Notes MC2 Biochemistry PDF

Biochemistry: Introduction to Biochemistry I. Introduction to Biochemistry Alkynes (Triple Bonds): CnH2n–2 Contains at least one triple bond, Highly reactive, Less common in I. Definition...

Biochemistry: Introduction to Biochemistry I. Introduction to Biochemistry Alkynes (Triple Bonds): CnH2n–2 Contains at least one triple bond, Highly reactive, Less common in I. Definition and Scope of Biochemistry biological systems Biochemistry is the study of the chemical processes Ex. Ethyne aka acetylene within and relating to living organisms. (C₂H₂) It seeks to understand the structure and function of bi- omolecules, as well as the metabolic pathways and regulatory mechanisms that govern life processes. Functional Groups II. Overview of Biomolecules Specific groups of atoms within molecules that confer Biomolecules are organic molecules essential for life. characteristic chemical properties and reactivity. Key classes of biomolecules include: o Hydroxyl (-OH) – found in alcohols o Carbohydrates - Provide and store energy; o Carbonyl (C=O) – found in aldehydes, ke- structural components. tones, acids, esters, amides o Lipids - Store energy, form cell membranes, act as signaling molecules (hormones). o Carboxyl (-COOH) – found in fatty acids o Proteins - Diverse functions, including catal- o Amino (-NH2) – found in proteins ysis (enzymes), structure, transport, defense o Phosphate (-PO4) – energy transfer in ATP (antibodies), and regulation. o Nucleic Acids - Store and transmit genetic information (DNA and RNA). III. Attributes of Life Biochemistry explores the chemical basis of key char- acteristics of living organisms, including: o Organization - Complex, hierarchical struc- tures from molecules to cells to organisms. o Metabolism - Chemical reactions for energy transformation and biosynthesis. o Growth and Development - Increase in size and complexity. o Responsiveness - Ability to react to environ- mental stimuli. o Adaptation - Evolutionary changes over Macromolecules vs Micromolecules time to enhance survival. o Reproduction - Ability to produce offspring. Macromolecules: Large polymers assembled from smaller repeating monomer units. IV. Basic Chemical Concepts o Proteins (amino acids) Hydrocarbons o Polysaccharides (sugars) o Nucleic Acids (nucleotides) Organic compounds consisting entirely of carbon and hydrogen; building blocks for complex biomolecules Micromolecules: Small molecules that are often building blocks for macromolecules or participate in Alkanes (Single Bonds): CnH2n+2 Saturated hydrocarbons, most stable, found in cell membranes. metabolic reactions. Ex. Methane (CH₄), o Glucose, fatty acids, amino acids, nucleo- Ethane (C₂H₆) Propane tides. (C₃H₈) V. Origins of Biochemistry Friedrich Wöhler synthesized urea, debunking the vi- Alkenes (Double Bonds): CnH2n talism theory. Unsaturated hydrocarbons, important in biological signaling, more o NH₄CNO (ammonium cyanate) → reactive than alkanes, contain at least one double bond NH₂CONH₂ (urea) Ex. Ethene (C₂H₄), Pro- Development of enzymology, genetics, and molecu- pene (C₃H₆) lar biology.  Biochemistry: Cellular Biology Foundations II. Cellular Biology Foundations Stages Glycolysis I. The Cell Structure and Function (Occurs in the cytoplasm): Breaks down one glucose 1 Cells are the fundamental units of life. They exhibit a molecule (C₆H₁₂O₆) into two pyruvate molecules, pro- high degree of organization and complexity. ducing a small amount of ATP. Eukaryotic cells, found in plants and animals, con- Citric Acid Cycle (Krebs Cycle) (Occurs in mitochondria): Pyruvate is further broken tain membrane-bound organelles such as the nucleus, 2 down, releasing CO₂ and producing more high-energy mitochondria, and endoplasmic reticulum. molecules (NADH, FADH₂). Prokaryotic cells, like bacteria, lack a true nucleus Electron Transport Chain (ETC) and membrane-bound organelles. (Occurs in mitochondria): NADH and FADH₂ donate 3 electrons, which flow through proteins in the inner mi- tochondrial membrane, ultimately producing a large amount of ATP via oxidative phosphorylation. Glycolysis Glycolysis breaks down one glucose molecule (C₆H₁₂O₆) into two pyruvate molecules (C₃H₄O₃), and it generates a small amount of ATP in the process. Here’s the chemical equation for that: C₆H₁₂O₆ + 2NAD+ + 2ADP + 2Pi → Prokaryotic cell vs Eukaryotic cell 2C₃H₄O₃ + 2NADH + 2H+ + 2ATP Key cellular components and their functions: One glucose molecule (C₆H₁₂O₆) is split into two py- o Cell membrane: Defines the cell boundary; ruvate molecules (C₃H₄O₃). regulates the passage of substances into and Two NAD⁺ are reduced to NADH, and two molecules out of the cell. of ATP are produced (net gain of 2 ATP). o Cytoplasm: The internal environment of the This process doesn’t require oxygen (it’s anaerobic), cell, containing the cytosol and organelles. and it occurs in the cytoplasm of the cell. o Nucleus: Contains DNA, the genetic mate- rial, and controls cellular activities In the absence of sufficient oxygen (anaerobic conditions), muscle cells o Mitochondria: The "powerhouses" of the convert pyruvate to lactate. This process, called lactic acid fermenta- cell, responsible for ATP production through tion, regenerates NAD+, which is necessary for glycolysis to proceed. cellular respiration. o Ribosomes: Sites of protein synthesis. Citric Acid Cycle (Krebs Cycle) o Endoplasmic Reticulum (ER): Network of Once glycolysis has split glucose into pyruvate, py- membranes involved in protein and lipid syn- ruvate enters the mitochondria, where it’s converted thesis and transport. into Acetyl-CoA and enters the citric acid cycle (aka o Golgi Apparatus: Modifies, sorts, and pack- Krebs cycle). Here’s the overall reaction for one cycle ages proteins and lipids. (but remember, two cycles occur for every glucose o Lysosomes: Contain enzymes for breaking molecule because glycolysis produces two pyruvate down cellular waste and debris. molecules): II. Cellular Processes and Regulation Acetyl-CoA + 3NAD⁺ + FAD + ADP + Pi + 2H2O → Metabolism 2CO₂ + 3NADH + FADH₂ + ATP The sum of all chemical reactions occurring within a cell, including both catabolic (breakdown) and ana- Acetyl-CoA (produced from pyruvate) enters the cy- bolic (building up) processes. cle. The cycle produces NADH (3 molecules), FADH₂ (1 Cellular Respiration molecule), ATP (or GTP, 1 molecule), and CO₂ The process by which cells convert glucose into ATP, (which is released as a waste product). the cell's energy currency. This process occurs in the mitochondrial matrix, and it’s aerobic (requires oxygen).  Biochemistry: Cellular Biology Foundations Electron Transport Chain (ETC) Response The NADH and FADH₂ produced in glycolysis and 3 The cell responds by activating certain genes, produc- ing proteins, or altering its activity (e.g., moving, divid- the citric acid cycle donate their electrons to the elec- ing, or secreting substances). tron transport chain, which takes place across the in- ner mitochondrial membrane. This is where most of the ATP is made via oxidative phosphorylation. The overall equation for the electron transport chain and oxidative phosphorylation is: NADH + FADH₂ + 6O₂ + 32ADP + 32Pi → 6H₂O + 32ATP + 2NAD+ + 2FAD NADH and FADH₂ donate electrons to the electron Cell Cycle transport chain (ETC), passing through protein com- The regulated sequence of events that cells go through plexes in the inner mitochondrial membrane. as they grow and divide. Oxygen (O₂) acts as the final electron acceptor and binds with electrons and protons (H⁺) to form water Interphase: The cell grows and prepares for di- (H₂O). vision. This includes: The energy from electrons moving through the chain o G1 Phase (Growth 1): The cell grows is used to pump protons into the intermembrane and carries out normal functions. space, creating a proton gradient. This gradient is o S Phase (Synthesis): DNA is replicated used by ATP synthase to produce ATP. (each chromosome now has a copy). The net result is 32 ATP molecules from one mole- o G2 Phase (Growth 2): The cell prepares cule of glucose (from NADH, FADH₂, and the proton for mitosis, producing proteins and orga- gradient). nelles needed for division. M Phase (Mitosis): The cell divides into two ge- Together, the processes generate about 36-38 ATP molecules from one glucose molecule. netically identical daughter cells. This involves: o Prophase: Chromosomes condense, and Protein Synthesis the nuclear envelope breaks down. The process of making proteins from amino acids, us- o Metaphase: Chromosomes align at the ing genetic information encoded in DNA. cell’s equator. Stages o Anaphase: Sister chromatids are pulled Transcription apart. 1 (Occurs in the nucleus): The DNA code is copied into messenger RNA (mRNA). o Telophase: New nuclear envelopes form Translation around the separated chromatids. (Occurs on ribosomes): The mRNA is read by ribo- o Cytokinesis: The cytoplasm divides, re- 2 somes in the cytoplasm, which assemble amino acids sulting in two separate cells. into a polypeptide chain according to the mRNA se- quence. Signal Transduction Cells communicate with each other and respond to their environment through complex signaling path- ways. Stages Reception A cell receives a signal (usually a molecule like a hor- 1 mone) from its environment or another cell. Transduction The signal is passed through a series of protein mole- III. Membrane Transport 2 cules inside the cell (often by phosphorylation), chang- The cell membrane is selectively permeable, meaning ing the cell's behavior or function. that it allows some substances to pass through while others are blocked.  Biochemistry: Cellular Biology Foundations Extracellular Osmolarity's Effect on Water Move- o Proton Pump (H⁺ pump): Moves protons ment: (H⁺) out of the cell or into organelles, im- Osmolarity (Osm/L): The concentration of solutes in portant for processes like acidifying the stom- a solution. High osmolarity = high concentration of ach. solutes Water moves across cell membranes by osmosis, from IV. Distribution of Water in the Body a region of lower osmolarity to a region of higher os- Water is the most abundant molecule in the human molarity. body, comprising approximately 60% of body weight. Hypotonic solution: Lower osmolarity outside the Water is distributed in various compartments: cell; water flows in, causing the cell to swell. o Intracellular fluid 2/3: Water within cells. Hypertonic solution: Higher osmolarity outside the o Extracellular fluid 1/3: Water outside cells cell; water flows out, causing the cell to shrink. ▪ Interstitial fluid – intermediary for Isotonic solution: Equal osmolarity inside and out- exchange between cells & blood side the cell; no net water movement. ▪ Plasma – contain water, electrolytes, proteins (e.g., albumin), & nutrients. ▪ Transcellular fluid – cerebrospinal fluid, synovial fluid in joints, aque- ous humor in the eye V. Processes That Regulate Cell Contents Endocytosis: The process of taking in substances from outside the cell by engulfing them in vesicles. o Phagocytosis (cell eating): Engulfing large particles. Performed by phagocytes (e.g., Transport Mechanisms Across Plasma Membrane macrophages and neutrophils). Passive Transport: Movement of substances down o Pinocytosis (cell drinking): Engulfing fluids their concentration gradient, requiring no energy in- and dissolved substances. put. o Simple Diffusion: Movement of small, non- polar molecules directly across the mem- brane. (E.g., Oxygen, Carbon Dioxide) o Facilitated Diffusion: Movement of larger or polar molecules through protein channels or carriers. (E.g., glucose, ions, amino acids) Exocytosis: The process of releasing substances from the cell by fusing vesicles with the cell membrane. o E.g., pancreas releasing insulin. Protein Sorting and Trafficking Proteins are synthesized in the ribosomes and then sorted and transported to their appropriate destina- tions (either inside the cell or outside) via the ER, Active Transport: Movement of substances against Golgi apparatus, and vesicles. This ensures proper their concentration gradient, requiring energy (often cellular function and efficiency in transporting and from ATP). delivering materials. o Sodium-Potassium Pump (Na⁺/K⁺ pump): Moves 3 sodium ions (Na⁺) out of the cell and 2 potassium ions (K⁺) into the cell, which helps maintain the cell's resting membrane potential.  Biochemistry: Water and Buffer Systems III. Water and Buffer Systems IV. Acid-Base Balance pH: Measures hydrogen ion concentration. I. Properties of Water Normal blood pH: 7.35–7.45. Polarity of Water o Acidosis: pH < 7.35; caused by excessive H+ Water molecules are polar, with a partial negative or CO2. charge on oxygen and partial positive charges on hy- o Alkalosis: pH > 7.45; caused by H+ loss or drogen. CO2 deficiency. Enables hydrogen bonding, critical for water's unique Regulation: properties. o Respiratory system adjusts CO2 levels. o Kidneys excrete H+ and reabsorb bicar- Role as Universal Solvent bonate. Dissolves ionic and polar compounds due to hydro- gen bonding and electrostatic interactions. V. Fluid-Electrolyte Balance Facilitates transport of nutrients and waste in biolog- Clinical Importance of Mineral Cations and Anions: ical systems. Cations: Sodium (Na+), Potassium (K+), Calcium (Ca2+), Magnesium (Mg2+). II. Four Types of Noncovalent Interactions Anions: Chloride (Cl-), Bicarbonate (HCO3-), Phos- Hydrogen Bonds: Occur between a hydrogen atom phate (PO4^3-). covalently bonded to an electronegative atom and an- Functions: other electronegative atom. o Maintain osmotic pressure and hydration. Ionic Bonds: Electrostatic attraction between posi- o Facilitate nerve transmission and muscle con- tively and negatively charged ions. traction. Van der Waals Interactions: Weak forces due to o Act as cofactors in enzymatic reactions. transient dipoles in molecules. Hydrophobic Interactions: Nonpolar molecules cluster to avoid water, stabilizing macromolecular structures like membranes. III. Buffer Systems Definition: Buffers maintain pH stability by neutral- izing acids and bases. Biological Buffers: o Bicarbonate Buffer System: Regulates blood pH. o Phosphate Buffer System: Important in in- tracellular fluid. o Protein Buffers: Hemoglobin acts as a buffer in blood.  Biochemistry: Carbohydrates IV. Carbohydrates Polysaccharides (Starch, Glycogen) Starch: The main form of energy storage in plants. I. Classification and Structure Glycogen: The energy storage polysaccharide in ani- Based on Number of Carbon Atoms mals, particularly in the liver and muscles. o Triose: 3 carbon atoms (like glyceraldehyde). Cellulose: A structural polysaccharide found in plant o Tetrose: 4 carbon atoms. cell walls. o Pentose: 5 carbon atoms (important in nucleic acids, like ribose in RNA). III. Stereoisomerism and Stereochemistry o Hexose: 6 carbon atoms (most common in energy metabolism, like glucose and fruc- Stereoisomerism – same chemical formula and bonds, tose). different spatial arrangement Chiral – a carbon is chiral of it has four different Based on Sugar Units groups attached. Many sugars are chiral, meaning Monosaccharides: Single sugar units (like glucose, they have asymmetric carbon atoms (carbons attached fructose, and galactose). These are the simplest sugars to four different groups), leading to mirror-image iso- mers called enantiomers. and building blocks for larger carbs. Disaccharides: Two monosaccharides joined to- D and L forms: Most naturally occurring sugars are gether by a glycosidic bond (like sucrose (glucose + in the D-form, though you can also have L-forms. fructose) and lactose (glucose + galactose)). Alpha and Beta Anomers: When monosaccharides Oligosaccharides: 3-10 monosaccharide units. cyclize (forming rings), they can create two forms: al- pha (α) and beta (β) anomers, depending on the orien- Polysaccharides: Large polymers of monosaccharides tation of the -OH group at the anomeric carbon (the (like starch, glycogen, and cellulose). These are en- carbon that was part of the carbonyl group in the ergy storage and structural forms of carbohydrates. open-chain form). Based on Functional Groups IV. Carbohydrate Metabolism Aldehydes (e.g., glucose): When the sugar has an al- General Principles of Metabolism dehyde group (-CHO). Involves catabolic and anabolic reactions. CHO pri- Ketones (e.g., fructose): When the sugar has a ketone marily undergo catabolic pathways to generate ATP. group (-CO). These functional groups determine whether the sugar Glycolysis will be an aldose (if it has an aldehyde group) or a Occurs in the cytoplasm, breakdown of glucose into ketose (if it has a ketone group). 2 pyruvate, 2 ATP (net) and 2 NADH. II. Types of Carbohydrates Gluconeogenesis Monosaccharides Occurs in the liver (mainly) and kidneys, formation of These are the building blocks of all carbohydrates. glucose from non-carbohydrate precursors like lac- They can’t be broken down further by hydrolysis. tate, glycerol, amino acids. (From fasting, or intense Some important monosaccharides: exercise) o Glucose (C₆H₁₂O₆): The most important sugar, providing energy to cells. Glycogen Synthesis (Glycogenesis) o Fructose: Found in fruits and honey. Occurs in the liver and muscles, conversion of glu- o Galactose: Found in milk sugar (lactose). cose into glycogen for storage. Enzyme: glycogen synthase Disaccharides Formed when two monosaccharides join by a glyco- Glycogen Breakdown (Glycogenolysis) sidic bond (a covalent bond formed through dehydra- Occurs in the liver and muscles, conversion of glyco- tion synthesis): gen back into glucose. Enzyme: glycogen phosphory- o Sucrose (glucose + fructose): Table sugar. lase o Lactose (glucose + galactose): Milk sugar. o Maltose (glucose + glucose): Found in germi- The Citric Acid Cycle nating seeds. Occurs in the mitochondria, where acetyl-CoA is ox- idized to produce ATP, NADH, and FADH₂.  Biochemistry: Carbohydrates Role of B-vitamins in the Citric Acid Cycle VII. Oxygen-Carbon Dioxide Cycle in Nature B vitamins (especially B1 (thiamine), B2 (riboflavin), The oxygen-carbon dioxide cycle is the process and B3 (niacin)) are essential as coenzymes in the cit- where oxygen is used in cellular respiration to pro- ric acid cycle and other metabolic pathways. duce energy, and carbon dioxide is released as a waste o Thiamine (Vitamin B1) is involved in the for- product. This CO₂ is then transported to the lungs and mation of acetyl-CoA. exhaled. Plants, through photosynthesis, absorb CO₂ o Riboflavin (Vitamin B2) and Niacin (Vita- and release O₂, completing the cycle. min B3) are critical for the production of FADH₂ and NADH, which are used in the electron transport chain. Oxidative Phosphorylation: ETS Occurs in the mitochondria, electrons from NADH and FADH₂ are transferred through protein com- plexes, ultimately producing ATP through chemios- mosis. Products: ATP, H₂O, and CO₂. Interconversion of Hexoses The conversion of one six-carbon sugar (hexose) to another, such as converting glucose to fructose, or vice versa. Purpose: To provide flexibility for energy production and storage, allowing the body to use different sugars. V. Blood Glucose Regulation Concentration of Sugar in the Blood The concentration of glucose in the blood is tightly regulated between 70-110 mg/dL in a healthy indi- vidual. Hypoglycemia (low blood sugar) and hyper- glycemia (high blood sugar) are both problematic. Hormones Involved in Blood Sugar Regulation Insulin: Produced by the pancreas, it lowers blood sugar by promoting glucose uptake by cells and gly- cogen synthesis. Glucagon: Also produced by the pancreas, it raises blood sugar by stimulating glycogenolysis and gluco- neogenesis. Cortisol: A stress hormone that increases glucose availability by promoting gluconeogenesis. Glucose Tolerance Test Measures how well the body processes glucose. VI. Overall Scheme of Metabolism 1. Carbs are ingested and broken down into glucose. 2. Glucose enters the bloodstream and is transported into cells. 3. Glycolysis breaks down glucose for energy. 4. Any excess glucose is stored as glycogen or con- verted to fat. 5. Gluconeogenesis and glycogenolysis regulate blood glucose when needed.  Biochemistry: Lipids V. Lipids Detergents I. Classification and Structure Detergents are special lipids with both hydrophilic (water- General Properties attracting) and hydrophobic (water-repelling) properties, Hydrophobicity: Lipids are mostly nonpolar, making making them effective at breaking down fats and oils. them insoluble in water. Sodium lauryl sulfate is a common detergent used in Energy Dense: Fat provides about 9 kcal/g, more than car- soaps. bohydrates or proteins (both provide 4 kcal/g). Diverse Functionality: Lipids can be involved in energy II. Biological Functions storage, signaling, membrane structure, and insulation. Use of Fats in the Body Energy Storage: Adipose tissue stores fat for long-term Fatty Acids energy. When energy is needed, fats are broken down into Basic Building Blocks of many lipids, fatty acids consist fatty acids and glycerol. of a long hydrocarbon chain with a carboxyl group (- Insulation: Fat also serves as an insulator, keeping us COOH) at one end. warm and protecting internal organs. Saturated Fatty Acids: No double bonds between carbon Hormone Production: Steroids, such as testosterone and atoms (e.g., palmitic acid). These are solid at room tem- estrogen, are made from cholesterol (a lipid). These hor- perature. mones regulate processes like metabolism, sexual func- Unsaturated Fatty Acids: Contain one or more double tion, and immune response. bonds. Monounsaturated (one double bond) and polyun- saturated (multiple double bonds) fats are liquid at room Membrane Structure (Fluid-Mosaic Model) temperature (like olive oil). Phospholipids are crucial in forming the lipid bilayer of cell membranes. The hydrophilic heads of the phospho- Fats and Oils lipids face outward toward the water inside and outside Both are triglycerides (molecules made from glycerol and the cell, while the hydrophobic tails face inward. three fatty acids). This forms a semi-permeable membrane that regulates Fats: Solid at room temperature (due to higher saturation). what enters and exits the cell. Oils: Liquid at room temperature (due to higher unsatura- Cholesterol in the membrane helps maintain its fluidity tion). and stability. Trans Fats: A type of unsaturated fat that’s chemically modified to be solid at room temperature. These are bad Energy Storage for health. Fats provide long-term storage of energy. When the body needs energy, lipases break down triglycerides into Complex Lipids fatty acids and glycerol, which can then be used in cellu- These are lipids that contain additional functional groups lar respiration to produce ATP. such as phosphates or sugars, which are added to fatty ac- ids and glycerol. III. Physical Properties Examples include phospholipids (like lecithin, which is Solubility: Lipids are insoluble in water but soluble in key in cell membranes) and glycolipids (lipids with sugar nonpolar solvents like ether, chloroform, and acetone. groups attached, important in cell recognition). Melting Point: Saturated fats (like butter) have higher melting points, while unsaturated fats (like olive oil) have Derived Lipids lower melting points. Derived lipids are metabolites of simple or complex li- pids. Density: Lipids are less dense than water, which is why Examples include steroids (like cholesterol) and eico- oil floats on water. sanoids (like prostaglandins), which are involved in cell signaling and immune responses. IV. Lipid Metabolism Absorption of Fats Waxes Fats are absorbed in the small intestine. Once broken Waxes are esters of fatty acids and alcohols (not glycerol). down into fatty acids and monoglycerides, they are They serve as a water-repellent layer in plants and ani- reassembled into triglycerides in the intestinal cells, mals. packed into chylomicrons, and transported via lym- They are found in skin, feathers, and leaf coatings, provid- phatic vessels into the bloodstream. ing protection and waterproofing.  Biochemistry: Lipids Oxidation of Fat V. Clinical Aspects Fat is primarily oxidized in the mitochondria to gen- Plasma Lipid Levels erate ATP through a process known as beta-oxida- Elevated blood lipid levels (especially triglycerides tion. Fatty acids are broken down into acetyl-CoA, and cholesterol) are associated with heart disease which then enters the Citric Acid Cycle to generate and stroke. energy. Lipoproteins, such as HDL (good cholesterol) and LDL (bad cholesterol), help transport lipids in the Oxidation of Fatty Acids bloodstream. Fatty acids are broken down into acetyl-CoA through the beta-oxidation pathway in the mitochondria, gen- Cholesterol Metabolism erating NADH and FADH₂, which enter the electron Cholesterol is produced in the liver and is a precursor transport chain to produce ATP. for steroid hormones and bile acids. High levels of LDL cholesterol can lead to athero- Energy Produced by Oxidation of Fatty Acids sclerosis (plaque buildup in arteries), increasing the Fatty acid oxidation is a high-yield process, produc- risk of cardiovascular disease. ing significantly more energy (ATP) per molecule than carbohydrates. Lowering the Serum Cholesterol Statins are drugs that lower LDL cholesterol by in- Storage of Fat hibiting the enzyme HMG-CoA reductase, which is Excess fatty acids are stored in adipose tissue as tri- involved in cholesterol production. glycerides. Dietary changes (low in saturated fats) and exercise Fat storage is regulated by insulin, which promotes also help reduce blood cholesterol levels. the uptake of glucose into cells and its conversion to fatty acids for storage. Lipid Storage Diseases These are genetic disorders that affect the body's Lipogenesis ability to break down or store lipids properly. Exam- Lipogenesis is the process of synthesizing fat from ples include Tay-Sachs disease and Gaucher dis- excess carbohydrates or proteins. This happens in ease, where lipids accumulate in tissues, leading to the liver and adipose tissue when caloric intake ex- organ damage. ceeds the body's immediate energy needs. Anabolic Steroids Anabolic steroids are synthetic derivatives of testos- terone and are used (sometimes abused) to increase muscle mass and strength. Long-term use can lead to liver damage, heart dis- ease, and endocrine disruption  Biochemistry: Amino Acids and Proteins VI. Amino Acids and Proteins Essential Amino Acids These are amino acids your body can’t synthesize, so you I. Sources of Proteins need to get them from your diet: Animal Sources: Meat, eggs, dairy. These contain Histidine, Isoleucine, Leucine, Lysine, Methio- complete proteins, which means they provide all the nine, Phenylalanine, Threonine, Tryptophan, essential amino acids your body can’t make on its Valine. own. Plant Sources: Legumes, nuts, seeds, and whole Acid-Base Properties grains. These are often incomplete proteins, mean- Amino acids can act as acids (donate a proton) or ba- ing they lack one or more essential amino acids. But ses (accept a proton). Their side chain can affect their when combined (like rice and beans), they can pro- pH and their role in buffering bodily fluids. vide a complete protein. Supplements: Protein powders (whey, soy, etc.) are Dipeptides often used for muscle repair or in diets requiring high When two amino acids bond through a peptide bond, protein intake. they form a dipeptide. Peptide bonds are strong and stable, linking amino acids in a chain. II. Functions of Protein in the Body Enzyme Catalysis: Proteins called enzymes speed up V. Protein Structure biochemical reactions, like digesting food or making The Peptide Bond ATP. Peptide bonds are covalent bonds formed between Structural Support: Proteins like collagen and ker- the carboxyl group of one amino acid and the amine atin form the building blocks of skin, hair, and nails. group of another. They’re strong and form the back- Transport: Hemoglobin, a protein in red blood cells, bone of protein chains. transports oxygen to tissues. Immune Defense: Antibodies are proteins that de- Primary Structure fend against pathogens. The primary structure is the sequence of amino ac- Hormonal Regulation: Some hormones like insulin ids in a polypeptide chain. This sequence is deter- are proteins that regulate metabolism and growth. mined by genetic code (DNA). Muscle Contraction: Actin and myosin are proteins responsible for muscle contraction. Secondary Structure The secondary structure refers to local folded shapes III. Molecular Masses formed by the peptide backbone due to hydrogen bond- Small proteins (e.g., insulin) weigh around 5,000 ing. Common secondary structures include: Daltons. Alpha helix: A spiral shape. Larger proteins (e.g., hemoglobin) can weigh up to Beta-pleated sheet: A folded sheet-like struc- 64,000 Daltons. ture. Titin, the largest protein, weighs over 3,000,000 Dal- tons! Tertiary Structure The tertiary structure is the 3D folding of the protein. IV. Amino Acid Structure and Properties It’s driven by interactions between the side chains (R Classification groups), including hydrophobic interactions, hydrogen Amino acids are the building blocks of proteins. Each has bonds, ionic bonds, and disulfide bridges. an amine group (-NH₂), a carboxyl group (-COOH), and a side chain (R group) that determines its properties. Quaternary Structure Amino acids are classified based on the properties of their The quaternary structure refers to the interaction be- side chains: tween multiple polypeptide chains to form a functional Nonpolar (Hydrophobic): E.g., glycine, ala- protein complex. Not all proteins have a quaternary nine. structure, but hemoglobin (with 4 subunits) does! Polar (Hydrophilic): E.g., serine, glutamine. Charged (Acidic or Basic): E.g., glutamate (acidic), lysine (basic).  Biochemistry: Amino Acids and Proteins VI. Protein Classification Synthesis of Protein According to Solubility Protein synthesis occurs in the ribosomes, using Globular Proteins: Water-soluble (e.g., hemoglo- mRNA as a template to link amino acids into a poly- bin, enzymes). peptide chain. Fibrous Proteins: Insoluble in water, structural (e.g., collagen, keratin). Biosynthesis of Nonessential Amino Acids The body can synthesize nonessential amino acids from According to Composition other compounds, such as pyruvate or glutamate. Simple Proteins: Composed only of amino acids The Body's Requirements of Protein (e.g., albumin). Protein intake varies based on age, activity level, and Conjugated Proteins: Contain a non-protein compo- health, with adults typically needing about 0.8 grams of nent (e.g., hemoglobin, which has a heme group). protein per kg of body weight. According to Function Catabolism of Amino Acids Amino acids are broken down in the liver, with their Enzymes: Catalyze biochemical reactions (e.g., am- amino groups removed to form urea (which is excreted ylase). via the kidneys) and the remaining carbon skeleton used Structural Proteins: Provide support (e.g., colla- in energy production or converted to glucose or fat. gen). Transport Proteins: Move molecules (e.g., hemo- Metabolic Disorders Associated with Urea Cycle globin). Disorders like urea cycle defects can cause the buildup of ammonia (toxic to the body) due to impaired urea pro- According to Shape duction. Fibrous Proteins: Elongated and tough (e.g., elas- tin). IX. Denaturation of Protein Globular Proteins: Spherical and functional (e.g., Denaturation refers to the loss of a protein's functional enzymes). 3D shape, usually caused by extreme heat, acid, or salt. Denatured proteins can no longer perform their biological Percent Classification functions—think of how egg whites turn white and firm Proteins can be classified based on their concentration in when cooked. This change is typically irreversible. a given sample, like collagen being a major protein in connective tissues. X. Overview of Protein Metabolism Protein metabolism involves a delicate balance between VII. Properties of Proteins synthesis, degradation, and energy production from Denaturation: Proteins can be denatured (lose their amino acids. Disruptions in this process can lead to dis- shape) by extreme conditions like heat, acid, or salt eases related to amino acid metabolism, muscle wast- concentration changes, which disrupt their second- ing, and protein-energy malnutrition. ary, tertiary, and quaternary structures. Solubility: A protein's solubility depends on its amino acid composition and environment. Binding: Many proteins bind to other molecules (e.g., ligands, substrates) in specific, often non-covalent ways, crucial for their function. VIII. Protein Metabolism Nitrogen Balance Positive nitrogen balance occurs when protein in- take exceeds breakdown, often during growth or muscle building. Negative nitrogen balance happens when protein breakdown exceeds intake, as seen in starvation or illness.  Biochemistry: Enzymes and Vitamins VII. Enzymes and Vitamins The rate of enzyme-catalyzed reactions is influenced by several factors: I. Enzyme Structure and Function Concentration of Substrate: As substrate con- Characteristics & Structure centration increases, reaction rate increases, but Enzymes are biological catalysts—they speed up chemi- only up to a point (saturation). cal reactions without being consumed in the process. Enzyme Concentration: More enzymes = faster Here’s what makes them tick: reactions. Proteins: Most enzymes are proteins, but some Temperature: Higher temperatures usually have RNA components (ribozymes). speed up reactions (until the enzyme denatures at Active Site: This is the specific region where the high heat). substrate binds. It’s often a pocket or groove in pH: Enzymes have an optimal pH—too acidic or the enzyme's 3D structure. too basic can denature them. Specificity: Enzymes are highly specific for their substrates, often likened to a lock-and-key The Effect of Enzymes on Activation Energy model (but there’s more to it, as you’ll see). Enzymes lower the activation energy required for a re- action, making it easier for the reaction to occur. They do Classification & Nomenclature this by: Enzymes are classified based on the reactions they cata- Stabilizing transition states (temporary, high- lyze: energy states). Oxidoreductases: Catalyze oxidation-reduc- Orienting substrates in the correct position for tion reactions. the reaction. Transferases: Transfer functional groups (like This is why enzymes are considered catalysts—they methyl or phosphate). speed up reactions without being consumed in the pro- Hydrolases: Break bonds using water (e.g., li- cess! pases, proteases). Lyases: Remove or add groups without hydroly- Enzyme Inhibition sis (e.g., decarboxylases). Enzyme activity can be inhibited in two main ways: Isomerases: Convert isomers (same molecular Competitive Inhibition: The inhibitor competes formula, different structure). with the substrate for the active site. Ligases: Form bonds by using ATP (e.g., DNA Non-Competitive Inhibition: The inhibitor ligase). binds to a different site (allosteric site), changing the enzyme's shape and reducing its activity. The nomenclature follows the EC (Enzyme Commis- sion) number system, where each class has a specific number. Cofactors and Coenzymes Cofactors are inorganic ions (like Zn²⁺ or Mg²⁺) that Models of Enzyme Action assist enzymes in catalyzing reactions. Lock-and-Key Model: The enzyme’s active site is a Coenzymes are organic molecules (often derived perfect match for the substrate, like a lock fitting a from vitamins) that work with enzymes, like NAD⁺ key. But this model doesn’t explain all enzyme be- (Nicotinamide adenine dinucleotide) or Coenzyme havior. A. Induced Fit Model: The active site is more flexible, adjusting its shape when the substrate binds, like a III. Vitamins hand shaking a hand. This model explains the dy- Fat-Soluble Vitamins namic nature of enzyme-substrate interactions bet- These vitamins dissolve in fat and are stored in the liver ter. and fatty tissues. They include: Vitamin A (Retinol): Essential for vision, immune The Enzyme-Substrate Complex function, and skin health. This is the intermediate stage where the enzyme and sub- o Deficiency: Night blindness, immune defi- strate are joined. Once formed, the enzyme either cata- ciencies. lyzes the reaction (turning substrate into product) or re- o Food Sources: Liver, carrots, spinach. leases the product. Vitamin D: Regulates calcium and phosphate me- tabolism, promoting bone health. II. Enzyme Kinetics and Regulation o Deficiency: Rickets, osteomalacia. Factors that Affect the Rate of Enzyme Activity  Biochemistry: Enzymes and Vitamins o Food Sources: Fatty fish, fortified milk, sun- ▪ Deficiency: Hair loss, skin rashes. light. ▪ Food Sources: Eggs, nuts, seeds. Vitamin E: Acts as an antioxidant, protecting cells o B9 (Folate): Vital for DNA synthesis and from oxidative damage. cell division. o Deficiency: Hemolytic anemia, muscle ▪ Deficiency: Neural tube defects, ane- weakness. mia. o Food Sources: Nuts, seeds, vegetable oils. ▪ Food Sources: Leafy vegetables, Vitamin K: Essential for blood clotting and bone legumes. health. o B12 (Cobalamin): Necessary for red blood o Deficiency: Easy bruising, bleeding disor- cell production and nerve function. ders. ▪ Deficiency: Pernicious anemia, neu- o Food Sources: Green leafy vegetables, broc- ropathy. coli. ▪ Food Sources: Animal products (meat, eggs, dairy). Water-Soluble Vitamins These dissolve in water and are not stored in the body, Role in Metabolism so they must be consumed regularly. They include: Both enzymes and vitamins are crucial for metabolic Vitamin C (Ascorbic acid): Important for collagen pathways in the body: synthesis, wound healing, and immune function. Enzymes catalyze the chemical reactions that o Deficiency: Scurvy (gums bleeding, slow convert nutrients into energy, structure, or wound healing). waste. o Food Sources: Citrus fruits, bell peppers, Vitamins act as coenzymes or precursors to co- broccoli. enzymes that assist enzymes in these reactions, Vitamin B Complex: ensuring the body runs like a well-oiled machine. o B1 (Thiamine): Helps convert food into en- ergy. ▪ Deficiency: Beriberi, Wernicke-Kor- sakoff syndrome. ▪ Food Sources: Whole grains, pork. o B2 (Riboflavin): Involved in energy pro- duction. ▪ Deficiency: Cracked lips, sore throat. ▪ Food Sources: Dairy, eggs, green leafy vegetables. o B3 (Niacin): Important for DNA repair and metabolism. ▪ Deficiency: Pellagra (dermatitis, di- arrhea, dementia). ▪ Food Sources: Poultry, fish, whole grains. o B5 (Pantothenic acid): Crucial for hormone production and energy metabolism. ▪ Deficiency: Rare, but can cause fa- tigue and mental confusion. ▪ Food Sources: Chicken, beef, pota- toes. o B6 (Pyridoxine): Involved in amino acid metabolism and neurotransmitter synthe- sis. ▪ Deficiency: Anemia, depression, confusion. ▪ Food Sources: Poultry, fish, pota- toes. o B7 (Biotin): Important for carbohydrate, fat, and protein metabolism.  Biochemistry: Nucleic Acids and Genetic Information VIII. Nucleic Acids and Genetic Infor- separating the strands of the DNA. This process is reversible once the conditions are normalized. mation I. Nucleic Acid Structure RNA Covalent Structure of Polynucleotide Structure: RNA is similar to DNA but with a few key Nucleic acids like DNA and RNA are polymers made up differences: of nucleotides, which are linked by covalent bonds to 1. Sugar: RNA contains ribose (not deoxyri- form long chains, or polynucleotides. bose). Phosphodiester Bond: The bond between the 2. Bases: Uracil (U) replaces thymine (T) in phosphate group of one nucleotide and the RNA. sugar molecule of the next. This forms the back- 3. Single-Stranded: Unlike DNA, RNA is usu- bone of the nucleic acid chain. ally single-stranded. Structure and Component of Nucleotides III. Central Dogma of Molecular Biology A nucleotide consists of: The Central Dogma explains the flow of genetic infor- 1. A Nitrogenous Base: These can be purines (ad- mation in cells: enine [A], guanine [G]) or pyrimidines (cytosine DNA → RNA → Protein [C], thymine [T], uracil [U]). This means DNA is transcribed into RNA, which is then 2. A Sugar: Either deoxyribose (in DNA) or ribose translated into a protein that carries out the cell's func- (in RNA). tions. 3. A Phosphate Group: This gives nucleic acids their acidic nature and links the nucleotides to- IV. DNA Processes gether. Mechanism of Prokaryotic DNA Replication DNA replication in prokaryotes (like bacteria) happens Formation of Nucleic Acids from Nucleotides in the cytoplasm and involves several key steps: When nucleotides are linked, they form polynucleotides 1. Origin of Replication: The DNA double helix is (like DNA or RNA), with the phosphate group of one unwound, forming a replication bubble. nucleotide connecting to the sugar of the next, creating 2. Helicase: This enzyme unwinds the DNA. the sugar-phosphate backbone. 3. Primase: Synthesizes an RNA primer to initiate DNA synthesis. Nomenclature of Nucleosides and Nucleotides 4. DNA Polymerase: Adds new nucleotides to the A nucleoside consists of a nitrogenous base + sugar. growing DNA strand (in the 5' to 3' direction). 5. Ligase: Seals any gaps between Okazaki frag- A nucleotide consists of a nucleoside + phosphate ments on the lagging strand. group. DNA Polymerase For example: The main enzyme that adds nucleotides to the growing Adenosine (nucleoside) + phosphate = Adenosine DNA strand during replication. There are different types Monophosphate (AMP) (nucleotide). of DNA polymerases in prokaryotes, but DNA polymer- ase III is the primary one involved in synthesis. II. Types of Nucleic Acids DNA Proteins Required for Replication Levels of Structure: Helicase: Unwinds the DNA double helix. 1. Primary Structure: The linear sequence of nu- cleotides. Primase: Synthesizes the RNA primer. 2. Secondary Structure: The famous double helix, Single-strand binding proteins (SSB): Keep the un- formed by two complementary strands of nu- wound DNA strands from reannealing. cleotides, held together by hydrogen bonds be- Topoisomerase: Relieves the torsional strain tween complementary base pairs (A-T and G-C). caused by the unwinding of DNA. 3. Tertiary Structure: The higher-order coiling and folding of the DNA molecule (e.g., super- Proofreading and Repair coiling). DNA polymerase has proofreading abilities to ensure Denaturation: Heat or chemicals can disrupt the hy- accurate replication by detecting and fixing errors (e.g., drogen bonds between complementary bases, mismatched bases). If an error is detected, the enzyme re- moves the incorrect nucleotide and adds the correct one.  Biochemistry: Nucleic Acids and Genetic Information V. Gene Expression Transcription Mechanism in Prokaryotes Initiation: RNA polymerase binds to the promoter region of the gene. Elongation: RNA polymerase synthesizes the RNA strand, moving along the DNA template strand. Termination: RNA polymerase reaches a termina- tor sequence, causing it to detach and release the newly synthesized RNA. Translation Mechanism in Prokaryotes Initiation: The ribosome assembles at the start co- don (AUG) on the mRNA. Elongation: tRNA molecules bring amino acids to the ribosome, where the mRNA is read in codons (three-nucleotide sequences) to form a polypeptide chain. Termination: When the ribosome reaches a stop co- don, the polypeptide is released. Genetic Code The genetic code is universal, with 64 codons (combina- tions of 3 nucleotides) encoding for the 20 amino acids used to build proteins. Start codon: AUG (Methionine), and stop codons signal the end of translation. VI. Mutations A mutation is a change in the DNA sequence. Mutations can arise due to: Point mutations (a change in one base). Insertions or deletions (addition or removal of bases). Frameshift mutations (caused by insertions or deletions that alter the reading frame). Mutations can lead to genetic disorders, but not all mu- tations are harmful—some may be neutral or even bene- ficial. VII. Protein Synthesis Protein synthesis involves two main processes: 1. Transcription (DNA → RNA): The gene is tran- scribed into mRNA. 2. Translation (RNA → Protein): The mRNA is translated into an amino acid sequence, forming a protein. This process ensures that genetic information encoded in DNA is accurately expressed as functional proteins, driv- ing cellular function and life processes.  Biochemistry: Integrated Metabolism IX. Integrated Metabolism metabolites like acetyl-CoA or intermediates in the Citric Acid Cycle for energy. I. Types of Metabolism Catabolism ATP: The Cellular Energy Catabolic processes involve the breakdown of ATP (adenosine triphosphate) is the primary en- larger molecules into smaller ones. This process re- ergy currency of the cell. It consists of an adenine leases energy in the form of ATP and is typically ex- base, a ribose sugar, and three phosphate groups. ergonic (releases energy). The energy stored in ATP is released when the high- Examples: The breakdown of glucose into pyruvate energy phosphate bonds are broken (by hydrolysis), in glycolysis, or the breakdown of fatty acids into ac- converting ATP to ADP (adenosine diphosphate) and etyl-CoA in beta-oxidation. These molecules then inorganic phosphate (Pi). This energy is used for cel- feed into the Citric Acid Cycle (Krebs Cycle) and ox- lular work, such as muscle contraction, protein syn- idative phosphorylation, ultimately producing ATP. thesis, and active transport. Anabolism III. Integration of Pathways Anabolic processes involve the synthesis of larger Carbohydrate Metabolism molecules from smaller ones, requiring energy. This Glycolysis provides pyruvate, which can either be process is endergonic (requires energy input). converted into acetyl-CoA (to enter the Citric Acid Examples: The synthesis of proteins from amino ac- Cycle) or used in lactate production under anaerobic ids (via translation), the formation of glycogen from conditions. glucose, and the synthesis of triglycerides from fatty When blood sugar levels are low, the liver performs acids and glycerol. gluconeogenesis (synthesis of glucose from non-car- bohydrate sources) to maintain blood glucose levels. II. Metabolic Pathways Glycogenolysis (breakdown of glycogen) is also cru- Overview of Catabolic Processes cial for maintaining glucose levels during periods of Catabolism focuses on energy release, as it involves the fasting or intense activity. breakdown of complex molecules: Lipid Metabolism in Animals Carbohydrate Metabolism Fatty acids are a key energy source. During periods Glycolysis: The breakdown of glucose into pyruvate, of starvation, stored triglycerides are broken down producing a small amount of ATP and NADH. via lipolysis into free fatty acids and glycerol. These Citric Acid Cycle: Acetyl-CoA (from glucose or fatty acids are then oxidized for ATP production. fatty acid metabolism) enters the cycle, generating Cholesterol plays a key role in membrane structure NADH, FADH₂, and ATP while releasing CO₂. and serves as a precursor for steroid hormones. Oxidative Phosphorylation: Electrons from NADH In times of excess energy, lipogenesis (synthesis of and FADH₂ pass through the electron transport fatty acids) occurs to store energy in the form of tri- chain (ETC), driving the production of large amounts glycerides. of ATP. Protein Metabolism Lipid Metabolism Proteins are primarily involved in anabolic pro- Fatty Acid Oxidation: Fatty acids are broken down cesses such as muscle growth and enzyme synthesis, into acetyl-CoA via beta-oxidation, which enters the but they can also be used for energy when needed. Citric Acid Cycle for further energy production. The urea cycle removes excess nitrogen produced Triglyceride Breakdown: Triglycerides are broken during amino acid catabolism. down into glycerol and fatty acids. Glycerol enters Amino acids can be converted into glucose (via glu- glycolysis, while fatty acids are oxidized to generate coneogenesis) or into ketone bodies (during starva- ATP. tion or diabetes) for energy. Protein Metabolism IV. The Regulation of Lipid and Carbohydrate Me- Proteins are broken down into amino acids, which tabolism can be used for energy if necessary, but they also con- Insulin and Glucagon tribute to anabolic processes (e.g., protein synthesis). Insulin is a hormone released from the pancreas Amino acids are deaminated (removal of the amino when blood glucose levels are high. It promotes group), and the carbon skeletons are converted into anabolism, encouraging the storage of glucose as  Biochemistry: Integrated Metabolism glycogen, the synthesis of fatty acids, and the up- take of amino acids into cells. Glucagon is released when blood glucose levels are low. It stimulates catabolic processes like glycogenolysis and gluconeogenesis, ensuring an adequate supply of glucose for energy. Cortisol and Epinephrine Cortisol and epinephrine are stress hormones that promote catabolism, increasing the break- down of glycogen, fats, and proteins to fuel the body during periods of stress or fasting. V. Utilization of Amino Acids Amino acids serve as building blocks for proteins, but they can also be used for energy under certain conditions. This occurs through deamination (re- moval of the amino group), with the resulting carbon skeletons entering various metabolic pathways, such as: o Gluconeogenesis (for glucose production). o Fatty acid synthesis (in case of excess amino ac- ids). o Ketogenesis (for ketone body production during starvation). The amino acid pool (a collection of free amino acids in the body) is constantly being replenished and broken down to meet the body’s needs. V. Summary of Integrated Metabolism Metabolism is a dynamic system, where catabolic processes release energy from nutrients, and ana- bolic processes use that energy to build and maintain cellular structures. Pathways like carbohydrate, lipid, and protein me- tabolism are interconnected, with key metabolites (like acetyl-CoA and pyruvate) acting as central hubs for energy production and biosynthesis. Regulation of metabolism occurs through hormones like insulin and glucagon, maintaining a balance be- tween energy storage and energy expenditure.  Biochemistry: Body Fluids X. Body Fluids affects blood flow and is critical for circulatory effi- ciency. I. Blood pH: Blood typically has a pH between 7.35 and 7.45, Functions of Blood which is slightly alkaline. This is essential for optimal Transport of Gases: Blood transports oxygen (O₂) enzyme function and cellular processes. from the lungs to tissues and carbon dioxide (CO₂) Temperature: Blood is slightly warmer than body from tissues to the lungs for exhalation. temperature, typically around 38°C (100.4°F), and Nutrient Transport: Blood carries nutrients from the helps regulate overall body temperature. digestive system to cells and organs, enabling metab- olism and energy production. Blood Analysis Waste Removal: Blood collects waste products, such Blood analysis involves various tests to assess health and as urea, creatinine, and CO₂, and transports them to detect diseases. Common tests include: organs like the kidneys and lungs for excretion. Complete Blood Count (CBC): Measures the num- Regulation of pH and Temperature: Blood helps ber and types of blood cells (RBCs, WBCs, platelets). maintain the acid-base balance (pH) and regulates Hemoglobin levels: Evaluates oxygen-carrying ca- body temperature by distributing heat. pacity. Immune Defense: White blood cells (leukocytes) are Blood Chemistry Panel: Assesses levels of glucose, essential for immune defense, attacking pathogens electrolytes, proteins, and other substances. and foreign substances. Blood Cultures: Detect infections in the blood- Clotting: Platelets and clotting factors in the blood stream. are crucial for blood clotting to prevent excessive Coagulation Tests: Assess blood clotting ability. bleeding after injury. Blood Volume Composition of Blood Blood volume typically accounts for 7-8% of body Blood is made up of plasma (the liquid component) and weight. In a healthy adult, this equates to approxi- formed elements (cells and cell fragments): mately 5 liters of blood. Plasma Blood volume can vary based on factors like body Mostly water (about 90%), plasma also contains pro- size, hydration status, and health conditions. teins, electrolytes, nutrients, hormones, gases, and waste products. Effects of Meals and Position on Concentrations of Major plasma proteins include albumin, globulins, Blood Substances and fibrinogen. Postprandial Effects: After eating, blood glucose and lipid levels can rise temporarily due to nutrient Formed Elements absorption in the digestive system. Red Blood Cells (RBCs): Carry oxygen using the Positional Effects: Changes in body position (e.g., protein hemoglobin. standing vs. lying down) can affect blood pressure, White Blood Cells (WBCs): Involved in immune de- hematocrit (the ratio of red blood cells to total blood fense. volume), and circulation. Platelets: Small cell fragments that play a role in blood clotting. Hemoglobin Hemoglobin (Hb) is a protein in red blood cells that Plasma Substitutes binds to oxygen and carries it from the lungs to the Plasma substitutes (also called volume expanders) tissues and organs. are fluids used to replace blood volume in cases of Hemoglobin also carries carbon dioxide back to the significant blood loss. lungs to be exhaled. Common substitutes include saline solutions (e.g., A healthy adult has a hemoglobin level around 12-18 normal saline) and colloids (e.g., dextran, albumin), grams per deciliter of blood, depending on gender. which help restore blood pressure and maintain fluid balance. Myoglobin Myoglobin is similar to hemoglobin but found in General Properties of Blood muscle cells. It stores oxygen within muscle tissue Viscosity: Blood is more viscous than water due to and facilitates oxygen transfer during periods of high the presence of cells and proteins. This property activity.  Biochemistry: Body Fluids Myoglobin's affinity for oxygen is higher than that of Secretion hemoglobin, allowing it to store oxygen effectively in 3 Excess ions and waste products are secreted into the muscle fibers. urine for excretion. Plasma Proteins General Properties of Urine Albumin: The most abundant plasma protein, respon- Color: Typically pale yellow to amber, depending on sible for maintaining osmotic pressure, helping to hydration levels and the concentration of waste prod- regulate fluid balance between blood and tissues. ucts. Globulins: Involved in immune function and Volume: An average of 1-2 liters per day in a transport of lipids and metal ions. healthy adult. Fibrinogen: A key protein in the blood clotting cas- pH: Urine is usually slightly acidic (pH 4.5-8.0) but cade, converting into fibrin during clot formation. can vary depending on diet and health. Blood Clotting Normal Constituents of Urine Coagulation is the process by which blood trans- Water (95%) forms from a liquid to a gel, helping to prevent exces- Urea sive bleeding. Creatinine Platelets (thrombocytes) form a plug at the site of in- Electrolytes (e.g., sodium, potassium, chloride) jury, and fibrinogen is activated to form fibrin, Hormones (e.g., aldosterone, antidiuretic hormone) which stabilizes the clot. Abnormal Constituents of Urine Respiration and Transport of Oxygen and Carbon Di- Glucose: Presence indicates diabetes mellitus. oxide Protein: Presence suggests kidney disease (pro- Oxygen Transport: Hemoglobin binds to oxygen in teinuria). the lungs, forming oxyhemoglobin, and releases it in Blood: Indicates hematuria, which can be due to kid- tissues where oxygen concentration is low. ney stones, infection, or trauma. Carbon Dioxide Transport: Carbon dioxide is trans- Bilirubin: Indicates liver disease. ported as bicarbonate ions in plasma, bound to he- moglobin, and dissolved in plasma. It is exhaled Diuretics through the lungs. Diuretics are drugs that promote the excretion of wa- ter and salts through urine, often used to treat hyper- Urine tension and edema. Urine is the liquid waste product of metabolism, produced They work by inhibiting sodium reabsorption in the by the kidneys to help regulate fluid balance, electrolyte kidneys, leading to increased urine output. levels, and excretion of metabolic waste. Reagent Tablets, Papers, and Dipsticks Excretion of Waste Material Reagent strips are commonly used for rapid urine Urine helps to eliminate metabolic wastes, such as testing. These strips change color in response to the urea (from protein metabolism), creatinine (from presence of specific substances like glucose, protein, muscle metabolism), and uric acid (from purine me- blood, or pH. tabolism). Dipstick tests are useful for detecting urinary tract It also removes excess ions, like sodium (Na⁺), po- infections, kidney function issues, and diabetes. tassium (K⁺), and phosphate (PO₄³⁻), which helps maintain homeostasis. Formation of Urine Urine formation involves 3 main processes in the kidneys: Stages Filtration 1 Blood is filtered in the glomerulus, where wa-ter, ions, and small molecules pass into the renal tubules. Reabsorption 2 Essential substances like glucose, amino ac-ids, and most water are reabsorbed back into the bloodstream.  Biochemistry: Experiments Biochemistry Experiments 2. Heat gently and observe for red precipi- tate. 1. Preparation of Phosphate Buffer Purpose: To prepare a buffer solution with a spe- 5. Bial’s Test cific pH. Purpose: To detect pentoses. Principle: Buffers resist changes in pH by neu- Principle: Pentoses react with orcinol and ferric tralizing added acids or bases. Phosphate buffer is chloride in acidic medium to form a green color. prepared using a mixture of monosodium phos- Procedure: phate (NaH₂PO₄) and disodium phosphate 1. Add Bial’s reagent to the sample. (Na₂HPO₄). 2. Heat in a boiling water bath and observe Procedure: for a green color. 1. Calculate the required amounts of NaH₂PO₄ and Na₂HPO₄ for the desired 6. Seliwanoff’s Test pH and molarity. Purpose: To distinguish ketoses from aldoses. 2. Dissolve both in distilled water. Principle: Ketoses react faster with resorcinol in 3. Adjust the final volume and check pH us- acidic medium, producing a cherry-red complex. ing a pH meter. Procedure: 1. Add Seliwanoff’s reagent to the sample. 2. Molisch Test 2. Heat gently and observe the color Purpose: To detect the presence of carbohy- change. drates. Principle: Carbohydrates undergo dehydration 7. Sucrose Hydrolysis Test with sulfuric acid to form furfural, which reacts Purpose: To detect glucose and fructose from hy- with α-naphthol to give a violet ring. drolyzed sucrose. Procedure: Principle: Hydrolysis of sucrose yields glucose 1. Add 2 drops of Molisch reagent to the and fructose, which can be tested with Benedict’s sample. or Seliwanoff’s reagent. 2. Carefully layer concentrated sulfuric acid Procedure: along the tube's wall. 1. Hydrolyze sucrose by heating with dilute 3. Observe a violet-colored ring at the inter- acid. face. 2. Neutralize and test for reducing sugars. 3. Benedict’s Test 8. Potassium Iodide Test Purpose: To identify reducing sugars. Purpose: To test for starch. Principle: Reducing sugars reduce copper(II) Principle: Iodine in potassium iodide binds with ions (blue) to copper(I) oxide (red precipitate) in starch to produce a blue-black color. an alkaline medium. Procedure: Procedure: 1. Add iodine solution to the sample. 1. Mix Benedict’s reagent with the test sam- 2. Observe the color change. ple. 9. Hydrolysis of Starch 2. Heat in a boiling water bath for 2–3 Purpose: To break starch into maltose and glu- minutes. cose. 3. Observe the color change (green, yellow, Principle: Starch hydrolyzes under acidic or en- or red, depending on sugar concentra- zymatic conditions. tion). Procedure: 1. Heat starch with dilute HCl or enzyme 4. Barfoed’s Test (amylase). Purpose: To differentiate monosaccharides from 2. Test the hydrolysate with Benedict’s rea- disaccharides. gent. Principle: Monosaccharides reduce copper(II) ions to copper(I) in acidic medium, producing a 10. Quantitative Measurement of Glucose by Enzy- red precipitate. matic Method Procedure: Purpose: To quantify glucose concentration. 1. Mix Barfoed’s reagent with the sample.  Biochemistry: Experiments Principle: Glucose oxidase enzyme oxidizes glu- Procedure: Mix fatty acid solution with calcium cose, producing a measurable product. or magnesium salts.Observe precipitate for- Procedure: mation. 1. React the sample with glucose oxidase reagent. 15. Copper Acetate Test 2. Measure absorbance at a specific wave- Purpose: To identify unsaturated fatty acids. length. Principle: Unsaturated fatty acids react with cop- per acetate to form a green complex. 11. Solubility Test Procedure: Purpose: To assess solubility of lipids in different 1. Add copper acetate to the sample. solvents. 2. Observe the green color. Principle: Lipids are nonpolar and dissolve in or- ganic solvents (e.g., ether). 16. Cholesterol Estimation by Liebermann-Burchard Procedure: Test 1. Add lipid to different solvents. Purpose: To quantify cholesterol. 2. Observe solubility. Principle: Cholesterol reacts with acetic anhy- dride and sulfuric acid to produce a green color. 12. Saponification Test Procedure: Purpose: To test for the formation of soap. 1. React the sample with the reagent. Principle: Hydrolysis of triglycerides with alkali 2. Measure the intensity of the green color produces soap and glycerol. spectrophotometrically. Procedure: 1. Heat lipid with NaOH. 17. Unsaturation Test 2. Observe soap formation. Purpose: To detect unsaturation in lipids. Principle: Bromine or iodine adds to double 13. Salting Out bonds, causing decolorization. Purpose: To isolate soap using NaCl. Procedure: Principle: Addition of salt reduces soap solubil- 1. Add bromine water to the lipid sample. ity, causing precipitation. 2. Observe for decolorization. Procedure: 1. Add NaCl to soap solution. 18. Acrolein Test 2. Observe precipitation. Purpose: To detect glycerol in fats. 14. Insoluble Fatty Acids Salt Formation Test Principle: Heating glycerol with potassium bisul- Purpose: To identify fatty acids. fate produces acrolein, which has a pungent Principle: Fatty acids form insoluble salts with smell. certain metal ions. Procedure: 1. Heat lipid with potassium bisulfate. 2. Detect the acrid odor of acrolein.