John E. McMurry et al. - Fundamentals of General, Organic and Biological Chemistry in SI Units Chapter 18

Amino Acids and Proteins Overview

18.1 Introduction to Biochemistry

Biochemistry: The study of molecules and reactions within living organisms that sustain life. This interdisciplinary field connects closely with areas such as nutrition, pharmaceuticals, and disease diagnosis, providing essential insights into how biological systems function at a molecular level.Biomolecules: The major classes of biomolecules include proteins, carbohydrates, lipids, and nucleic acids, each playing vital roles in biological processes.

18.2 Proteins and Their Functions

Definition: Proteins are primary biological macromolecules essential to all forms of life. They constitute approximately 50% of the body's dry mass and participate in nearly every cellular function.

Functions of Proteins:

• Structural: Proteins like keratin provide structural integrity; keratin is found in hair, nails, and the outer layer of skin.

• Support: Structural proteins such as actin filaments are critical for cellular shape and motility, serving as tracks for cellular transport and muscle contraction.

• Enzymatic: Many proteins function as enzymes, catalytic agents that accelerate metabolic reactions; for example, catalase decomposes hydrogen peroxide into water and oxygen.

• Transport: Proteins like transferrin transport essential metals, such as iron, in the bloodstream, ensuring proper cellular function.

• Protective: Immunoglobulins, or antibodies, are proteins that play a crucial role in the immune response by identifying and neutralizing pathogens.

• Hormonal: Hormonal proteins like insulin are key regulators of physiological processes, including the maintenance of blood glucose levels.

18.3 Amino Acids

Building Blocks of Proteins: Proteins are composed of 20 standard alpha-amino acids, each characterized by distinct functional groups:

• Amino Group (NH2): Acts as a base and accepts protons in acidic environments.

• Carboxyl Group (COOH): Functions as an acid, donating protons in basic environments.

• R Group (Side Chain): Varies among amino acids and determines the unique properties of each amino acid.

• Alpha-Carbon: The central carbon atom to which the amino group, carboxyl group, and R group are attached.

• Chirality: All amino acids, except glycine, are chiral, existing in two stereoisomers: D- and L- forms, crucial for protein synthesis in organisms.

18.4 Acid-Base Properties of Amino Acids

• Zwitterions: Amino acids can exist as zwitterions—dipolar ions that have both a positive and a negative charge, depending on the pH of the solution they are in. In neutral conditions, they behave as both acids (by donating protons from COOH) and bases (by accepting protons to NH2).

• Isoelectric Point (pI): The pH at which an amino acid carries no net electrical charge, which varies for different amino acids based on their side chains.

18.5 Peptides

• Peptide Bond: A covalent bond formed between the carboxyl group of one amino acid and the amino group of another, resulting in the release of a water molecule through a dehydration reaction.

• Dipeptides and Tripeptides: A dipeptide consists of two amino acids linked by a peptide bond, while a tripeptide consists of three.

• Naming: Peptides are named according to the sequence of the amino acids they contain (e.g., an alanine-glycine dipeptide is labeled Ala-Gly).

18.6 Protein Structure Overview

• Primary Structure: The linear sequence of amino acids in a protein, defining its unique characteristics.

• Secondary Structure: Local folding patterns within the protein, such as α-helices and β-sheets, which are stabilized by hydrogen bonds between amine and carbonyl groups of the polypeptide backbone.

• Tertiary Structure: The overall three-dimensional shape of a single polypeptide, determined by interactions among R groups, including hydrophobic interactions, salt bridges, hydrogen bonds, and disulfide bonds.

• Quaternary Structure: The association of multiple polypeptide chains into a functional protein complex, exemplified by hemoglobin which contains four polypeptide subunits.

18.10 Chemical Properties of Proteins

• Protein Hydrolysis: The biochemical process that breaks down proteins into amino acids through enzymatic action or chemical hydrolysis, effectively reversing protein synthesis.

• Denaturation: The alteration of a protein's shape without breaking the primary sequence, caused by factors such as heat, pH changes, or chemical exposure, which can affect the protein's functionality.

Important Concepts to Review

• Types of Bonds: Understand the roles of hydrogen bonds, ionic bonds, and hydrophobic interactions in determining protein folding and stability.

• Protein Classification: Differentiate between fibrous and globular proteins, as well as between simple and conjugated proteins.

• Functional Importance: Recognize how the specific structure of proteins is related to their function, along with understanding how alterations in amino acid sequences can significantly impact functionality (e.g., the genetic mutation causing sickle-cell anemia).

Summary

Proteins play crucial biological roles informed by their intricate structures, which result from various combinations of amino acids. Their vast array of functions is intimately linked to their specific conformation, directly determined by the sequences and interactions of amino acids throughout the polypeptide chain.