Amino Acids and Proteins Overview

Amino Acids

• Amino acids consist of an α carbon bonded to four substituents: a carboxyl group, an amino group, a hydrogen atom, and a unique R group (side chain).
• Glycine is unique with a second hydrogen atom in place of an R group.
• Amino acid residues in proteins are L stereoisomers, making them optically active.
• Amino acids are classified into five main groups based on their R groups: nonpolar aliphatic, aromatic, polar uncharged, positively charged, and negatively charged.

pKa Values

• Cysteine features three pKa values:
  • pK1 for the carboxyl group: 1.96
  • pK2 for the amino group: 10.28
  • pK3 for its side chain: 8.18

Types of R Groups

• Nonpolar, Aliphatic R Groups: Contribute to protein structure stability via the hydrophobic effect.
• Aromatic R Groups: Absorb UV light at 270-280 nm and can enhance hydrophobic effects.
• Polar, Uncharged R Groups: Capable of forming hydrogen bonds and disulfide bonds (e.g., cysteine).
• Positively Charged R Groups: Display significant positive charge at physiological pH (7.0).
• Negatively Charged R Groups: Carry a net negative charge at physiological pH (7.0).

Protonation States and Isoelectric Point (pI)

• Amino acids can act as weak acids or bases; zwitterions dominate at neutral pH.
• Titration reveals cation, zwitterion, and anion forms, with pK1 and pK2 defining acidic and basic characteristics, respectively.
• For amino acids without ionizable side chains, pI is calculated as (pK1 + pK2) / 2.

Peptides

• Peptides are chains of amino acids linked by covalent peptide bonds formed via condensation and cleaved by hydrolysis.
• Types of peptides vary by the number of amino acids: dipeptide (2), tripeptide (3), oligopeptide (a few), polypeptide (many, <10 kDa), protein (thousands, >10 kDa).
• Peptides are named from the amino-terminal (N-terminal) to the carboxyl-terminal (C-terminal) residue.

Peptide Composition and Subunits

• Peptides can be multisubunit, formed from multiple polypeptides noncovalently, or oligomeric with identical subunits (protomers).

Protein Composition

• Proteins have highly variable amino acid composition, exemplified by differences in bovine cytochrome c and chymotrypsinogen.

Estimation of Amino Acid Residues

• The number of amino acid residues can be estimated as molecular weight/110, factoring out the water molecule lost during peptide bond formation.

Conjugated Proteins

• Conjugated proteins contain non-amino acid components known as prosthetic groups, including lipids, carbohydrates, phosphate groups, heme, and specific metals.

Protein Separation and Purification

• Proteins can be separated based on size, charge, binding properties, and solubility. Common methods include salt precipitation, fractionation, dialysis, and chromatography.

Column Chromatography

• Protein migration utilizes a buffered solution through a solid phase, with the rate affected by protein properties.

Electrophoresis

• Utilized to visualize and analyze purified proteins based on charge-to-mass ratios. Involves polyacrylamide gels and staining methods for visualization.

Protein Structure Levels

• Four structural levels:
  • Primary: Linear sequence and covalent bonds of amino acids.
  • Secondary: Patterns like alpha-helices and beta-sheets.
  • Tertiary: 3D folding configuration.
  • Quaternary: Assembly of multiple polypeptide chains.

Protein Structural Analysis Techniques

• Traditional protein sequencing methods involve protein labeling and protease digestion.
• Advanced techniques include X-ray crystallography, NMR spectroscopy, and Cryo-EM for atomic resolution structure.
• Mass spectrometry offers insights into molecular mass, amino acid sequences, and proteomes.

This quiz covers the structural features of amino acids, including the α carbon and its four substituents. Dive into the unique characteristics of various amino acids and their role in forming peptides and proteins. Ideal for students studying biochemistry or molecular biology.