Amino Acids & Proteins: Fundamentals

Amino Acids & Proteins

• Amino acids are the basic building blocks of proteins.
• Each amino acid has a central carbon atom bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable side chain (R-group).
• The R-group distinguishes one amino acid from another, determining its chemical properties.
• Amino acids exist as L-stereoisomers in most proteins.
• Amino acids are classified based on the chemical properties of their side chains (e.g., hydrophobic, polar, acidic, basic).
• Examples include aliphatic amino acids (Leu, Ile, Ala, Val), aromatic amino acids (Phe, Trp, Tyr), amino acids containing sulfur (Cys, Met), amino acids with hydroxyl groups (Thr, Ser), acidic amino acids (Asp, Glu), basic amino acids (Lys, Arg, His), imino acids (Pro), and amides (Gln, Asn).
• Proteins vary greatly in size, ranging from small proteins with fewer than 100 amino acids to large proteins with thousands.
• Examples of proteins with varying sizes include insulin and collagen.
• Myoglobin, a protein, has 153 amino acids, while hemoglobin has ~574 amino acids.
• Proteins are categorized as globular or fibrous proteins, performing diverse functions such as enzymes, structural components, and transport.
• Proteins can be conjugated containing a non-protein moiety such as heme.

Protein Structure

• Proteins are biopolymers composed of amino acids linked by peptide bonds.

• The linear sequence of amino acids in a protein is called the primary structure.

• The polypeptide chain folds into local conformations (secondary structures) stabilized by hydrogen bonds between backbone atoms.

• Common secondary structures include alpha-helices (a lot of hydrogen bonding between C=O and N-H groups of neighboring peptide bonds) and beta-sheets (hydrogen bonds between neighboring peptide bonds of the same or different chains).

• Local conformations of the polypeptide chain formed as a result of the regular folding of backbone atoms or common patterns within protein structures

• These patterns result from hydrogen bonds between neighboring peptide bonds

• Secondary structure gives rise to Super secondary structure(conformations of particular group of secondary structures)

• The 3-dimensional arrangement of the polypeptide chain is called the tertiary structure. This is a result of interactions between amino acids that are far apart in the primary sequence of the protein.

• The association of multiple polypeptide chains forms the quaternary structure of certain proteins, as seen in oligomeric proteins.

• Large proteins may contain multiple subunits.

• The arrangement of polypeptide chains (subunits) results in the quaternary structure in oligomeric proteins.

Forces Influencing Protein Structure

• The peptide bond has a planar structure. The degree of rotation depends upon the sizes of the R groups
• Hydrogen bonds form between the N-H and C=O groups of peptide bonds.
• Hydrophobic interactions occur between non-polar amino acid side chains, driving them to cluster together in the protein interior.
• Electrostatic interactions occur between charged amino acid side chains.
• Van der Waals interactions are weak attractions between atoms.
• Disulfide bonds (covalent bonds between cysteine residues) contribute to protein stability, particularly in certain proteins.