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Semester 2: Biochemistry and Physiology
Structure and Function of Biomolecules: carbohydrates, lipids, amino acids, proteins
Structure and Function of Biomolecules
Carbohydrates
Carbohydrates are organic compounds made of carbon, hydrogen, and oxygen. They are categorized into monosaccharides, disaccharides, and polysaccharides. Monosaccharides like glucose serve as immediate energy sources, while polysaccharides such as starch and glycogen function in energy storage and structural support in plants and animals.
Lipids
Lipids are hydrophobic molecules composed mainly of hydrocarbons. They include fats, oils, phospholipids, and steroids. Lipids serve multiple roles such as energy storage, cell membrane formation, and signaling molecules. Fatty acids can be saturated or unsaturated, influencing their physical properties and functions.
Amino Acids
Amino acids are organic molecules that serve as the building blocks of proteins. There are 20 standard amino acids, each with a unique side chain determining its properties. They contain an amino group, carboxyl group, and a variable side chain. Amino acids link through peptide bonds to form polypeptides and proteins.
Proteins
Proteins are large, complex molecules composed of one or more polypeptides. They play crucial roles in biological processes, including catalyzing reactions (enzymes), transporting molecules, and providing structure. The function of a protein is determined by its structure, which is divided into four levels: primary, secondary, tertiary, and quaternary.
Enzyme Action and Regulation: enzyme nomenclature, mechanism, kinetics, allosteric enzymes
Enzyme Action and Regulation
Enzyme Nomenclature
Enzyme Mechanisms
Enzyme Kinetics
Allosteric Enzymes
Enzymes are named based on the substrate they act upon and the type of reaction they catalyze. The International Union of Biochemistry and Molecular Biology (IUBMB) classifies enzymes into six main classes: oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases. Each enzyme has a unique Enzyme Commission (EC) number that provides precise information about its function.
Enzyme action involves several fundamental steps: substrate binding, catalysis, and product release. The active site is the specific region of the enzyme where the substrate binds. The catalytic mechanism can include various processes such as acid-base catalysis, covalent catalysis, and metal ion catalysis. Understanding these mechanisms provides insight into how enzymes lower activation energy and increase reaction rates.
Enzyme kinetics studies the rates of enzyme-catalyzed reactions. Michaelis-Menten kinetics is a common model that describes the relationship between the rate of reaction and substrate concentration. Key parameters include Vmax (maximum velocity) and Km (Michaelis constant), which indicates the substrate concentration at which the reaction rate is half of Vmax. Kinetic studies help in understanding enzyme efficiency and inhibition.
Allosteric enzymes have unique regulatory sites apart from the active site, allowing them to change conformation upon binding of effectors (activators or inhibitors). This process alters the enzyme's activity, enabling fine-tuning of metabolic pathways. The sigmoid shape of the enzyme activity versus substrate concentration graph indicates cooperative binding, showing that allosteric regulation is crucial for maintaining homeostasis in biological systems.
Metabolism of Carbohydrates and Lipids: glycolysis, citric acid cycle, gluconeogenesis, fatty acid metabolism
Metabolism of Carbohydrates and Lipids
Glycolysis
Glycolysis is the metabolic pathway that converts glucose into pyruvate, generating ATP and NADH in the process. It occurs in the cytoplasm and is anaerobic. The pathway consists of ten enzyme-catalyzed reactions divided into two phases: the energy investment phase and the energy payoff phase. Key intermediates include glucose 6-phosphate, fructose 1,6-bisphosphate, and pyruvate.
Citric Acid Cycle
The Citric Acid Cycle, also known as the Krebs cycle, is a key metabolic pathway that takes place in the mitochondria. It oxidizes acetyl-CoA to CO2, capturing energy in the form of ATP, NADH, and FADH2. Each turn of the cycle involves the condensation of acetyl-CoA with oxaloacetate to form citrate, followed by a series of enzymatic reactions that regenerate oxaloacetate.
Gluconeogenesis
Gluconeogenesis is the metabolic process that synthesizes glucose from non-carbohydrate precursors, primarily occurring in the liver and kidneys. It takes place mainly during fasting or intense exercise when glucose levels are low. Key substrates include lactate, glycerol, and amino acids. The pathway bypasses three irreversible steps of glycolysis using distinct enzymes like pyruvate carboxylase and phosphoenolpyruvate carboxykinase.
Fatty Acid Metabolism
Fatty acid metabolism involves both catabolic and anabolic pathways. Beta-oxidation is the primary catabolic pathway, breaking down fatty acids into acetyl-CoA units for energy production in the mitochondria. Fatty acid synthesis, on the other hand, occurs in the cytoplasm and uses acetyl-CoA and NADPH to form long-chain fatty acids. Regulation of these pathways is crucial for maintaining energy homeostasis.
Metabolism of Proteins and Nucleotides: amino acid catabolism, urea cycle, nucleotides and vitamins, oxidative phosphorylation
Metabolism of Proteins and Nucleotides
Amino Acid Catabolism
Amino acid catabolism involves the breakdown of amino acids for energy and the production of metabolic intermediates. The process begins with the removal of the amino group through deamination, leading to the formation of ammonia and a corresponding keto acid. Ammonia is toxic and is converted to urea in the liver via the urea cycle. The remaining carbon skeleton can enter various metabolic pathways, including gluconeogenesis or the citric acid cycle.
Urea Cycle
The urea cycle is a series of reactions that convert ammonia into urea for excretion. It occurs primarily in the liver and involves the coordination of several enzymes. The key steps include the formation of carbamoyl phosphate, the condensation with ornithine to produce citrulline, and then the formation of arginine, which is ultimately split to release urea and regenerate ornithine. This cycle is crucial for detoxifying ammonia derived from amino acid catabolism.
Nucleotide Metabolism
Nucleotide metabolism encompasses the synthesis and degradation of nucleotides, which are the building blocks of DNA and RNA. Nucleotide synthesis can be de novo or salvage pathways. The degradation of nucleotides generates nucleosides and eventually uric acid. Disruptions in nucleotide metabolism can lead to diseases such as gout or purine metabolism disorders.
Vitamins in Metabolism
Vitamins play essential roles as coenzymes and cofactors in many metabolic pathways. Water-soluble vitamins, such as B vitamins, are critical in energy production and amino acid metabolism. Fat-soluble vitamins, like A, D, E, and K, also participate in metabolic processes, including antioxidant activity and calcium homeostasis. Deficiencies in vitamins can impair protein and nucleotide metabolism.
Oxidative Phosphorylation
Oxidative phosphorylation is the final stage of cellular respiration, occurring in the mitochondria. It involves the electron transport chain and chemiosmosis. Electrons from NADH and FADH2 are transferred through a series of proteins, creating a proton gradient across the inner mitochondrial membrane. The flow of protons back into the mitochondrial matrix through ATP synthase drives the production of ATP. This process is tightly linked to metabolic pathways, including those of proteins and nucleotides.
Digestion and Respiration: gastrointestinal tract, digestion, respiration mechanisms, respiratory pigments
Digestion and Respiration
Gastrointestinal Tract
The gastrointestinal tract is a series of hollow organs that work together to convert food into energy and basic nutrients to feed the entire body. It includes the mouth, esophagus, stomach, small intestine, large intestine, rectum, and anus. Each segment plays a crucial role in the mechanical and chemical breakdown of food.
Digestion
Digestion is the biochemical process through which food is broken down into smaller components that can be absorbed by the body. This process comprises two main types: mechanical digestion, which includes chewing and the churning of food in the stomach, and chemical digestion, which involves enzymes breaking down food into molecules. Key enzymes include amylase for carbohydrates, pepsin for proteins, and lipase for fats.
Respiration Mechanisms
Respiration refers to the processes through which organisms exchange gases with their environment, primarily involving the intake of oxygen and the expulsion of carbon dioxide. In mammals, respiration occurs in two stages: external respiration, which is the exchange of gases between the lungs and the blood, and internal respiration, which occurs at the cellular level where oxygen is utilized for energy production and carbon dioxide is produced as a waste product.
Respiratory Pigments
Respiratory pigments are proteins that transport oxygen in the blood. The most common respiratory pigment in vertebrates is hemoglobin, found in red blood cells. Hemoglobin binds oxygen in the lungs and releases it in the tissues. In some invertebrates, such as mollusks and some arthropods, hemocyanin, which contains copper, serves a similar function and has a blue color when oxygenated.
Circulation and Excretion: blood components, haemostasis, heart structure, cardiac cycle, kidney structure and urine formation
Circulation and Excretion
Blood Components
Blood consists of three main components: red blood cells, white blood cells, and platelets. Red blood cells are responsible for transporting oxygen and carbon dioxide. White blood cells are involved in immune response. Platelets play a vital role in blood clotting.
Haemostasis
Haemostasis is the process of stopping bleeding, which involves vascular spasm, platelet plug formation, and coagulation. The coagulation cascade leads to the formation of fibrin clots, which help seal wounds and prevent blood loss.
Heart Structure
The heart has four chambers: two atria and two ventricles. It is divided into the right and left sides, with the right side pumping deoxygenated blood to the lungs and the left side pumping oxygenated blood to the body.
Cardiac Cycle
The cardiac cycle includes all the events of one heartbeat, comprising diastole (relaxation) and systole (contraction). During diastole, the heart fills with blood, and during systole, the heart pumps blood out.
Kidney Structure
The kidney has multiple functional units called nephrons. Each nephron consists of a renal corpuscle and a renal tubule. The kidneys filter blood, remove waste, and regulate fluid balance.
Urine Formation
Urine formation involves three main processes: filtration, reabsorption, and secretion. Filtration occurs in the glomerulus, reabsorption happens in the renal tubules, and secretion involves the transfer of additional waste from blood to urine.
Nervous System and Endocrinology: neuron structure, action potential, synapses, endocrine glands and hormones
Nervous System and Endocrinology
Neuron Structure
Neurons are specialized cells that transmit nerve impulses. They consist of three main parts: the cell body (soma), dendrites, and axon. The soma contains the nucleus and organelles, the dendrites receive signals from other neurons, and the axon sends impulses away from the cell body. Neurons can be classified into sensory, motor, and interneurons based on their function.
Action Potential
An action potential is a rapid, temporary change in the membrane potential of a neuron. It is generated when the neuron's membrane depolarizes to a threshold level, resulting in the opening of voltage-gated sodium channels. This influx of sodium ions causes the membrane potential to become positive before repolarization occurs as potassium channels open, restoring the resting potential.
Synapses
Synapses are specialized junctions where neurons communicate with each other or with other types of cells. There are two main types of synapses: electrical and chemical. Chemical synapses involve the release of neurotransmitters from the presynaptic neuron, which bind to receptors on the postsynaptic neuron, leading to either excitation or inhibition of the postsynaptic neuron.
Endocrine Glands
Endocrine glands are responsible for hormone production and release into the bloodstream. Major endocrine glands include the pituitary, thyroid, adrenal glands, and pancreas. Each gland produces specific hormones that regulate various bodily functions such as metabolism, growth, and stress responses.
Hormones
Hormones are chemical messengers that travel through the bloodstream to target organs and tissues, eliciting specific biological responses. Some key hormones include insulin (regulates blood glucose levels), adrenaline (increases heart rate during stress), and thyroxine (regulates metabolism). Hormones play crucial roles in maintaining homeostasis in the body.
Muscular System: histology of muscle types, ultrastructure, muscle contraction mechanisms
Muscular System
Histology of Muscle Types
The muscular system consists of three main types of muscle: skeletal, cardiac, and smooth. Skeletal muscles are striated and under voluntary control, while cardiac muscle is striated but involuntary, found only in the heart. Smooth muscle is non-striated and also involuntary, located in walls of hollow organs. Histologically, skeletal muscle fibers are multinucleated and organized in bundles, while cardiac muscle features intercalated discs. Smooth muscle cells are spindle-shaped and arranged in sheets.
Ultrastructure of Muscle Tissue
The ultrastructure of muscle tissue is characterized by the presence of myofibrils within muscle fibers. Myofibrils contain thick filaments made of myosin and thin filaments composed of actin, tropomyosin, and troponin. The organization of these filaments forms sarcomeres, the basic contractile units of muscle. The sarcoplasmic reticulum surrounds myofibrils and regulates calcium ion concentrations during muscle contraction.
Muscle Contraction Mechanisms
Muscle contraction occurs via the sliding filament theory, where myosin heads bind to actin filaments, creating cross-bridges. This process is regulated by the availability of calcium ions and ATP. Upon stimulation by a motor neuron, calcium is released from the sarcoplasmic reticulum, allowing myosin to attach to actin, initiating contraction. The force generated is a result of repeated cycles of cross-bridge formation and detachment.
