In-Depth Notes on Peptides and Peptide Bonds

Chapter 3.2: Introduction to Proteins - BCM 251 Lecture 4: Peptides and Peptide Bonds

Exercises from Lecture 2

  • Exercise 3: Identify amino acids with certain characteristics.

  • Positively charged at neutral pH: Arg (R), Lys (K), His (H)

  • Negatively charged at neutral pH: Asp (D), Glu (E)

  • Form disulphide bonds: Cys (C)

  • Aromatic character: Tyr (Y), Phe (F), Trp (W)

  • Not chiral: Gly (G)

  • More than one chiral carbon: Thr (T), Ile (I), etc.

Peptide Bonding

  • A peptide bond is a covalent bond formed between the a-carboxyl group of one amino acid and the a-amino group of another.

  • The formation of this bond involves a dehydration (or condensation) reaction where water is eliminated.

  • The resulting bond is called an amide bond.

Nature of Peptide Bonds

  • Peptide bonds do not allow free rotation because of resonance stabilization, which results in a shorter and stronger bond compared to a typical single bond.

  • Peptide bonds are represented as planar and rigid structures due to this restriction.

  • Characteristics of peptide bonds:

  • Shorter than C-C single bonds

  • Longer than C=C double bonds

Peptides vs. Proteins

  • Peptides are polymer chains of amino acids linked by peptide bonds, typically comprising 2 to several hundred amino acids.

  • Proteins are larger polypeptides, usually with more than 100 amino acids, synthesized by ribosomes.

  • Directionality of peptide chains: N-terminal (amino group) to C-terminal (carboxyl group).

Nomenclature of Peptides

  • Naming conventions:

  • Use the name of amino acids with the suffix 'yl' for the acyl group leading to the C-terminal.

    • Example: Alanyl (Ala) → Alanylleucine (Ala-Leu)

  • C-terminal is named by the standard amino acid name without a change.

  • Unique example: Glutathione is known as L-g-glutamyl-L-cysteinylglycine, reflecting participation of side chains in bonding.

Titration of Peptides

  • Peptides can be titrated similarly to individual amino acids with two or more titratable groups.

  • Typical titratable groups include:

  • C-terminal a-carboxyl group

  • N-terminal a-amino group

  • Additional groups may be present depending on amino acid composition.

Isoelectric Points

  • The isoelectric point (pI) is the pH at which a peptide has no net charge. Calculating pI involves taking the average of pKa values of the ionizing groups.

  • Examples of pI calculation:

    • Peptide: Ala-Gly → pI = (pKa of COOH + pKa of NH2)/2

Important Exercises and Self-Control Questions

  • Draw structures of proteinogenic amino acids with names and abbreviations.

  • Detail the reactions involved in the formation and hydrolysis of peptide bonds.

  • Identify key characteristics of peptide bonds and compare peptides with proteins.

Final Notes

  • Understanding the characteristics of amino acids and peptides is crucial for comprehension in biochemistry.

  • Pay attention to the structural features influencing peptide bonding and stability, as well as amino acid interactions and their implications for protein structure and function.