Amino Acids and Protein Structure

Amino Acids, Peptides, and Proteins

• Proteins are composed of amino acids (AA)
• There are 20 standard amino acids
• Additional 2 (selenocysteine and pyrrolysine)
• Amino acids are linked by peptide bonds
• forming linear chains
• Individual proteins differ in their AA sequence
• This sequence determines their chemical and functional properties
• Proteins have many vital functions
• Protein structure is crucial for their function
• Protein structure is determined by their sequence of amino acids

Biomolecules

• Proteins, carbohydrates, lipids, and nucleic acids are vital biomolecules
• These are the fundamental components of all life forms

Polymers

• Most biomolecules are polymers
• Polymers are composed of repeating units called monomers

Protein Structure Principles

• The structure of a macromolecule determines its function
• Non-covalent interactions are vital for protein structure and function
• A specific sequence of monomeric subunits can hold information essential to the ordered biological life states

Water's Influence on Biomolecules

• Water and its ionization products (H+ and OH−) significantly affect the structure, organization, and properties of cellular components, including proteins, nucleic acids, and lipids
• Non-covalent interactions between biomolecules are heavily influenced by water's solvent properties, especially its capacity to form hydrogen bonds with itself and other molecules.

Key Principles of Proteins

• Proteins in all living organisms are built from 20 common amino acids
• The amino acids are linked via peptide bonds to form polypeptide chains of varying lengths
• Individual proteins differ significantly in their AA sequence
• This unique sequence determines their structure and function

Amino Acids

• Amino acids have an amino and carboxylic acid group bonded to the same carbon atom (α-carbon)
• The side chain (R group) differentiates amino acids
• Side chains vary in structure, size, and electrical charge, consequently influencing water solubility

Chiral Centers

• The α-carbon atom is a chiral center
• The four different groups attached to the α-carbon can form two distinct spatial arrangements
• These arrangements are called stereoisomers (enantiomers)
• They interact differently with light

Classification of Amino Acids by R-Groups

• Amino acids are classified into major groups based on properties of their R-groups
• This is helpful in characterizing/grouping amino acids

Nonpolar, Aliphatic R Groups

• Amino acids in this group are nonpolar and hydrophobic (water-insoluble)
• Their side chain's structures contribute to their hydrophobic effects

Aromatic R Groups

• These aromatic (ring-containing) side chains are typically nonpolar and hydrophobic and contribute to the hydrophobic effect
• The hydroxyl group in tyrosine can form hydrogen bonds
• Tyrosine and tryptophan are more polar than phenylalanine

Polar, Uncharged R Groups

• These amino acids have differing degrees of polarity, and their side chains can form hydrogen bonds
• Cysteine is an important outlier due to its sulfur-containing group

Positively Charged (Basic) R Groups

• The amino acids in this group carry a positive charge at neutral pH (7.0) due to an amine group
• Lysine, arginine and histidine are relevant examples of this class

Negatively Charged (Acidic) R Groups

• Aspartate and glutamate are negatively charged amino acids due to their carboxyl group side chains

Non-Standard Amino Acids

• Some amino acids are not common constituents of proteins but play important roles in other biological processes

AA Derivatives

• The body converts some amino acids into important molecules like neurotransmitters or other bioactive compounds

AA; Acids or Bases

• The amino acids' amine and carboxyl groups make them weak acids or bases
• Zwitterions form at neutral pH

Protein Terminology

• Two amino acids bonded are dipeptides, three are tripeptides, 3-10 are oligopeptides, and >10 are polypeptides

Protein Classification

• Simple proteins contain only amino acids
• Compound proteins have additional non-amino acid components (prosthetic groups)
• Derived proteins are products of protein breakdown
• Proteins can be classified by their function (e.g., catalytic enzymes, structural proteins)

Protein Structure Levels

• Primary structure: linear sequence of amino acids
• Secondary structure: local folding patterns, such as α-helices and β-sheets
• Tertiary structure: overall three-dimensional shape of the polypeptide chain; this is the 3-D structure
• Quaternary structure: arrangement of multiple polypeptide chains (subunits); this is the arrangement of multiple 3-D structures
• Non-covalent interactions determine the folded structure
• The structure determines function, and denaturation disrupts this relationship.

Biologically Active Peptides and Polypeptides Occur in a Vast Range of Sizes

• Many proteins have a wide range of sizes

Protein Structure: Tertiary Structure

• Tertiary structure in proteins refers to the overall three-dimensional arrangement of the polypeptide chain or polypeptide subunits.

Protein Structure: Quaternary Structure

• Quaternary structure refers to the arrangement of different polypeptide chains or subunits to form a functional protein/complex

Loss of Protein Structure Results in Loss of Function

• Denaturation causes loss of protein function
• Denaturation can be brought about by different factors like Heat, X-Rays, and Ultrasonic Waves. Specific pH values, salts of heavy metals, Urea, alcohol, and acetone can also cause denaturation

Essential vs. Non-essential Amino Acids

• Some amino acids are essential, meaning the body cannot make them. They must be consumed in the diet
• Other amino acids are nonessential, meaning the body can synthesize them

Protein Intake

• Adequate protein intake is necessary in daily diets.
• Protein intake standards (recommendations) are often dependent on factors including age, gender, activity level, whether pregnant, or consuming a plant-based diet.