. The sequence starts with alanine's free amino group at the N-end and ends with serine's free carboxyl at the C-end.

Amino acid residues. Refers to amino acids that have lost water during peptide bond formation and are now integral parts of the chain.

$n-1$ molecules of $H_2O$. Each peptide bond formation eliminates one water molecule, so for $n$ amino acids, $n-1$ bonds release that many waters.

$n-1$ peptide bonds. In a chain of $n$ residues, each internal linkage is a peptide bond, totaling one less than the number of residues.

Carbonyl carbon ($C=O$) bonded to amide nitrogen ($N$). Constitutes the amide linkage where the carbonyl carbon from one residue covalently attaches to the nitrogen of the next.

Partial double-bond character from resonance. Arises from electron delocalization between the carbonyl and nitrogen, restricting rotation and enforcing planarity.

Rotation about the $C-N$ peptide bond. Resonance stabilization imparts partial double-bond nature, limiting free rotation and contributing to backbone rigidity.

Rotation about $N-C_$ ($$) and $C_-C$ ($$) bonds. These single bonds allow torsional flexibility, enabling diverse conformations in the protein's secondary and tertiary structures.

Trans configuration. Minimizes steric hindrance between side chains, making it energetically favorable in most peptide bonds except near proline.

Proline. Its cyclic side chain reduces the energy difference between cis and trans, allowing cis configurations more frequently.

Dipeptide. Consists of exactly two amino acids joined by one peptide bond, representing the smallest polypeptide unit.

Carboxyl group of one amino acid and amino group of the next. These groups undergo dehydration synthesis, eliminating water to establish the covalent amide bond in the protein chain.

Peptide (amide) bond between the $$-carboxyl and $$-amino groups. Forms via condensation between the carboxyl group of one amino acid and the amino group of another, creating a rigid linkage in the polypeptide backbone.

Condensation (dehydration) reaction releasing $H_2O$. Involves the loss of a water molecule as the carboxyl group of one amino acid reacts with the amino group of another to form the amide linkage.

Tripeptide. Comprises three amino acids connected by two peptide bonds, serving as a basic model for studying peptide properties.

Oligopeptide (short peptide). Describes peptides with a limited number of residues, often functioning as signaling molecules or hormones in biology.

Peptide (amide) bond hydrolysis. Enzymatic cleavage adds water across the amide bond, reversing condensation to degrade proteins into smaller fragments.

$6$ peptide bonds and $6$ molecules of $H_2O$. For 7 residues, 6 internal linkages form, each releasing one water molecule during condensation synthesis.

Amide bond (peptide bond in proteins). Results from nucleophilic attack by the amino nitrogen on the carbonyl carbon, forming a stable covalent connection in peptides.