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Semester 3: Biochemistry and Biochemical tools
Amino acids and Protein: Structure and properties of amino acids, types and classification of proteins, forces stabilizing protein structure, levels of structural organization, denaturation and renaturation
Amino acids and Protein
Amino acids are organic compounds that serve as the building blocks of proteins.
They contain an amino group, a carboxyl group, a hydrogen atom, and a distinctive R group.
Properties include polarity, charge, and side chain structure influencing protein interactions.
Proteins are classified into fibrous, globular, and membrane proteins.
These proteins have elongated shapes and are typically structural proteins such as collagen.
These are more spherical and perform dynamic functions like enzymes and antibodies.
These proteins are embedded in cell membranes and are involved in signaling and transport.
They occur between polar side chains and contribute to secondary structure.
These involve charged side chains and help maintain protein shape.
Non-polar side chains cluster away from water, stabilizing the core of the protein.
Covalent bonds between cysteine residues providing additional stability.
The sequence of amino acids linked by peptide bonds.
Local folding into structures like alpha helices and beta sheets.
The overall three-dimensional shape of a protein.
Complexes formed from multiple polypeptide chains.
The process where proteins lose their native structure due to external stress like heat or pH change.
Refolding of a protein to its original structure under favorable conditions, often restoring functionality.
Carbohydrates: Structure, function and properties of monosaccharides, disaccharides and polysaccharides, mucopolysaccharides, bacterial cell wall polysaccharides, glycoproteins
Carbohydrates: Structure, function and properties
Monosaccharides
Monosaccharides are the simplest form of carbohydrates, consisting of single sugar units. They are categorized based on the number of carbon atoms they contain, typically 3 to 7. Common examples include glucose, fructose, and galactose. Monosaccharides serve as energy sources and building blocks for larger carbohydrates. They can exist in linear or cyclic forms, with the cyclic forms being more stable in solution.
Disaccharides
Disaccharides are formed by the combination of two monosaccharides through a glycosidic bond. Common disaccharides include sucrose (glucose + fructose), lactose (glucose + galactose), and maltose (glucose + glucose). These compounds play essential roles in energy metabolism, and their breakdown is crucial for providing monosaccharides to the body.
Polysaccharides
Polysaccharides are long chains of monosaccharide units linked by glycosidic bonds. They can be linear or branched and serve various structural and storage functions. Common polysaccharides include starch, glycogen, and cellulose. Starch serves as an energy storage molecule in plants, while glycogen performs a similar function in animals. Cellulose provides structural support in plant cell walls.
Mucopolysaccharides
Mucopolysaccharides, also known as glycosaminoglycans, are a group of polysaccharides that play key roles in connective tissues and cellular functions. They consist of repeating disaccharide units that often contain amino sugars and uronic acids. Functions include providing structural support, lubrication, and facilitating cell signaling. Examples include hyaluronic acid and chondroitin sulfate.
Bacterial Cell Wall Polysaccharides
Bacterial cell walls are primarily composed of peptidoglycan, a complex structure made of polysaccharide chains cross-linked by peptide bridges. This structure is crucial for maintaining cell shape and preventing lysis in hypotonic environments. Other polysaccharides, such as lipopolysaccharides, also contribute to bacterial virulence and interactions with the host immune system.
Glycoproteins
Glycoproteins are proteins that have carbohydrate components attached. These carbohydrates can influence protein folding, stability, and function. Glycoproteins play essential roles in cell recognition, signaling, and immune responses. Examples include antibodies and certain hormones. The carbohydrate moiety can vary significantly, affecting the properties and functions of the glycoprotein.
Nucleic acids: Structure and functions, physical and chemical properties of nucleic acids, nucleosides and nucleotides, purines and pyrimidines, DNA double helix models, denaturation and renaturation
Nucleic Acids: Structure and Functions
Structure of Nucleic Acids
Nucleic acids include DNA and RNA, composed of long chains of nucleotides. Each nucleotide consists of a sugar, phosphate group, and a nitrogenous base. DNA has a double helix structure, while RNA is usually single-stranded. The structure determines the genetic information they carry.
Functions of Nucleic Acids
Nucleic acids play critical roles in biological processes. DNA serves as the genetic blueprint for the organism, transmitting hereditary information. RNA is involved in protein synthesis, acting as a messenger between DNA and ribosomes, and has roles in catalysis and regulation.
Physical and Chemical Properties of Nucleic Acids
Nucleic acids exhibit various properties, such as absorbance at specific wavelengths due to their aromatic bases. They are soluble in water, and their stability depends on the pH and ionic strength of the solution. Hydrogen bonding in DNA contributes to its stability.
Nucleosides and Nucleotides
Nucleosides are composed of a nitrogenous base bonded to a sugar, while nucleotides consist of a nucleoside with one or more phosphate groups. Nucleotides are the monomer units of nucleic acids and are essential for energy transfer and signaling (e.g., ATP).
Purines and Pyrimidines
Purines are double-ringed nitrogenous bases, including adenine and guanine. Pyrimidines are single-ringed bases, such as cytosine, thymine, and uracil. The arrangement of these bases in nucleic acids impacts base pairing and genetic encoding.
DNA Double Helix Models
The DNA double helix is characterized by two complementary strands held together by hydrogen bonds between purines and pyrimidines. Watson-Crick model illustrates base pairing (A-T and G-C). The anti-parallel orientation and helical twist are crucial for DNA's stability and function.
Denaturation and Renaturation
Denaturation involves the breaking of hydrogen bonds between DNA strands due to heat or chemical agents, leading to strand separation. Renaturation is the process where separated strands come back together under appropriate conditions, allowing the restoration of the double helix structure.
Lipids: Structure and functions of lipids, classification, nomenclature and properties of fatty acids, phospholipids, sphingolipids, glycolipids, prostaglandins, cholesterol
Lipids: Structure and functions of lipids, classification, nomenclature and properties of fatty acids, phospholipids, sphingolipids, glycolipids, prostaglandins, cholesterol
Introduction to Lipids
Lipids are a diverse group of hydrophobic organic molecules. They play key roles in energy storage, cellular structure, and signaling.
Structure of Lipids
Lipids are primarily composed of hydrocarbons. They can be categorized into fatty acids, triglycerides, phospholipids, and sterols.
Classification of Lipids
Lipids are classified into simple lipids (fatty acids, triglycerides), compound lipids (phospholipids, glycolipids), and derived lipids (steroids, prostaglandins).
Fatty Acids
Fatty acids are long hydrocarbon chains with a carboxylic acid group. They are classified as saturated or unsaturated based on the presence of double bonds.
Phospholipids
Phospholipids consist of two fatty acids, glycerol, and a phosphate group. They are key components of cell membranes, forming bilayers.
Sphingolipids
Sphingolipids are important in cell membrane structure and signal transduction. They contain a sphingosine backbone.
Glycolipids
Glycolipids contain carbohydrates and are found in cell membranes, contributing to cell recognition and signaling.
Prostaglandins
Prostaglandins are lipid compounds derived from fatty acids and have roles in inflammation, pain, and other physiological functions.
Cholesterol
Cholesterol is a type of sterol that is vital for maintaining cell membrane integrity and serves as a precursor for steroid hormones.
Enzymes and Enzyme classification: Nomenclature and classification, enzyme kinetics, cofactors, coenzymes, prosthetic groups, holoenzyme and apoenzyme, enzyme inhibition
Enzymes and Enzyme Classification
Nomenclature and Classification
Enzymes are categorized based on the type of reaction they catalyze. The International Union of Biochemistry and Molecular Biology (IUBMB) classifies enzymes into six main classes: oxioreductases, transferases, hydrolases, lyases, isomerases, and ligases. Each class is further divided into subclasses and specific enzymes are named based on their substrate and type of reaction.
Enzyme Kinetics
Enzyme kinetics studies the rates of enzyme-catalyzed reactions. Key parameters include substrate concentration, enzyme concentration, temperature, and pH. The Michaelis-Menten equation describes the relationship between reaction rate and substrate concentration, yielding critical values like Vmax and Km, which provide insights into enzyme efficiency and affinity.
Cofactors, Coenzymes, and Prosthetic Groups
Cofactors are non-protein molecules that assist enzyme activity. These can be inorganic ions (like Mg2+, Zn2+) or organic molecules (coenzymes). Coenzymes are organic cofactor molecules that often act as carriers for chemical groups during enzymatic reactions. Prosthetic groups are tightly bound cofactors that remain attached to the enzyme throughout its function.
Holoenzyme and Apoenzyme
A holoenzyme is the complete, active form of an enzyme that includes its apoenzyme and any required cofactors. The apoenzyme is the protein component of the enzyme, inactive without its cofactor. The presence of the cofactor converts the apoenzyme into a functional holoenzyme.
Enzyme Inhibition
Enzyme inhibition refers to the decrease in enzyme activity due to various inhibitors. Competitive inhibition involves an inhibitor competing with the substrate for the active site, whereas non-competitive inhibition involves an inhibitor binding to a different site on the enzyme, reducing its activity regardless of substrate concentration. Understanding these mechanisms is crucial for drug design and understanding metabolic regulation.
Metabolism: Metabolism of carbohydrates—gluconeogenesis, glycolysis, TCA cycle, glyoxylate cycle; Metabolism of fatty acids; Oxidation of amino acids and urea cycle
Metabolism of carbohydrates and fatty acids and amino acids
Glycolysis
Glycolysis is the metabolic pathway that converts glucose into pyruvate, releasing energy in the form of ATP. This process occurs in the cytoplasm and involves ten enzymatic reactions that can be divided into two phases: the energy investment phase and the energy payoff phase.
Gluconeogenesis
Gluconeogenesis is the synthesis of glucose from non-carbohydrate precursors, primarily occurring in the liver. It is essentially the reverse of glycolysis, with some unique enzymes that bypass the irreversible steps of glycolysis.
TCA Cycle (Citric Acid Cycle)
The TCA cycle, also known as the Krebs cycle, is a key metabolic pathway that takes place in the mitochondrial matrix. It processes acetyl-CoA derived from carbohydrates, fats, and proteins into carbon dioxide and high-energy electron carriers (NADH and FADH2) for ATP production.
Glyoxylate Cycle
The glyoxylate cycle is a variant of the TCA cycle found in plants, bacteria, and fungi. It allows the conversion of fats into carbohydrates, facilitating growth in organisms that do not have a source of carbohydrates.
Metabolism of Fatty Acids
Fatty acid metabolism involves the catabolism of fatty acids for energy, primarily through beta-oxidation, which occurs in the mitochondria. It produces acetyl-CoA, which enters the TCA cycle, and generates NADH and FADH2 for ATP production.
Oxidation of Amino Acids
The oxidation of amino acids serves as a source of energy and involves the removal of the amino group followed by the conversion of the remaining carbon skeleton into various intermediates that enter the TCA cycle.
Urea Cycle
The urea cycle is a series of reactions that convert ammonia, which is toxic at high levels, into urea, which is excreted from the body. This cycle occurs primarily in the liver and is crucial for nitrogen metabolism.
Vitamins and Hormones: Introduction to vitamins, hormones, phytohormones, deficiency diseases
Vitamins and Hormones
Introduction to Vitamins
Vitamins are organic compounds that are crucial for various metabolic processes in the body. They are categorized into two groups: water-soluble (B-complex and vitamin C) and fat-soluble (vitamins A, D, E, K). Each vitamin serves distinct roles, such as aiding in energy production, immune function, and maintaining healthy skin.
Introduction to Hormones
Hormones are chemical messengers produced by glands in the endocrine system. They regulate numerous physiological processes, including metabolism, growth, and mood. Key hormones include insulin, adrenaline, cortisol, and estrogen, each having specific functions and effects on body organs.
Phytohormones
Phytohormones, or plant hormones, are natural substances produced by plants that regulate growth, development, and responses to environmental stimuli. There are several types, including auxins, gibberellins, cytokinins, ethylene, and abscisic acid. They play significant roles in processes such as seed germination and fruit ripening.
Deficiency Diseases
Deficiency diseases occur when the body does not receive adequate vitamins or hormones. For example, vitamin A deficiency can lead to vision problems, while vitamin D deficiency can cause rickets. Hormonal imbalances, like diabetes from insufficient insulin, also illustrate the significance of proper hormone levels for health.
Conclusion
Understanding the roles of vitamins, hormones, and phytohormones is vital for maintaining health. Awareness of deficiency diseases reinforces the importance of a balanced diet and health monitoring for hormone levels.
Techniques: Chromatography (various types), Spectroscopy (UV-Vis), NMR, X-ray diffraction, Centrifugation, Mass spectrometry
Biochemistry and Biochemical tools
Chromatography
Chromatography is a technique used for separating components of a mixture based on their different interactions with a stationary phase and a mobile phase. Various types of chromatography include: 1. Gas Chromatography (GC) - Separates volatile compounds based on their vaporization. 2. Liquid Chromatography (LC) - Utilizes liquid mobile phases for separation, with High-Performance Liquid Chromatography (HPLC) being a notable variant. 3. Thin Layer Chromatography (TLC) - A simple and rapid method performed on a flat surface to separate small quantities.
Spectroscopy
Spectroscopy involves the study of the interaction between matter and electromagnetic radiation. UV-Vis spectroscopy focuses on the absorption of ultraviolet and visible light by biomolecules, allowing for the analysis of concentration and electronic transitions in molecules.
NMR
Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful tool for determining the structure of organic compounds. It relies on the magnetic properties of nuclei, particularly hydrogen, to provide information about molecular structure, dynamics, and environment.
X-ray Diffraction
X-ray diffraction is a technique used to determine the atomic and molecular structure of a crystal. By directing X-rays at a crystal, one can observe the resulting diffraction pattern to discern the positions of atoms within the crystal lattice.
Centrifugation
Centrifugation is a method employed to separate particles from a solution based on their size, shape, and density. By spinning samples at high speeds, denser components sediment to the bottom, allowing for separation.
Mass Spectrometry
Mass spectrometry is an analytical technique used to measure the mass-to-charge ratio of ions. It provides detailed information about molecular weights and structural information, useful in the analysis of complex mixtures.
