2: Amino Acids and Proteins Introduction

Amino Acids and Proteins Introduction

• Amino acids are the building blocks of proteins
• Amino acids are linked together by peptide bonds
• Functional groups on amino acid side chains determine protein activity
• There are 20 amino acids
• Amino acids can be electrically charged, polar, or nonpolar, depending on the side chain
• Side chains affect how proteins behave in different environments
• Amino acids differ in their behavior depending on pH

Objectives

• Compare and contrast the chemical and structural features of amino acids to understand how they contribute to protein behavior. This will focus on functional groups
• Explain how side chains on amino acids affect behavior and function
• Explain the formation of peptide bonds and their relationship to protein function
• Evaluate protein structures:
  • Identify and describe the different levels of protein structure (primary, secondary, tertiary, and quaternary), and the importance of amino acid structure on protein folding.
  • Compare and contrast denaturation and renaturation/protein folding.
  • Explain how altered protein folding impacts human health.
• Explain protein classification and list categories.
• Determine how environmental conditions, specifically pH, affect amino acid behavior and relate it to the Henderson-Hasselbalch equation.
• Calculate pH, pKa, and pI values.
• Calculate changes in pH and pKa.

Amino Acids

• Amino acids have an amino group, a carboxyl group, and a side chain (R group)
• Each side chain has unique chemical properties, influencing the properties of the protein as a whole
• 20 different amino acids are used in protein synthesis in humans
• Structure of the R group determines the protein's polarity
• Polar side chains are hydrophilic (water-loving) while nonpolar side chains are hydrophobic (water-fearing)

Basic Structure and Stereochemistry

• Amino acids are amphoteric (both acidic and basic)
• Amino acids that have asymmetric carbon are stereoisomers (typically L-amino acids)
• All amino acids are L-amino acids found in proteins
• The different arrangements of the side chain on the central carbon make the molecule either D or L

Protein Structure

• Primary structure: The linear sequence of amino acids
• Secondary structure: Local folding of the polypeptide chain into alpha helices or beta pleated sheets; these depend on primary structure
• Tertiary structure: 3D folding of the entire polypeptide chain; depends on both primary and secondary structures
• Quaternary structure: Interaction of two or more polypeptide chains, not all proteins have this structure

Protein Folding

• Protein folding is essential for function
• Dependent on hydrogen bonds and non-covalent bonds
• Protein folding is determined by the structure of amino acid side chains
• Denaturation is the loss of secondary and tertiary structure, often irreversible
• Conditions like high temperature or pH changes can cause denaturation
• Misfolded proteins can have negative effects on the organism

Importance of Primary Structure

• Primary structure determines the secondary and tertiary structures of proteins
• A single change in primary structure can have a drastic effect on protein function, as seen in sickle cell anemia

Types of Proteins

• Proteins can be classified by structure, composition, and function
• Common categories include: simple, conjugated, and derived proteins
• Other categories include: antibodies, contractile, enzymes, hormonal, structural, storage, and transport proteins
• Enzymes are important biological catalysts that are proteins
• Other proteins are important for structure, regulation, and transport

Polarity and Ionization of Amino Acids

• Amino acids have different ionization and polarity properties due to the side chains
• pKa values of amino acids vary depending on temperature, buffers, and ligands.
• pKa values of different side chains vary significantly and can be used to determine pH in specific conditions.
• Buffering capacity at specific pH levels is related to the amino group and carboxyl group pKa values of the amino acid, influencing its behavior.

Amino Acid Structure and Protein Relationship

• Proline is an imino acid and its side chain contributes to kinks and bends in polypeptide structure
• Cysteine is a special case due to its sulfhydryl group, which can react with other cysteine residues to form disulfide bonds, impacting structure.

Introduction to Henderson-Hasselbalch

• Amino acids exhibit different behaviors at different pHs
• In physiological conditions, amino acids act as buffers
• Amino acids in solution at different pHs can be in various states including protonated, zwitterions, and unprotonated states
• The pI (isoelectric point) is the pH where the amino acid has a net zero charge and minimum buffering capacity.

This quiz explores the essential concepts of amino acids and proteins, including their structures and functions. It focuses on the chemical and structural features that determine protein behavior and the significance of side chains. Candidates will evaluate different levels of protein structure and the role of peptide bonds in protein functionality.