Lecture_2_Le_Nours_2025

Course Overview

Course Title: BMS1021 BiochemistryInstructor: Ass. Professor Jérôme Le NoursContact: Jerome.lenours@monash.eduInstitution: Comparative Immunology Laboratory, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute

Main Biochemical Categories

• Carbohydrates: Essential biomolecules that serve as energy sources, structural components, and cell recognition elements. They consist of monosaccharides, oligosaccharides, and polysaccharides.

• Proteins: Complex macromolecules composed of amino acids linked by peptide bonds. They play crucial roles in catalyzing biochemical reactions, providing structural support, and facilitating communication within and between cells.

• Lipids: A diverse group of hydrophobic molecules including fats, oils, and phospholipids, which are pivotal in energy storage, membrane structure, and signaling pathways.

• Nucleic Acids: Polymers such as DNA and RNA that carry genetic information and are essential for inheritance, coding, and regulation of genes.

• Water: The most abundant molecule in cells, serving as a solvent, reactant, and medium for biochemical reactions. Its properties are fundamental to life.

E. coli in Human Gut

• The human gut hosts approximately 100 billion E. coli cells per gram of intestinal content, outnumbering human cells by a ratio of 2:1, reflecting their importance in gut health and function.

• A single cm² of the intestinal epithelium can contain about 100 million E. coli cells, highlighting their density and influence on the gastrointestinal microbial ecosystem.

Learning Objectives

• Describe the major macromolecule categories within cells, emphasizing their structures and functions.

• Understand the various levels of protein structure and how these levels correlate with protein function and activity.

• Outline the significant biological functions of proteins and carbohydrates in cellular contexts.

• Focus Areas: Explore the intricate structure and biological importance of proteins and carbohydrates, discussing their dynamics and regulatory roles.

Recommended Resources

• Biology Textbook: Campbell (10/11th edition)

  • Chapter 5: pp. 66-72, 75-83

  • Chapter 6: pp. 102-108, 115-119

• Principles of Biochemistry Textbook: Lehninger (7th edition, 2017)

  • Chapter 3: pp. 75-113

  • Chapter 4: pp. 115-155

  • Chapter 7: pp. 241-278

• Lectures: BMS1011 covering essential topics on Carbohydrates, Amino Acids, and Proteins

Levels of Structure Within a Cell

• Level 1: Monomeric Units: Basic building blocks such as nucleotides, amino acids, and sugars that combine to form larger structures.

• Level 2: Macromolecules: Complex molecules like proteins, DNA, and polysaccharides that are formed from monomer units.

• Level 3: Supramolecular Complexes: Higher-order assemblies including chromatin and various cell organelles that play vital roles in biological functions.

• Level 4: The Cell and Its Organelles: The entire cellular structure, including various organelles like the nucleus, mitochondria, and Golgi apparatus that perform specific functions necessary for cell survival.

Carbohydrates (Polysaccharides)

• Definition: Polysaccharides formed from monosaccharide building blocks, essential for energy storage and structural integrity.

• Examples of Monosaccharides:

  • Common Monosaccharides: Include glucose (primary energy source), fructose, ribose (significant in nucleic acids), galactose, and xylose.

  • Glucose: This monosaccharide can exist in both alpha and beta configurations, with the alpha form having the hydroxyl group on the first carbon positioned downward.

• Glycosidic Linkages:

  • Monosaccharides bond through glycosidic linkages formed via condensation reactions, facilitating the formation of more complex carbohydrates.

  • Reaction is reversible, facilitated by specific enzymes, through hydrolisis to reform the saccharides

  • Example Disaccharides:

    • Maltose: (sugar) Composed of two glucose units linked through an α(1-4) bond.

    • Sucrose: A glucose-fructose combination (α-D-glucopyranosyl β-D-fructofuranoside), notable in dietary sources.

• Polysaccharides:

  • Classification: Differentiation between homopolysaccharides and heteropolysaccharides.

  • Homopolysaccharides- All of the monosaccharides are the same (glucose joined to glucose)

  • Heteropolysaccharide: Different monosaccharides liinked together (sucorse and fructose etc)

  • Storage Polysaccharides:

    • Starch: A polymer composed entirely of glucose (from 500-20,000), serving as primary energy storage in plants, existing as amylose (unbranched) or amylopectin (branched).

  • Structural Polysaccharides:

    • Cellulose: Composed of glucose units; provides rigidity and structural support due to extensive hydrogen bonding between chains.

    • Chitin: A nitrogenous polymer of N-Acetylglucosamine found in fungal cell walls and the exoskeletons of crustaceans, contributing to structural integrity.

• Extracellular Polysaccharides:

  • Glycosaminoglycans: Heteropolysaccharides acting as lubricants and shock absorbers in tissues as highly polar.

  • Examples:

    • Hyaluronic Acid: A high molecular weight polysaccharide contributing to tissue hydration and elasticity, particularly in cartilage.

    • Proteoglycans: Complexes consisting of glycosaminoglycans covalently linked to proteins, crucial for the organization of tissues and regulation of extracellular matrix assembly. Made of polysaccharides

    • They are actually glycosaminoglycan (polysaccharides with amino acids containing sugars) molecules attached covalently to a membrane portine molecule or secreted protein

    • Polysachharides help protect proteins from action of proteases (degration) and helps protein folding by stabilizing the protein structure and preventing misfolding.

Proteins and Their Functions

• Proteins: polymer made up of amino acids (polypeptides)

• They: - function as enzymes in cellular metabolism, provide structural support, can be hormones, receptor molecules, antibodies, transportes inide and out of cell, move muscles and cilia

• Glycoproteins are chains with covaelently linked sugar (carbohyrate) chains -

• General Structure: Proteins are polymers formed from amino acids linked by peptide bonds, characterized by diverse structures and functions.

• Functions of Proteins:

  • Enzymatic catalysis, providing structural support, participating in hormonal signaling, serving as receptors, facilitating transport across membranes, and enabling motor functions, such as muscle contraction.

• Composition: Comprised of 20 different amino acids; the unique side chains (R-groups) confer specific properties and functions to the resulting proteins - important for the archetecture and overall function

• Joining amino acids is a hydrolisis reaction/ condensation reaction. they join via peptides bonds to form dipeptides. This reaction can be catalysed by specific enzymes

• N terminus - amino end of polypeptide

• C terminus - Carboxyl end of polypeptide

Protein Structure

• Levels of Structure:

  • Primary Structure: Denotes the linear sequence of amino acids in a polypeptide chain, determined by genetic coding. In nature dont actually exist in linear form

  • Secondary Structure: Involves the formation of local folding patterns, such as α-helix and β-sheets, stabilized by hydrogen bonds.

    • α-helix: One turn every 3.6 residues, where the H from the amino group will bond through hydrogen bonding to an oxygen 4 residues away. The R groups project outwards.

    • β-sheets: Relativly flat. Side chains projecting above and below the plane. Sheets held together by h-bonding between the carbonyl oxygen of one amino acid and the amide hydrogen of another.

      • a) Antiparalell: Each row of chain is going in opposite directions (N-terminus to C-terminus), allowing for optimal hydrogen bonding between adjacent strands, which enhances the stability of the sheet.

      • b) Parellel: direction of the chans are all the same

  • Tertiary Structure: The three-dimensional arrangement of polypeptides driven by interactions among side chains, including hydrogen bonds, ionic bonds, and hydrophobic interactions.

    • Held together through hydrogen, ionic, covalent, di-sulfide (give regidiity to protiens) hydrophobic and van der waals interactions.

    • Eg) Myoglobin - a globular protein that facilitates oxygen transport in muscle tissues. Consists entirely of alpha-helix, and hydrophobic residues

  • Quaternary Structure: The assembly of multiple polypeptide chains (tertiary structure) into a functional protein, exemplified by hemoglobin's complex structure with multiple subunits. Forms through ionic, hydrogen bonds etc

    • Eg) Haemoglobin - found in red blood cells. Made of four proteins that each bind oxugen. Realeases ocygen more readily than myoglobin bc of allosteric cooperativity btw subunits of quaternary structure

Protein Dynamics

• The dynamic nature of protein structure is crucial; conformational changes can significantly affect functionality, making it a relevant consideration in pharmacology and drug design strategies.

Summary

• Carbohydrates: Represent polysaccharides originating from monosaccharide building blocks, playing key roles in energy storage and cellular structure.

• Proteins: Polypeptides composed of amino acids, exhibiting intricate structures essential for diverse biological functions.