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Semester 2: Bioorganic and Medicinal Chemistry
Chemistry of Carbohydrates: Classification, properties, structures, interconversions
Chemistry of Carbohydrates
Classification of Carbohydrates
Carbohydrates can be classified into three main categories: monosaccharides, oligosaccharides, and polysaccharides. Monosaccharides are simple sugars like glucose and fructose. Oligosaccharides consist of 2 to 10 monosaccharide units, such as sucrose and lactose. Polysaccharides are large molecules composed of many monosaccharide units, like starch, glycogen, and cellulose.
Properties of Carbohydrates
Carbohydrates possess various chemical and physical properties. They are generally soluble in water, especially monosaccharides and some oligosaccharides. They can undergo hydrolysis, oxidation, and reduction reactions. Carbohydrates also have the ability to form glycosidic bonds, which are essential for creating larger carbohydrate structures.
Structures of Carbohydrates
The structure of carbohydrates can be either linear or cyclic. The linear form consists mainly of a chain of carbon atoms, while the cyclic form is often represented in a ring structure. Monosaccharides can be classified based on the number of carbon atoms they contain, such as trioses, tetroses, pentoses, and hexoses. The specific arrangement of hydroxyl groups and the presence of functional groups determine the specific properties and functions of each carbohydrate.
Interconversions of Carbohydrates
Carbohydrates can undergo interconversion through various biochemical pathways. For instance, glucose can be converted to fructose through an isomerization reaction. Glycogen can be broken down into glucose for energy through glycogenolysis. Additionally, carbohydrate metabolism pathways such as glycolysis and gluconeogenesis are crucial for converting carbohydrates into usable energy forms in living organisms.
Chemistry of Proteins: Classification of amino acids, protein structures, peptide synthesis, enzyme action and inhibition
Chemistry of Proteins
Classification of Amino Acids
Amino acids are the building blocks of proteins. They can be classified into several categories based on their properties: 1. Essential amino acids: Cannot be synthesized by the body and must be obtained from the diet. 2. Non-essential amino acids: Can be synthesized by the body. 3. Polar and nonpolar amino acids: Polar amino acids have side chains that are charged or contain electronegative atoms, while nonpolar amino acids have hydrophobic side chains. 4. Acidic and basic amino acids: Acidic amino acids have a carboxylic acid functional group, while basic amino acids have amino groups in their side chains.
Protein Structures
Proteins exhibit four levels of structure: 1. Primary structure: The linear sequence of amino acids in a polypeptide chain. 2. Secondary structure: Local folding into alpha-helices and beta-pleated sheets stabilized by hydrogen bonds. 3. Tertiary structure: The overall three-dimensional shape of a single polypeptide chain, determined by interactions among side chains. 4. Quaternary structure: The arrangement of multiple polypeptide chains into a functional protein complex.
Peptide Synthesis
Peptide synthesis involves the formation of peptide bonds between amino acids. Techniques include: 1. Solid-phase peptide synthesis (SPPS): A method where amino acids are sequentially added to a growing chain attached to a solid support. 2. Liquid-phase synthesis: Involves mixing amino acids in solution to facilitate peptide bond formation. 3. Protecting groups: Chemical groups used to protect reactive sites on amino acids during synthesis.
Enzyme Action and Inhibition
Enzymes are biological catalysts that speed up chemical reactions. Key concepts include: 1. Active site: The specific region of an enzyme where substrates bind and reactions occur. 2. Enzyme-substrate complex: Temporary complex formed when an enzyme binds to its substrate. 3. Types of inhibition: Enzyme inhibitors can be competitive, non-competitive, or uncompetitive, affecting enzyme activity by binding to the active site or altering the enzyme's shape.
Chemistry of Nucleic Acids: Constituents, structure of DNA and RNA, biological roles
Chemistry of Nucleic Acids
Introduction to Nucleic Acids
Nucleic acids are biopolymers essential for all known forms of life. They are primarily categorized into DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). Both types are crucial for storing and transferring genetic information.
Constituents of Nucleic Acids
Nucleic acids consist of nucleotides, which are the monomeric units. A nucleotide is composed of three components: a phosphate group, a sugar (ribose in RNA and deoxyribose in DNA), and a nitrogenous base (adenine, thymine, cytosine, and guanine for DNA; adenine, uracil, cytosine, and guanine for RNA).
Structure of DNA
DNA is a double helix structure, composed of two strands that wind around each other. The strands are antiparallel and held together by hydrogen bonds between complementary base pairs (adenine-thymine and cytosine-guanine). The backbone of DNA is formed by alternating sugar and phosphate groups.
Structure of RNA
RNA is typically single-stranded and can fold into various shapes due to intra-strand hydrogen bonding. The primary types of RNA include messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). RNA contains ribose sugar and uracil instead of thymine.
Biological Roles of Nucleic Acids
DNA is responsible for the storage and transmission of genetic information. It guides the synthesis of RNA during transcription, which in turn guides protein synthesis during translation. RNA plays various roles, including serving as a template for protein synthesis and functioning in regulatory and catalytic capacities.
Conclusion
Understanding the chemistry of nucleic acids is fundamental to molecular biology and biochemistry. Their structure and function are tightly linked to biological processes such as replication, transcription, and translation.
Introductory Medicinal Chemistry: Drug discovery, design, drug action theory, synthesis of representative drugs
Introductory Medicinal Chemistry
Drug Discovery
Drug discovery is the process of identifying new candidates for inhaled or injected drug products. It involves target identification, hit discovery, lead optimization, and preclinical studies. Techniques include high-throughput screening, structure-based drug design, and pharmacodynamics assessment.
Drug Design
Drug design focuses on the creation of new drugs based on the biological target. It uses computational chemistry, molecular modeling, and structure-activity relationship analysis. Understanding the physicochemical properties and the biological activity of compounds is crucial in this phase.
Drug Action Theory
Drug action theory elaborates on how drugs produce their effects at the molecular level. This includes concepts such as receptor binding, enzyme inhibition, and signal transduction pathways. Knowledge of pharmacodynamics and pharmacokinetics is essential to predict drug behavior in biological systems.
Synthesis of Representative Drugs
The synthesis of drugs involves the chemical processes used to create pharmaceutical substances. It covers basic organic synthesis techniques, chiral synthesis, and methods for optimizing yields and purities. Case studies of specific drug syntheses provide insight into practical applications of medicinal chemistry.
Solid State: Space lattice, unit cell, laws of crystallography, X-ray diffraction, crystal structures of salts
Solid State
Space Lattice
A space lattice is a three-dimensional arrangement of points that represent the positions of atoms, ions, or molecules in a crystalline solid. Each point represents an identical environment, and the entire lattice can be translationally repeated throughout space. The lattice is defined by lattice parameters, which include the lengths of the unit cell edges and the angles between them.
Unit Cell
The unit cell is the simplest repeating unit in a crystal structure. It is defined by its dimensions (lattice parameters) and the arrangement of atoms within it. The unit cell can be classified into different types based on symmetry and dimensions, including cubic, tetragonal, orthorhombic, hexagonal, and monoclinic.
Laws of Crystallography
The laws of crystallography describe the symmetrical properties of crystals and their growth patterns. Key laws include Bravais lattices, which classify the 14 distinct three-dimensional lattices; Miller indices, which are a notation system to describe orientations of planes in crystals; and the law of constancy of interfacial angles, stating that the angles between corresponding faces of crystals are constant.
X-ray Diffraction
X-ray diffraction (XRD) is a technique used to study the crystalline structure of materials. When X-rays are directed at a crystalline sample, they are scattered by the electrons in the atoms. The resulting diffraction pattern provides information about the arrangement of atoms in the crystal. XRD is essential for determining unit cell dimensions and confirming the symmetry of a crystal.
Crystal Structures of Salts
In crystallography, salts can form various crystal structures depending on the types of ions present and their interactions. Common examples include ionic crystals such as sodium chloride (NaCl) which adopts a face-centered cubic structure. The arrangement of cations and anions in these structures follows specific stoichiometries and can influence properties such as solubility, melting point, and hardness.
Introduction to Polymer: Classification, bonding, molecular mass determination, inorganic polymers
Introduction to Polymer
Classification of Polymers
Polymers can be classified based on various criteria. They can be categorized as natural or synthetic. Natural polymers include cellulose, proteins, and nucleic acids, while synthetic polymers include plastics like polyethylene and polystyrene. Further classification can be done based on structure, as in linear, branched, or cross-linked polymers. Additionally, they can be classified by their thermal properties into thermoplastics and thermosetting polymers.
Bonding in Polymers
The properties of polymers greatly depend on the type of bonding present. The primary bonding within the polymer chain is covalent bonding, which connects monomers to form long chains. Secondary interactions, such as hydrogen bonding, van der Waals forces, and ionic interactions, also play a significant role in determining the physical properties of polymers.
Molecular Mass Determination
Determining the molecular mass of polymers can be complex due to their large and varying sizes. Techniques such as gel permeation chromatography (GPC), viscometry, and light scattering are commonly used to assess polymer molecular weight. These methods help in understanding the molecular distribution, which is crucial for predicting the behavior of polymers in different applications.
Inorganic Polymers
Inorganic polymers differ from organic polymers by containing elements other than carbon in their backbone. Common examples include silicones, which have a silicon-oxygen backbone, and phosphazenes, which contain alternating phosphorus and nitrogen. Inorganic polymers often exhibit unique properties such as high thermal stability and chemical resistance, making them suitable for various industrial applications.
Kinetics and Mechanism of Polymerization: Polymerization techniques and mechanisms
Kinetics and Mechanism of Polymerization
Introduction to Polymerization
Polymerization is the process of reacting monomer molecules together in a chemical reaction to form three-dimensional networks or polymer chains. It can occur via different mechanisms and under various conditions.
Types of Polymerization Techniques
1. Addition Polymerization: Involves the joining of monomers with unsaturated bonds. Common methods include free radical, ionic, and coordination polymerization. 2. Condensation Polymerization: Involves the reaction between two different types of monomers leading to the loss of small molecules (e.g., water).
Kinetics of Polymerization
Kinetic studies help in understanding the rates of polymerization reactions. Rate equations can differ based on the mechanism (chain-growth or step-growth), influencing the molecular weight and structure of the resulting polymer.
Mechanisms of Polymerization
1. Free Radical Polymerization: Initiated by free radicals, leading to chain initiation, propagation, and termination. 2. Ionic Polymerization: Utilizes ionic species as initiators, can be cationic or anionic, impacting the polymer characteristics.
Factors Affecting Polymerization Rate
Key factors include temperature, concentration of monomers, presence of catalysts, and solvent effects. These factors significantly influence molecular weight and polydispersity.
Applications of Polymerization Techniques
Polymerization techniques are employed in the production of various materials, including plastics, fibers, and elastomers, essential in multiple industries such as packaging, textiles, and pharmaceuticals.
Synthetic Dyes: Colour and constitution, classification, chemistry and synthesis of common dyes
Synthetic Dyes
Introduction to Synthetic Dyes
Synthetic dyes are organic compounds used to impart color to fabric, paper, and other materials. They are widely used due to their vibrant hues, versatility, and ability to be produced in large quantities.
Colour and Constitution
The color of synthetic dyes is influenced by their molecular structure and the presence of chromophores, which are responsible for the absorption of specific wavelengths of light. The interaction of dyes with materials is also influenced by the constitution of the dye molecule.
Classification
Synthetic dyes can be classified based on various criteria such as structure, application, and reactivity. Common classifications include acid dyes, basic dyes, reactive dyes, and disperse dyes.
Chemistry of Common Dyes
The chemistry of synthetic dyes involves various types of chemical bonds and functional groups. For example, azo dyes contain an azo group (-N=N-), while anthraquinone dyes contain an anthraquinone structure, which contributes to their color properties.
Synthesis of Common Dyes
The synthesis of synthetic dyes often involves organic reactions such as azo coupling, nitration, and reduction. For instance, azo dyes are commonly synthesized by coupling diazonium salts with phenolic compounds.
Applications of Synthetic Dyes
Synthetic dyes have a wide range of applications including textile dyeing, food coloring, biological staining, and in the production of inks and plastics.
Environmental Impact
The production and disposal of synthetic dyes can pose environmental hazards. Efforts are being made to develop eco-friendly dyes and improve waste management in the dye industry.
