Amino Acids and Protein Structure

Study Notes

Amino Acid Structure

Amino acids consist of an alpha carbon (Cα), a carboxylic acid group (-COOH), an amino group (-NH2), a hydrogen atom, and a unique R group.
Alpha amino acids have an amino group directly bonded to the alpha carbon.
Cα serves as a chiral center, resulting in optical activity of amino acids, except for glycine (where R = H).

Proteins

Proteins are large, complex molecules vital for normal bodily functions, including tissue and organ structure, function, and regulation.
Composed of hundreds of amino acids linked by peptide bonds, forming long chains likened to a string of beads.

L and D Amino Acids

L and D amino acids are enantiomers, mirroring each other and non-superimposable, like left and right hands.
Only L-amino acids are incorporated into proteins, synthesized by the body and crucial for catalyzing biochemical reactions.
Proteins, alongside DNA and RNA, are integral components of living organisms' genetic machinery and termed "building blocks of life."

Isoelectric Point (pI)

The isoelectric point is the pH level where an amino acid carries a net zero charge, forming a zwitterion.
For glycine, as pH increases, it transitions through different charged forms: a positive charge (+1), zwitterion (net zero), and a negative charge (-1).

Glycine Titration Curve

At pH 2.34 (pKa1), forms A and B of glycine are in equilibrium; at pH 9.6, forms B and C are in equilibrium.
The isoelectric point (pI) for glycine can be mathematically calculated using specific formulas.

Classification of Amino Acids

There are 20 common amino acids categorized based on the nature of their R groups.

Peptide Bond Formation

Amino acids connect through peptide bonds, which are covalent bonds formed via a nucleophilic addition-elimination reaction.
This reaction occurs between the carboxylic group of one amino acid and the amino group of another, producing a molecule of water as a byproduct.

Mechanism of Peptide Bond Formation

The nucleophilic amino group attacks the carbonyl group of the first amino acid, leading to the formation of a peptide bond.
This reaction involves steps of bond reformation, hydroxide ion elimination, and proton abstraction, culminating in the creation of a stable peptide bond.
Biological peptide bond synthesis is more complex, involving catalysts, cofactors, and enzymes.

Peptide Bond Characteristics

The peptide bond exhibits a double-bond character, which affects the structure and stability of protein chains.

Description

This quiz explores the fundamental concepts of amino acids and their role in protein structure. Learn about the components of amino acids, the distinction between L and D forms, and their significance in biological processes. Test your knowledge on how these molecules contribute to the functioning of living organisms.