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Semester 1: M.Sc. Biotechnology Syllabus 2023-2024
pH, pK, Acid, base. Buffers- Henderson-Hasselbach equation, biological buffer system Phosphate buffer system, protein buffer system, bicarbonate buffer system, amino acid buffer system and Hb buffer system
pH, pK, Acid, Base and Buffers
pH
pH is a measure of the hydrogen ion concentration in a solution. It indicates whether a solution is acidic (pH less than 7), neutral (pH equal to 7), or basic (pH greater than 7). The pH scale is logarithmic, meaning each whole number change on the scale represents a tenfold change in hydrogen ion concentration.
pK
pK is the negative logarithm of the acid dissociation constant (Ka) and indicates the strength of an acid in solution. A lower pK value indicates a stronger acid that dissociates more readily to produce hydrogen ions. pK values are crucial for understanding the behavior of acids and bases in biological systems.
Acids
Acids are substances that donate protons (H+) in a solution. Strong acids completely dissociate in water, while weak acids only partially dissociate. The strength of an acid is determined by its pK value. Biological acids, such as amino acids and nucleic acids, play essential roles in metabolic processes.
Bases
Bases are substances that accept protons or donate hydroxide ions (OH-) in a solution. Like acids, bases can also be classified as strong or weak based on their dissociation in water. The presence of bases is important in biological systems for maintaining pH balance.
Buffers
Buffers are solutions that resist changes in pH upon the addition of small amounts of acid or base. They are vital in biological systems to maintain a stable pH. Buffers consist of a weak acid and its conjugate base (or vice versa).
Henderson-Hasselbalch Equation
The Henderson-Hasselbalch equation relates the pH of a buffer solution to the pKa of the acid and the ratio of the concentrations of its dissociated and undissociated forms. It is expressed as pH = pKa + log([A-]/[HA]), where [A-] is the concentration of the conjugate base and [HA] is the concentration of the acid.
Phosphate Buffer System
The phosphate buffer system is one of the key buffering systems in biological fluids, especially in the cytoplasm of cells. It consists mainly of dihydrogen phosphate (H2PO4-) and hydrogen phosphate (HPO4^2-). This system helps maintain pH within the physiological range.
Protein Buffer System
Proteins can act as buffers due to their amino acid residues, which can donate or accept protons. The buffering capacity of proteins is significant in maintaining pH in blood and tissues. Hemoglobin, for example, acts as a buffer in blood by binding to protons.
Bicarbonate Buffer System
The bicarbonate buffer system is crucial for regulating pH in the blood and consists of carbonic acid (H2CO3) and bicarbonate (HCO3-). This system allows for the dynamic regulation of pH in response to metabolic processes and respiratory activities.
Amino Acid Buffer System
Amino acids can function as buffers due to the presence of both carboxyl and amino groups, allowing them to donate or accept protons. The buffering capacity varies with the side chains of the amino acids.
Hemoglobin Buffer System
Hemoglobin functions as a buffer by binding to CO2 and protons (H+) in the blood. It helps transport CO2 from tissues to the lungs and plays a critical role in maintaining blood pH.
Carbohydrates - Nomenclature, classification, structure, chemical and physical properties of carbohydrates. Metabolism: glycogenesis, glycogenolysis, gluconeogenesis, pentose phosphate pathway, glycolysis, citric acid cycle, Cori cycle, glyoxalate pathway
Carbohydrates
Nomenclature
Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen, typically with a general formula (CH2O)n. The nomenclature often includes terms like monosaccharides, disaccharides, oligosaccharides, and polysaccharides, reflecting their structure and complexity.
Classification
Carbohydrates are classified based on their structure: monosaccharides (simple sugars like glucose and fructose), disaccharides (two monosaccharides linked such as sucrose and lactose), oligosaccharides (short chains of monosaccharides), and polysaccharides (long chains, e.g., starch, glycogen, cellulose).
Structure
Monosaccharides are single sugar units with a backbone of carbon atoms and hydroxyl groups. Disaccharides consist of two monosaccharides joined by a glycosidic bond. Polysaccharides are branched or linear chains of monosaccharides, forming complex structures.
Chemical Properties
Carbohydrates can undergo various chemical reactions, including hydrolysis, oxidation, and reduction. They are known for their ability to form glycosidic bonds and participate in redox reactions, influencing their functionality in biological systems.
Physical Properties
Carbohydrates are generally soluble in water, with their solubility decreasing with increasing molecular weight. They can exist in crystalline forms and have distinctive melting points. Their taste can vary from sweet (sugars) to bland (polysaccharides).
Metabolism
Carbohydrate metabolism refers to the biochemical processes that convert carbohydrates into energy and other metabolites. Key pathways include:
Glycogenesis
The process of converting glucose into glycogen for storage in liver and muscle tissues. It involves the enzyme glycogen synthase.
Glycogenolysis
The breakdown of glycogen into glucose when energy is needed. It is regulated by hormones such as glucagon and epinephrine.
Gluconeogenesis
The synthesis of glucose from non-carbohydrate precursors. Occurs mainly in the liver and is vital during fasting.
Pentose Phosphate Pathway
A metabolic pathway parallel to glycolysis that generates NADPH and pentoses (5-carbon sugars) for nucleotide synthesis.
Glycolysis
The breakdown of glucose into pyruvate, yielding ATP and NADH. It occurs in the cytoplasm and is the first step of cellular respiration.
Citric Acid Cycle
Also known as the Krebs cycle, it takes place in the mitochondria, oxidizing acetyl-CoA to produce CO2, ATP, NADH, and FADH2.
Cori Cycle
The metabolic pathway that recycles lactate produced during anaerobic glycolysis in muscles back to glucose in the liver.
Glyoxalate Pathway
A variant of the citric acid cycle that allows organisms like plants and some microbes to convert fatty acids into carbohydrates.
Lipids - Nomenclature, classification, structure, chemical and physical properties of fatty acids. Metabolism: biosynthesis of fatty acids, triglycerols, phospholipids, glycolipids. Cholesterol biosynthesis, bile acids and salt formation. Oxidation of fatty acids, beta-oxidation, alpha and gamma oxidation
Lipids
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Lipids are a diverse group of hydrophobic or amphipathic organic compounds characterized by their solubility in nonpolar solvents and insolubility in water.
fatty acids
triglycerides
phospholipids
glycolipids
steroids
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Composed of long hydrocarbon chains with a carboxylic acid group at one end.
saturated
unsaturated
acidity
derivatization
melting point
solubility
boiling point
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Produced through the fatty acid synthase complex, utilizing acetyl-CoA as the building block.
Synthesized from glycerol and fatty acids and stored in adipose tissue.
Formed from fatty acids, glycerol, and phosphate groups, vital for cell membranes.
Comprised of carbohydrates and lipids, important for cell recognition.
Involves multiple enzymatic steps starting from acetyl-CoA with HMG-CoA reductase as a key regulator.
Cholesterol is essential for cell membrane integrity and as a precursor for steroid hormones and bile acids.
Cholesterol is converted to bile acids in the liver, aiding in the emulsification and digestion of dietary fats.
Formed from bile acids and conjugated with amino acids for improved solubility.
Primary method for fatty acid degradation in mitochondria, producing acetyl-CoA, NADH, and FADH2.
Occurs in peroxisomes and involves the removal of one carbon at a time from the fatty acid chain.
Primarily occurs in specific metabolic adaptations, producing similar energy carriers.
Bioenergetics - Concept of energy, Principle of thermodynamics. Laws of thermodynamics, Biological oxidation Electron transport chain, oxidative phosphorylation. Photosynthesis Oxygenic and Anoxygenic, Hormonal regulation of fatty acids and carbohydrate metabolisms
Bioenergetics
Concept of Energy
Energy is the capacity to do work. In biological systems, energy is crucial for processes like metabolism, growth, and reproduction. It exists in various forms, including kinetic, potential, thermal, and chemical energy. Organisms obtain energy primarily through the catabolism of nutrients.
Principle of Thermodynamics
Thermodynamics governs energy transformations. The first law states that energy cannot be created or destroyed, only transformed. The second law introduces entropy, indicating that systems tend to move towards disorder unless energy is expended to maintain order.
Laws of Thermodynamics
1. First Law: Conservation of Energy - energy in an isolated system remains constant. 2. Second Law: Entropy increases in natural processes - systems evolve towards thermodynamic equilibrium.
Biological Oxidation
Biological oxidation involves the enzymatic breakdown of substrates in the presence of oxygen. It releases energy stored in chemical bonds, primarily through the processes of glycolysis, the Krebs cycle, and oxidative phosphorylation.
Electron Transport Chain (ETC)
The ETC is a series of protein complexes located in the inner mitochondrial membrane. It transfers electrons from NADH and FADH2 to oxygen, creating a proton gradient that drives ATP synthesis via chemiosmosis.
Oxidative Phosphorylation
Oxidative phosphorylation occurs in the mitochondria where ATP is produced using energy from the ETC. Protons flow back into the mitochondrial matrix through ATP synthase, catalyzing the conversion of ADP and inorganic phosphate to ATP.
Photosynthesis
Photosynthesis is the process by which autotrophs convert light energy into chemical energy stored in glucose. It occurs in two stages: the light-dependent reactions and the Calvin cycle.
Oxygenic and Anoxygenic Photosynthesis
Oxygenic photosynthesis, performed by plants and cyanobacteria, produces oxygen as a byproduct. Anoxygenic photosynthesis, found in some bacteria, does not produce oxygen and relies on alternative electron donors such as hydrogen sulfide.
Hormonal Regulation of Fatty Acids and Carbohydrate Metabolisms
Hormones like insulin, glucagon, and epinephrine play key roles in metabolic regulation. Insulin promotes glucose uptake and fatty acid synthesis, while glucagon stimulates glycogenolysis and lipolysis, maintaining homeostasis.
Amino acids and Protein - Nomenclature, Classification, structure, chemical and physical properties. Metabolism: Biosynthesis of amino acids. Degradation of proteins, nitrogen metabolism and carbon skeleton of amino acids, Urea cycle. Overall inborn errors of metabolism
Amino Acids and Protein
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Amino acids are organic compounds characterized by the presence of both an amino group and a carboxyl group. They are classified based on the nature of their side chains, which can be categorized as non-polar, polar, acidic, or basic. Standard amino acids are encoded by the genetic code, while non-standard amino acids may occur in proteins or be intermediates in metabolic pathways.
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Amino acids can be classified into essential and non-essential amino acids. Essential amino acids cannot be synthesized by the body and must be obtained from the diet, whereas non-essential amino acids can be synthesized by the body.
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The general structure of amino acids includes a central carbon atom, an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom, and a variable side chain (R group). The specific properties of each amino acid are determined by the unique structure of its side chain.
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The chemical properties of amino acids are influenced by their functional groups. They can act as both acids and bases, exhibit zwitterionic character in solution, and participate in peptide bond formation, leading to protein structure.
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Physical properties include melting points, solubility, and the ability to form crystalline structures. These properties vary widely among the different amino acids and influence protein folding and stability.
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Amino acids can be synthesized through various pathways, including transamination and amidation. The biosynthesis often begins with substrates derived from the glycolytic pathway or the TCA cycle.
The degradation of proteins involves proteolytic enzymes that break down proteins into polypeptides and then into individual amino acids. These amino acids can then enter various metabolic pathways.
Nitrogen metabolism is critical for amino acid synthesis and degradation, focusing on the incorporation of nitrogen into organic molecules and the removal of excess nitrogen.
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The carbon skeleton of amino acids is the backbone that provides the framework for metabolic processes. Different amino acids have unique carbon skeletons that influence their role in cellular metabolism.
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The urea cycle is a metabolic pathway that converts excess nitrogen from amino acid degradation into urea for excretion. This cycle helps to maintain nitrogen balance in the body.
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Inborn errors of metabolism refer to genetic disorders that result in metabolic dysfunction. These can result from defects in enzymes involved in amino acid metabolism, leading to conditions such as phenylketonuria or maple syrup urine disease.
Nucleic acids - Nomenclature, Classification, structure, chemical and physical properties. De novo and salvage synthesis of purine and pyrimidine bases, nucleosides and nucleotides. Catabolism of purine and pyrimidine bases. Synthetic analogues of nitrogenous bases
Nucleic acids
Nomenclature
Nucleic acids are classified primarily into DNA and RNA. The nomenclature involves specific naming conventions for nucleotides, nucleosides, and bases. Nucleotides are named based on the nitrogenous base, sugar (ribose or deoxyribose), and phosphate group location. Common bases include adenine, guanine, cytosine, thymine, and uracil.
Classification
Nucleic acids are classified into two main types: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is typically double-stranded, containing deoxyribose sugar, while RNA is usually single-stranded and contains ribose. RNA can be further classified into mRNA, tRNA, rRNA, and others based on function.
Structure
Nucleotides comprise a nitrogenous base, a five-carbon sugar, and one or more phosphate groups. The sugar-phosphate backbone forms the structural framework of nucleic acids, while the bases provide coding information. DNA has a double helix structure stabilized by hydrogen bonds between complementary bases.
Chemical properties
Nucleic acids are acidic in nature due to the presence of phosphate groups. They can participate in hydrogen bonding and interactions with proteins and other biomolecules. The stability of nucleic acids is affected by factors like pH, temperature, and ionic strength.
Physical properties
Nucleic acids exhibit unique physical properties such as UV absorbance due to aromatic bases. The melting temperature (Tm) indicates the stability of the double helix; higher GC content generally increases Tm due to stronger hydrogen bonding.
De novo synthesis and salvage synthesis
De novo synthesis of purine and pyrimidine bases occurs from simpler molecules, while salvage pathways recover bases and nucleotides from degradation products. Key enzymes include ribonucleotide reductase for reducing ribonucleotides to deoxyribonucleotides.
Catabolism of purine and pyrimidine bases
Purine catabolism leads to the formation of uric acid, which is excreted. Pyrimidine catabolism results in the production of ammonia and other metabolites. Disorders in catabolism can result in metabolic diseases.
Synthetic analogues of nitrogenous bases
Synthetic analogues, such as azathioprine or 5-fluorouracil, are used in therapy to interfere with nucleic acid synthesis. These analogues can disrupt the function of nucleic acids and are utilized in cancer treatment and immunosuppressive therapy.
