Lecture 2 : Biological Macro molecules and Small molecules: Importance and functions

Organic Chemistry in Biology and Drug Design Overview

Essential Molecules of Life

• The course focuses on the essential molecules for living organisms: proteins, nucleic acids, carbohydrates, and lipids.

• These molecules are termed biological macromolecules due to their large molecular weight compared to small organic molecules.

• Proteins are formed from amino acids as building blocks; nucleic acids consist of nucleotides or deoxynucleotides.

• Carbohydrates are made up of monosaccharides; some exist in free form (e.g., glucose), while others serve as storage (e.g., glycogen).

• Glycogen is a branched polymer of glucose that can be broken down for energy when needed.

Understanding Lipids

• Lipids are defined as water-insoluble molecules, soluble in nonpolar solvents like organic solvents.

• They include various classes such as fatty acid derivatives, steroids, and terpenes found in plants.

• Lipids primarily consist of hydrophobic carbon chains with fewer functionalized carbons compared to other macromolecules.

Small Molecules in Biology

• In addition to macromolecules, small molecules like coenzymes and neurotransmitters play crucial roles in biological processes.

• Coenzymes assist enzymes in catalyzing reactions; neurotransmitters facilitate signal transduction within organisms.

Central Dogma of Molecular Biology

• The central dogma describes the flow of genetic information from DNA to RNA to proteins, emphasizing the role of nucleic acids in protein synthesis.

• Some viruses deviate from this model by using only RNA instead of DNA, highlighting exceptions to the central dogma.

Structural Insights into Proteins

• The lecture will explore three-dimensional structures of proteins and how they fold into functional forms within cells.

Understanding Biological Systems and Carbohydrates

Hierarchical Structure of Biological Systems

• The biological system is organized hierarchically, starting from organs, then tissues, followed by cells, and finally the internal structures of cells.

• Proteins fold not only due to their linear structure but also to create functional pockets essential for their biological roles.

Protein Structures

• A protein's crystal structure includes various formations such as helices (green and red), sheet structures, and random loop structures.

Carbohydrate Basics

• Glucose is a simple monosaccharide that exists in two forms: alpha and beta. It can undergo mutarotation when subjected to an amphoteric pH.

• Monosaccharides like glucose serve as building blocks for carbohydrates; they can also exist in deoxy forms which are crucial in biological systems.

Importance of Ribose and Deoxyribose

• Ribonucleic acid (RNA) contains ribose with all hydroxy groups intact, while deoxyribonucleic acid (DNA) lacks the 2' hydroxy group, highlighting its significance in genetic material.

Structural Variations in Carbohydrates

• Ribose typically appears in a furanose structure (5-membered ring), while glucose can form both furanose (5-membered) and pyranose (6-membered) structures.

• Glucosamine is derived from glucose where one hydroxyl group is replaced by an amino group; it plays a vital role in bacterial cell wall formation.

Functions of Carbohydrates

• Glycogen serves as a storage form of glucose; it consists of branched structures representing multiple glucose units.

• Carbohydrates are essential energy sources for organisms; they provide necessary energy through daily consumption of starches.

Understanding Carbohydrates and Lipids in Biological Systems

The Role of Carbohydrates

• Plants utilize solar energy to convert carbon dioxide into carbohydrates, which serve as a primary food source for many organisms.

• Carbohydrates are crucial in biological systems, acting as an energy storehouse and precursors for various biomolecules, including fatty acids like palmitic and stearic acid.

• They also contribute to the structure of cell walls, providing essential energy to plants.

Introduction to Lipids

• Lipids are defined by their solubility in organic solvents and insolubility in water, leading to a diverse range of lipid molecules such as fatty acids, steroids, and terpenes.

• Tristearin (a triglyceride) is highlighted as a fat that is soluble in organic solvents; cholesterol is identified as a non-polar steroid lipid with no functional groups.

Types of Fatty Acids

• Various saturated and unsaturated fatty acids exist; common examples include lauric acid (C12), myristic acid, palmitic acid, stearic acid, and arachidonic acid (C20).

• Isopentenyl diphosphate serves as a precursor for synthesizing steroids and terpenes through biosynthesis processes.

Steroid Structure and Function

• Steroids consist of three fused 6-membered rings (A, B, C) attached to a 5-membered ring (D), derived from phenanthrene without double bonds.

• Isopentenyl pyrophosphate is noted as the precursor for steroid synthesis; molecular modeling reveals crowded atomic structures within steroid molecules.

Prostaglandins: Importance and Functions

• Prostaglandins originate from arachidonic acid (C20 carboxylic acid); they possess significant physiological effects including blood pressure regulation.

• These compounds play roles in inflammation control, kidney function regulation, blood clotting management, and stimulating uterine contractions during childbirth. Aspirin inhibits prostaglandin biosynthesis.

Understanding the Role of Nucleic Acids and Small Molecules in Biological Systems

The Importance of Nucleic Acids

• Nucleic acids are essential biological molecules, composed of polymers of nucleotides, which include a phosphate group, sugar, and a nitrogenous base.

• There are two main types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), with DNA serving as the genetic material in all eukaryotic cells.

• Eukaryotic cells have compartmentalized structures including a nucleus where DNA is housed; prokaryotes like bacteria lack this compartmentalization.

• DNA consists of four different bases, while RNA has uracil instead of thymine found in DNA. This distinction is crucial for understanding their functions.

• The double helical structure proposed by Watson and Crick is fundamental to our understanding of DNA's role in genetics.

The Significance of Small Molecules

• Small molecules such as neurotransmitters play critical roles in signal transduction within biological systems, influencing various physiological processes.

• Acetylcholine is highlighted as an essential small molecule; its proper secretion levels are vital for health, with imbalances leading to diseases.

• Dopamine is another simple yet crucial molecule necessary for the functioning of biological systems; both acetylcholine and dopamine exemplify the importance of small molecules alongside macromolecules.

• Just as electricity powers a house, small molecules are essential for cellular function; without them, life can become compromised or lead to severe complications.

• Vitamins serve as medium-sized molecules that catalyze reactions and support enzyme functions; they bridge the gap between small and large biomolecules.

Medium-Sized Molecules

• Bradykinin is identified as a hormone that regulates blood pressure by acting as a vasodilator; it illustrates the diverse roles medium-sized molecules play in biological regulation.