MSc Microbiology Semester I comprehensive theory notes covering biochemical principles, metabolic pathways, enzymology and microbial biotechnology with mechanisms, pathways, flowcharts and applications.
Major syllabus areas covered in this page
Carbohydrates, amino acids, proteins, lipids, fatty acids and nucleic acids.
Fat-soluble and water-soluble vitamins, absorption, sources and functions.
Michaelis-Menten kinetics, Lineweaver-Burk plot and enzyme inhibition.
Glycolysis, glycogen metabolism, gluconeogenesis, PPP, uronic acid pathway and disaccharides.
TCA cycle, glyoxylate cycle, ETC, oxidative phosphorylation and substrate-level phosphorylation.
Protein metabolism, ammonia, amino acid biosynthesis, catabolism and urea cycle.
Beta oxidation, alpha and omega oxidation, ketone bodies and lipid biosynthesis.
Purine and pyrimidine de novo and salvage pathways and deoxyribonucleotide formation.
Vectors, Agrobacterium-mediated transfer, animal cell culture and plant tissue culture.
Antibiotics, vitamins, amino acids, organic acids, enzymes, beverages and fermented foods.
Production and recovery of insulin, interferon and human growth hormone.
Rhizobium, Azotobacter, Bacillus, cyanobacteria and VAM.
Bacterial, fungal and viral biological control agents and their applications.
Biomolecules are organic molecules synthesized and utilized by living organisms. They form the structural components of cells and participate in energy storage, catalysis, information transfer, cellular signaling and regulation of metabolism.
The major classes emphasized in biochemistry are carbohydrates, amino acids and proteins, lipids and fatty acids, and nucleic acids. Their properties depend on their chemical structure, functional groups, three-dimensional organization and interactions with water and other cellular components.
| Biomolecule | Basic Components | Major Functions |
|---|---|---|
| Carbohydrates | Monosaccharides | Energy, storage, structural components and cell recognition |
| Proteins | Amino acids | Enzymes, transport, structure, receptors, antibodies and regulation |
| Lipids | Fatty acids, glycerol and other hydrophobic components | Energy storage, membranes, signaling and insulation |
| Nucleic acids | Nucleotides | Genetic information storage, expression and energy transfer |
Carbohydrates are polyhydroxy aldehydes or ketones, or substances that yield such compounds on hydrolysis. They are classified into monosaccharides, oligosaccharides and polysaccharides.
| Class | Definition | Examples |
|---|---|---|
| Monosaccharides | Single sugar unit | Glucose, fructose, galactose, ribose |
| Disaccharides | Two monosaccharides joined by glycosidic bond | Sucrose, lactose, maltose |
| Oligosaccharides | Few monosaccharide residues | Raffinose, stachyose |
| Polysaccharides | Long chains of monosaccharides | Glycogen, starch, cellulose |
Amino acids are the monomeric units of proteins. Proteinogenic amino acids generally contain an amino group, carboxyl group, hydrogen atom and variable side chain attached to the α-carbon.
At physiological pH, amino acids commonly exist as zwitterions containing both positively and negatively charged groups.
Lipids are chemically diverse, largely hydrophobic or amphipathic molecules. They include fatty acids, triacylglycerols, phospholipids, glycolipids and sterols.
| Type | Example | Function |
|---|---|---|
| Triacylglycerol | Fat/oil | Long-term energy storage |
| Phospholipid | Phosphatidylcholine | Membrane structure |
| Sterol | Cholesterol | Membrane organization and precursor of steroid molecules |
| Glycolipid | Cerebrosides | Membrane structure and recognition |
Fatty acids may be saturated or unsaturated. Unsaturated fatty acids contain one or more carbon-carbon double bonds. The degree of unsaturation influences membrane fluidity and the physical properties of fats.
Nucleic acids are polymers of nucleotides. Each nucleotide contains a nitrogenous base, pentose sugar and phosphate group.
| Feature | DNA | RNA |
|---|---|---|
| Sugar | Deoxyribose | Ribose |
| Major bases | A, G, C, T | A, G, C, U |
| Typical structure | Double-stranded | Usually single-stranded |
| Main role | Genetic information storage | Gene expression and regulation |
Vitamins are organic micronutrients required in relatively small amounts for normal metabolism. Many vitamins act as precursors of coenzymes or cofactors involved in enzymatic reactions.
| Fat-soluble | Water-soluble |
|---|---|
| A, D, E and K | B-complex and C |
| Stored relatively readily in tissues | Generally limited storage and regular intake is important |
| Vitamin | Major Function | Important Sources |
|---|---|---|
| A | Vision, epithelial integrity and growth | Animal foods, carotenoid-rich plants |
| D | Calcium and phosphate homeostasis | Sunlight, fish oils, fortified foods |
| E | Antioxidant protection of membranes | Vegetable oils, nuts, seeds |
| K | Blood coagulation protein activation | Green leafy vegetables and intestinal microbial sources |
| B1 | Thiamine pyrophosphate-dependent metabolism | Whole grains, legumes, meat |
| B2 | FAD and FMN formation | Milk, eggs, meat |
| B3 | NAD/NADP-dependent oxidation-reduction reactions | Meat, grains, legumes |
| B6 | PLP-dependent amino acid metabolism | Meat, cereals, legumes |
| B12 | DNA synthesis and one-carbon metabolism | Animal-derived foods and fortified foods |
| C | Collagen synthesis and antioxidant activity | Fruits and vegetables |
Enzymes are biological catalysts that accelerate chemical reactions by lowering activation energy without being consumed in the overall reaction. Most enzymes are proteins, although some catalytic RNA molecules, called ribozymes, also exist.
For a simple enzyme-catalyzed reaction:
Vmax is the maximum reaction velocity when the enzyme is saturated with substrate. Km is the substrate concentration at which the reaction velocity is half of Vmax.
The Lineweaver-Burk plot is the double-reciprocal representation of the Michaelis-Menten equation.
| Inhibition | Binding Site | Effect on Km | Effect on Vmax |
|---|---|---|---|
| Competitive | Active site | Increases | No change |
| Non-competitive | Allosteric site | Usually unchanged in pure form | Decreases |
| Uncompetitive | ES complex | Decreases | Decreases |
Carbohydrate metabolism involves the digestion, absorption, utilization and storage of carbohydrates. Major pathways include glycolysis, glycogenesis, glycogenolysis, gluconeogenesis, pentose phosphate pathway and the uronic acid pathway.
Glycolysis is the sequence of reactions by which one molecule of glucose is converted into two molecules of pyruvate. It occurs in the cytosol and can operate in the presence or absence of oxygen.
The major regulatory enzymes are hexokinase/glucokinase, phosphofructokinase-1 and pyruvate kinase. Among these, phosphofructokinase-1 is the major rate-limiting enzyme.
Glycogenesis is the synthesis of glycogen from glucose. It is favored when glucose availability and cellular energy are relatively high.
Glycogenolysis is the breakdown of glycogen. Glycogen phosphorylase releases glucose-1-phosphate from glycogen branches. Debranching enzyme assists removal of branch points.
Gluconeogenesis is the synthesis of glucose from non-carbohydrate precursors such as lactate, glycerol and glucogenic amino acids. It is particularly important during fasting.
The pentose phosphate pathway operates in the cytosol and has two major functions: production of NADPH and production of ribose-5-phosphate.
| Phase | Main Function |
|---|---|
| Oxidative phase | Produces NADPH and ribulose-5-phosphate |
| Non-oxidative phase | Interconversion of pentose phosphates with glycolytic intermediates |
The uronic acid pathway participates in carbohydrate metabolism and provides intermediates for the synthesis and degradation of certain carbohydrate derivatives. It is also associated with glucuronide formation, an important mechanism for conjugation and elimination of several endogenous and exogenous compounds.
| Disaccharide | Components | Major Enzyme |
|---|---|---|
| Sucrose | Glucose + Fructose | Sucrase |
| Maltose | Glucose + Glucose | Maltase |
| Lactose | Glucose + Galactose | Lactase |
The Krebs cycle, also called the citric acid cycle or TCA cycle, is a central amphibolic pathway. It oxidizes acetyl-CoA and generates reduced electron carriers that subsequently contribute to ATP production through oxidative phosphorylation.
The TCA cycle is amphibolic because it participates in both catabolism and anabolism. It oxidizes acetyl-CoA while also supplying intermediates for biosynthetic pathways.
| Intermediate | Important Biosynthetic Connection |
|---|---|
| Citrate | Fatty acid synthesis |
| α-Ketoglutarate | Amino acid metabolism |
| Succinyl-CoA | Heme biosynthesis |
| Oxaloacetate | Amino acid synthesis and gluconeogenesis |
The glyoxylate cycle is a modified version of the TCA cycle found in many microorganisms and plants. It allows acetyl-CoA to contribute to the net synthesis of four-carbon compounds without complete loss of carbon as CO₂.
Oxidative phosphorylation is the process in which oxidation of reduced electron carriers is coupled to ATP synthesis through an electrochemical proton gradient.
According to the chemiosmotic model, electron transport is coupled to proton translocation across a membrane. The resulting proton-motive force provides the energy required by ATP synthase to convert ADP and inorganic phosphate into ATP.
Substrate-level phosphorylation involves direct transfer of a high-energy phosphate group from a metabolic intermediate to ADP or another nucleotide diphosphate.
Examples occur in glycolysis and the TCA cycle.
Amino acid metabolism includes digestion and absorption of dietary proteins, amino acid biosynthesis, degradation, nitrogen metabolism and disposal of ammonia.
Transamination transfers an amino group from an amino acid to an α-keto acid. Aminotransferases generally use pyridoxal phosphate (PLP), derived from vitamin B6, as a cofactor.
Oxidative deamination releases ammonia from glutamate. Glutamate dehydrogenase is an important enzyme in this process.
The urea cycle converts toxic ammonia into urea, which can be safely transported and excreted. In mammals, the pathway is associated mainly with the liver.
Lipid metabolism includes digestion and transport of dietary lipids, fatty acid oxidation, ketone body formation and biosynthesis of fatty acids, triacylglycerols and other lipids.
β-oxidation is the major pathway for degradation of fatty acids. It occurs mainly in mitochondria in eukaryotic cells and involves repeated removal of two-carbon units as acetyl-CoA.
Fatty acids are highly reduced molecules and therefore provide substantial energy upon complete oxidation. The acetyl-CoA generated enters the TCA cycle, while NADH and FADH₂ contribute electrons to oxidative phosphorylation.
Alpha oxidation is involved in the metabolism of certain branched-chain fatty acids that cannot be efficiently processed by the conventional β-oxidation pathway.
Omega oxidation occurs at the terminal carbon of fatty acids and provides an alternative route of fatty acid metabolism, particularly when β-oxidation is impaired or overwhelmed.
Excess acetyl-CoA generated during fatty acid oxidation can be converted into ketone bodies. Major ketone bodies include acetoacetate, β-hydroxybutyrate and acetone.
Fatty acid synthesis is a reductive anabolic process. Acetyl-CoA is converted into malonyl-CoA and then elongated through repeated condensation, reduction and dehydration reactions.
Triacylglycerol synthesis involves esterification of fatty acyl groups with glycerol-derived intermediates and serves as a major mechanism for long-term energy storage.
Nucleotide metabolism provides the precursors required for DNA and RNA synthesis. It includes de novo synthesis, salvage pathways, interconversion and degradation.
In de novo purine synthesis, the purine ring is constructed progressively on a ribose-phosphate scaffold. IMP is the central precursor for AMP and GMP.
Pyrimidine biosynthesis differs from purine biosynthesis because the pyrimidine ring is assembled before being attached to ribose phosphate.
Salvage pathways recover preformed purine or pyrimidine bases and convert them back into nucleotides. They are energetically less expensive than complete de novo synthesis.
Ribonucleotide reductase converts ribonucleotides into deoxyribonucleotides, providing precursors for DNA synthesis.
Applications of biological systems for production and improvement of useful products
Biotechnology uses living cells, organisms or biological molecules to develop products and processes of practical value. Modern biotechnology combines molecular biology, genetics, cell culture, microbiology and biochemical engineering.
Agrobacterium-mediated transformation is an important method for introducing foreign DNA into plant cells. Agrobacterium naturally transfers T-DNA from its Ti plasmid into plant cells. Biotechnology modifies this system to deliver desired genes.
| Component | Function |
|---|---|
| T-DNA | Region transferred into plant genome |
| Virulence genes | Assist processing and transfer of T-DNA |
| Border sequences | Define the transferable T-DNA region |
A binary vector system separates the T-DNA region from the virulence functions. The engineered vector carries the desired gene, while helper functions are supplied by another plasmid system within the Agrobacterium strain.
The ability of plant cells to regenerate into complete plants is related to cellular totipotency.
Animal cell culture involves maintaining animal cells under controlled nutritional, physical and environmental conditions. It is important in vaccine development, recombinant protein production, drug screening and research.
Microorganisms are used as biological production systems because of their rapid growth, metabolic diversity, genetic manipulability and ability to produce valuable metabolites and enzymes.
Penicillin is a β-lactam antibiotic produced industrially using selected strains of Penicillium. Large-scale production involves strain improvement, submerged fermentation and downstream recovery.
Streptomycin is an aminoglycoside antibiotic associated with Streptomyces griseus. Industrial production involves fermentation, biomass separation and recovery of the antibiotic from the fermentation broth.
Riboflavin (vitamin B2) can be produced by microbial fermentation. Industrial strains are selected or improved for high productivity, followed by recovery and purification of the vitamin.
Vitamin B12 production involves selected microorganisms capable of synthesizing cobalamin. Process optimization is important because vitamin biosynthesis depends on appropriate nutrients and growth conditions.
Microorganisms are extensively used for commercial production of amino acids because their metabolic pathways can be manipulated to increase accumulation of desired products.
| Product | Major Application |
|---|---|
| Glutamic acid | Food flavoring and fermentation industry |
| Lysine | Animal feed and nutritional supplementation |
| Tryptophan | Pharmaceutical and nutritional applications |
Citric acid is commercially produced using microorganisms, particularly Aspergillus niger. Industrial production depends strongly on medium composition, carbon source, pH, temperature and aeration.
Lactic acid can be produced by lactic acid bacteria through carbohydrate fermentation. Depending on the organism and pathway, glucose can be converted primarily to lactic acid.
Kojic acid is a microbial metabolite produced by selected fungi and has applications in cosmetic and pharmaceutical-related formulations.
| Enzyme | Major Function | Applications |
|---|---|---|
| Amylase | Hydrolysis of starch | Food, textile, detergent and starch industries |
| Protease | Protein hydrolysis | Detergent, food and leather industries |
| Glucose isomerase | Conversion of glucose to fructose | High-fructose syrup production |
Yeasts convert fermentable sugars into ethanol and carbon dioxide under anaerobic or oxygen-limited conditions.
Wine production generally involves alcoholic fermentation of grape juice by yeasts, followed by clarification, maturation and stabilization processes depending on the product.
Beer production involves malting, mashing, wort preparation, boiling, fermentation, maturation and clarification.
| Food | Important Microbial Role |
|---|---|
| Kinema | Bacillus-associated alkaline fermentation of soybean |
| Soya sauce | Mixed microbial fermentation involving molds, yeasts and bacteria |
| Natto | Bacillus subtilis-associated soybean fermentation |
| Kimchi | Lactic acid bacterial fermentation of vegetables |
Single cell protein (SCP) refers to microbial biomass used as a protein-rich food or feed source. Organisms used may include yeasts, bacteria, algae and fungi.
Recombinant DNA technology allows genes encoding valuable proteins to be expressed in suitable host organisms. Microbial systems are widely used because of their rapid growth and ease of genetic manipulation.
Recombinant insulin production involves expression of insulin precursor or appropriate insulin-related sequences in a host, followed by processing, purification and formulation.
Recombinant human growth hormone can be produced using expression systems carrying the gene encoding human growth hormone. Downstream processing is required to obtain a purified product.
Recombinant interferons are produced using genetically engineered host systems and are purified for therapeutic applications.
Biofertilizers are preparations containing living microorganisms that enhance nutrient availability or promote plant growth. They can improve nutrient cycling and reduce dependence on certain chemical fertilizers.
| Microorganism | Major Role |
|---|---|
| Rhizobium | Symbiotic nitrogen fixation in legumes |
| Azotobacter | Free-living nitrogen fixation and plant growth promotion |
| Bacillus | Plant growth promotion and nutrient mobilization |
| Cyanobacteria | Nitrogen fixation, particularly important in some aquatic/agricultural systems |
| VAM / AM fungi | Improved phosphorus and mineral uptake |
Nitrogenase catalyzes the reduction of atmospheric nitrogen to ammonia. The reaction requires substantial ATP and reducing power.
Biopesticides use microorganisms or microbial products to control pests. Bioherbicides are biological agents used to suppress unwanted plants or weeds.
Bacillus thuringiensis is one of the most important bacterial biopesticide organisms. It produces insecticidal crystal proteins that can be toxic to susceptible insect larvae after ingestion.
Entomopathogenic fungi can infect insects through the external cuticle. Examples include Beauveria and Metarhizium species.
Baculoviruses are important viral agents used for biological control of specific insect pests. Their high host specificity can be useful in integrated pest management.
Microbial bioherbicides use pathogens or microbial metabolites to suppress specific weeds. Their effectiveness depends on host specificity, environmental conditions and application strategy.
High-yield concepts for MSc preparation
| Concept | Key Difference |
|---|---|
| Glycolysis vs Gluconeogenesis | Glycolysis breaks glucose down; gluconeogenesis synthesizes glucose from non-carbohydrate precursors. |
| β-Oxidation vs Fatty Acid Synthesis | β-oxidation is mainly catabolic and produces acetyl-CoA; fatty acid synthesis is anabolic and consumes reducing power. |
| De novo vs Salvage pathway | De novo synthesis builds nucleotides from simple precursors; salvage pathways recycle preformed bases. |
| Competitive vs Non-competitive inhibition | Competitive inhibition affects apparent Km but not Vmax; pure non-competitive inhibition decreases Vmax without changing Km. |
| Biofertilizer vs Biopesticide | Biofertilizers improve nutrient availability or plant growth; biopesticides suppress pests. |
| Topic | Remember |
|---|---|
| Glycolysis | Glucose → Pyruvate; cytosolic pathway; ATP and NADH generation |
| TCA cycle | Acetyl-CoA oxidation; NADH/FADH₂/GTP production; amphibolic role |
| PPP | NADPH + ribose-5-phosphate |
| Urea cycle | Ammonia detoxification through urea formation |
| β-oxidation | Fatty acid → acetyl-CoA + NADH + FADH₂ |
| Purine pathway | IMP → AMP/GMP |
| Enzyme kinetics | Km, Vmax, Michaelis-Menten and inhibition |
| Plant biotechnology | Agrobacterium, Ti plasmid, T-DNA, binary vector |
| Industrial microbiology | Strain → fermentation → recovery → purification |
| Biofertilizer | Rhizobium, Azotobacter, Bacillus, cyanobacteria, VAM |
| Biopesticide | Bt, entomopathogenic fungi, baculoviruses |
This page is organized according to the MB 504 Biochemistry and Biotechnology theory syllabus of Tribhuvan University, with additional explanatory material for postgraduate study.