Biochemistry Basics

Biochemistry Basics

Introduction

Biochemistry focuses on the study of chemistry in living organisms and the vital biochemical processes that sustain life. This field has unique aspects that differentiate it from other branches of chemistry. The primary areas of focus include carbohydrates, lipids, proteins, and nucleic acids, which form the basis of biological molecules.

Objectives

The core objectives of studying biochemistry include:

  • Defining biochemistry: Understanding its scope and differentiating it from other chemistry branches.

  • Identifying biomolecule characteristics: Recognizing the distinctive features of carbohydrates, lipids, and proteins.

  • Amino acid chain bonding: Explaining the special binding characteristics of amino acid chains.

  • Stereochemistry and Hydrogen Bonding: Exploring the relevance of stereochemistry and hydrogen bonding for drug receptors.

  • Genetic Code Structure: Describing the structure and functions of messenger nucleotides, DNA, and RNA.

Major Categories of Bioactive Substances

  1. Carbohydrates

    • Defined as sugars represented chemically as Cx(H2O)y.

    • Sugars can take the form of aldehydes or ketones.

    • Monosaccharides, such as glucose, cannot be broken down into simpler forms.

    • Chirality refers to the property of a molecule having non-superimposable mirror images; it encompasses left (L) and right (D) enantiomers.

    • CHO (carbohydrate) drugs include many important pharmacological compounds like antibiotics, chemotherapeutic agents, and anti-inflammatory medications.

  2. Lipids

    • Lipids, commonly referred to as fats, are characterized by their hydrophobic nature, making them poorly soluble or insoluble in water.

    • Their structures vary significantly, including components such as glycerides and fatty acids.

    • Fatty acids are long-chain carboxylic acids, categorized based on the number of unsaturated double bonds.

    • Examples include triglycerides, which consist of a glycerol molecule bonded to three long fatty acid chains, reacting similarly to esters.

    • Steroids constitute a significant category of lipids, characterized by a specific skeletal structure; ketones also exhibit hydrophobic properties.

  3. Proteins and Amino Acids

    • Proteins are versatile biomolecules serving numerous roles: transportation (e.g., hemoglobin), structural components (receptors), movement, and as enzymes.

    • Polypeptides are molecules comprising numerous amino acid segments. Each protein is formed from chains of amino acids linked by peptide bonds, which connect amino (NH2) and carboxylic (COOH) functional groups.

G Protein Ligand Receptors

  • A ligand is defined as a molecule that generates a signal by binding to a specific site on a target protein, known as a receptor.

  • The binding interactions of drugs with receptors vary based on the type of bonding, which may include:

    • Ionic bonds

    • Covalent bonds

    • Hydrogen bonds

    • Van der Waals forces

    • Mechanical interactions

Protein Structure and Function

  • The protein structure starts with chains of amino acids communicated through peptide bonds.

  • A peptide bond is formed between the carboxyl group of one amino acid and the amino group of another amino acid, enabling the formation of polypeptides.

  • Proteins can comprise hundreds of amino acids. Drug interactions with proteins can lead to effective binding, but it’s important to note that bound drugs are not available to activate receptors. For example, Coumadin exhibits about 95% protein binding.

Nucleic Acids

  • Nucleic acids consist of chains of nucleotide bases bonded to a sugar backbone and play a crucial role in the synthesis of biological proteins.

  • The genetic code is conveyed in sequences of three base pairs (codons) along a sugar chain. DNA is a biopolymer consisting of two chains (double helix) that encodes genetic information, whereas RNA is a single-stranded molecule carrying the message required for protein synthesis.

Comparison of DNA and RNA

  • Location:

    • DNA: Located primarily in the nucleus of the cell.

    • RNA: Found in both the nucleus and cytoplasm.

  • Nucleotide Bases:

    • DNA contains thymine, while RNA contains uracil.

  • Sugar Components:

    • DNA has a deoxyribose backbone, contrasted with RNA's ribose structure.

  • Structural Differences:

    • DNA is comprised of two strands, making it longer and more stable than RNA, which is typically a single-stranded molecule.

  • Functional Differences:

    • DNA retains the genetic code, while RNA transmits and converts this code into amino acids required for protein synthesis.

Summary

  • Biochemistry is the study of fundamental chemical processes in living organisms.

  • Carbohydrates are categorized as sugar molecules, often exhibiting chirality.

  • Lipids display minimal water solubility and can be saturated or unsaturated, with triglycerides being a primary example.

  • Proteins consist of amino acids linked through peptide bonds, showing diverse functionalities including enzymatic and structural roles.

  • Drug receptors are primarily proteins allowing for geometric recognition and bonding interactions with various ligands, facilitating signal transduction.

  • Nucleic acids (RNA and DNA) are structured as chains of nucleotides along a sugar backbone, serving critical roles in genetic coding (DNA) and translation of this code into proteins (RNA).