Amino Acids & Proteins Overview

Amino Acids & Proteins

• Amino acids are the basic units of proteins.
• An amino acid has a central carbon atom bonded to an amino group (+H₃N), a carboxyl group (-COOH), a hydrogen atom, and a variable R-group (or side chain).
• Stereoisomerism (D/L): Amino acids exist as L and D isomers, determined by the spatial arrangement around the central carbon. L-amino acids are the predominant type in biological systems.
• Classification of Amino Acids: Classified based on the chemical properties of their R-groups, including: hydrophobic/non-polar, polar/uncharged, polar/negatively charged, and polar/positively charged. Further sub-classifications exist based on specific R-group characteristics.
• Examples of classified amino acids include: aliphatic/nonpolar, aromatic, sulfur-containing, hydroxyl-containing, acidic, basic, imino, and amides.
• Naturally occurring amino acids were presented in diagram examples.
• Some properties of amino acids include: solubility in polar solvents (e.g., water), insolubility in non-polar solvents, high melting points due to crystalline structure, ability of aromatic amino acids to absorb UV light.
• Amino acids are amphoteric (zwitterionic) molecules. They can act as either acids or bases depending on the surrounding pH.
• The formation of a peptide bond involves the removal of a water molecule between the carboxyl group of one amino acid and the amino group of another. This creates a peptide linkage.
• Proteins are biopolymers of amino acids. The size of proteins varies greatly; from smaller ones containing less than 100, to larger ones containing many hundreds or even thousands of amino acids.
• Two main protein classes include: globular and fibrous. Globular proteins typically function as enzymes, hormones or in transport, while fibrous proteins provide structural roles.
• Proteins also include conjugated proteins which contain a non-protein moiety. Examples include hemoglobin's heme component.

Organizational Levels in Protein Structure

• Primary structure: The linear sequence of amino acids in a protein.
• Secondary structure: Local conformations of the polypeptide chain, often resulting from hydrogen bonding between the backbone atoms (e.g., α-helix, β-sheet). Hydrogen bonding of neighboring peptide bonds creates common folding patterns. The arrangement of secondary structural regions within a protein is called supersecondary structure.
• Tertiary structure: The 3-dimensional structure formed by interactions among amino acids across long distances, often involving side chain interactions like hydrophobic, electrostatic, hydrogen, van de Waals forces, and disulfide bonds.
• Quaternary structure: The association of multiple polypeptide chains (subunits) to form a larger protein complex. This interaction leads to the overall final structure of the protein.

Secondary Structures

• α-helix: A right-handed helical structure stabilized by hydrogen bonds between the amide hydrogen of one peptide bond and the carbonyl oxygen of another, four residues down the chain. Globular proteins average about 11 amino acids (aa) per α-helix, but up to 53 are possible.
• β-sheet: A sheet-like structure formed by hydrogen bonds between amino acid residues in different strands. Can be parallel or anti-parallel, with amino acid side chains extending above and below the pleated sheet. Globular proteins have beta structures in the range of 2-15 amino acids.

Tertiary Structures

• The three-dimensional arrangement of a polypeptide chain.
• Interactions among amino acid side chains (R-groups) are crucial, including hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bonds.
• Super-secondary structures, or motifs are common arrangements of secondary structure elements.
• Many proteins contain domains – distinct functional regions within the polypeptide chain.
• The folded configuration largely depends on the amino acid sequence and thus the R-groups.
• Factors like hydrophobicity of a-amino acids play an important role in tertiary structures.

Forces Influencing Protein Structure

• Peptide bond geometry: Planar structure and restricted rotation around the peptide bond determines folding pattern.
• Hydrogen bonds: Stabilizing interactions between peptide bonds influence local structure.
• Hydrophobic interactions: Nonpolar amino acid side chains cluster together in the protein interior.
• Electrostatic interactions: Attractions and repulsions among charged side chains are significant.
• Van der Waals interactions: Weak attractive forces between atoms.
• Disulphide Bonds: Covalent linkages formed between cysteine residues are structural stabilizing force.