Introduction to Proteins: The Primary Level of Protein Structure (Chapter 5 Study Notes)

Introduction to Proteins: The Primary Level of Protein Structure

Overview

This chapter introduces the foundational concepts of protein structure, focusing on amino acids, peptide bonds, and the primary structure of proteins. Understanding these topics is essential for grasping the molecular basis of biochemistry and the function of proteins in living systems.

5.1 Amino Acids

Structure of Amino Acids

• Amino acids are organic molecules containing an amino group (–NH2), a carboxyl group (–COOH), a hydrogen atom, and a unique side chain (R group) all bonded to a central α-carbon.

• The α-carbon is the central atom; when the R group is not hydrogen, it is a chiral center (asymmetric carbon).

• At physiological pH (~7), the amino group is protonated (–NH3+) and the carboxyl group is deprotonated (–COO–), forming a zwitterion (a molecule with both positive and negative charges but overall neutral).

Stereochemistry of Amino Acids

• Most amino acids (except glycine) are chiral and exist as two stereoisomers: L- and D-amino acids, based on their similarity to glyceraldehyde.

• Enantiomers are mirror-image isomers; in proteins, only L-amino acids are commonly found.

• The Fischer projection is a 2D representation of stereochemistry.

Classification of Amino Acids

The 20 common amino acids are classified based on the chemical properties of their side chains:

• Nonpolar Aliphatic: Glycine, Alanine, Valine, Leucine, Isoleucine

• Nonpolar Aromatic: Phenylalanine, Tyrosine, Tryptophan

• Polar Uncharged: Serine, Threonine, Asparagine, Glutamine

• Positively Charged (Basic): Lysine, Arginine, Histidine

• Negatively Charged (Acidic): Aspartic acid, Glutamic acid

Properties and Codes

• Each amino acid can be referred to by a three-letter or one-letter code (e.g., Gly for glycine, G for glycine).

• Side chain carbons are designated with Greek letters (β, γ, δ, ε, ω).

Net Charges and Ionization of Amino Acids

Net Charge at Different pH

• At neutral pH, the carboxyl group is negatively charged and the amino group is positively charged.

• Amino acids without charged side chains exist as zwitterions at neutral pH.

Ionization States

• The ionization state of amino acids depends on the pH and the pKa values of their ionizable groups.

• Example: Histidine has three ionizable groups and its charge varies from +2 to –1 depending on pH.

Titration Curves

• Titration curves show how the net charge of an amino acid changes as pH increases.

• Alanine (diprotic acid) and histidine (triprotic acid) have characteristic titration curves.

UV Absorption

• Aromatic amino acids (tyrosine and tryptophan) absorb UV light at 280 nm, which is used to quantify proteins.

• Nucleic acids absorb most strongly at 260 nm.

Isoelectric Point (pI)

Definition and Calculation

• The isoelectric point (pI) is the pH at which an amino acid or peptide has no net charge.

• For amino acids with only two ionizable groups (e.g., glycine), the pI is calculated as: $pI = \frac{pK_{a1} + pK_{a2}}{2}$ Example for glycine: $pI = \frac{2.34 + 9.60}{2} = 5.97$

Charge States at Different pH

• At low pH, amino acids with basic side chains (arginine, lysine) have net charges of +2.

• At high pH, amino acids with acidic side chains (aspartic acid, glutamic acid) have net charges of –2.

5.2 Peptides and the Peptide Bond

Peptide Bond Formation

• Peptide bonds are formed by the condensation of two amino acids, releasing water.

• This reaction is thermodynamically unfavorable and requires energy input, typically coupled to ATP hydrolysis during protein biosynthesis.

Structure of Peptides

• The peptide bond is an amide bond between the α-carboxyl group of one amino acid and the α-amino group of the next.

• Peptides are molecules formed by linking two to several dozen amino acids by amide bonds.

• Polypeptide chain is the backbone of a protein, formed by linking amino acids via peptide bonds.

Small Peptides with Physiological Activity

• Oxytocin and vasopressin are small cyclic peptides with important hormonal functions.

Peptide Bond Cleavage

• Peptide bond hydrolysis is energetically favorable ($\Delta G^\circ$ ≈ –10 kJ/mol) but peptides are stable under physiological conditions.

• Proteases are enzymes that cleave specific peptide bonds, often with sequence specificity.

Sequence Specificities for Proteases

Proteolytic enzymes and chemical reagents cleave peptide bonds at specific amino acid residues:

Enzyme/Reagent	Preferred Site	Source
Trypsin	R (Arg), K (Lys)	Digestive systems of animals
Chymotrypsin	F (Phe), Y (Tyr), W (Trp)	Digestive systems of animals
V-8 protease	E (Glu), D (Asp)	Staphylococcus aureus
Cyanogen bromide	M (Met)	Chemical reagent
Thrombin	R (Arg)	Blood plasma
Carboxypeptidase	C-terminal residues	Digestive systems of animals
Thermolysin	F (Phe), L (Leu), I (Ile), V (Val), M (Met)	Bacillus thermoproteolyticus

Chapter 5 Summary

• Proteins are polymers of α-amino acids, with twenty common amino acids (and two rare) incorporated into proteins.

• Proteins are produced by condensation of amino acids via peptide bond formation.

• The unique, defined sequence of amino acids constitutes the primary structure of proteins.

• In cells, genes are transcribed into messenger RNA (mRNA), which is then translated into a polypeptide strand at the ribosomes.