Introduction to Biochemistry PDF

INTRODUCTION TO BIOCHEMISTRY Cell Components Biochemistry is the study of the chemical processes that Plasma membrane: Controls the movement of occur within and related to living organisms. It's a field that...

INTRODUCTION TO BIOCHEMISTRY Cell Components Biochemistry is the study of the chemical processes that Plasma membrane: Controls the movement of occur within and related to living organisms. It's a field that substances in and out of the cell. bridges biology and chemistry, exploring the molecular Cytoplasm: A jelly-like substance that fills the cell. basis of life through examining the structure, function, and Nucleus: Contains DNA and controls cell activities. interactions of biomolecules. Cytoskeleton: Provides structural support and facilitates cell movement. Significance of Biochemistry ○ Microfilaments: Composed of actin, they Molecular mechanisms: It unravels the underlying are involved in cell shape, movement, and processes of biological functions. muscle contraction. Genetics: It provides insights into DNA, RNA, and ○ Intermediate filaments: Provide structural protein synthesis. support and help maintain cell shape. Disease development: It helps identify the Organelles: Specialized structures with specific molecular causes of diseases, leading to targeted functions. therapies. Metabolism: It explains how organisms convert Cell Functions food into energy and other biomolecules. 1. Energy production (e.g., cellular respiration) 2. Protein synthesis Applications of Biochemistry 3. Cell division and reproduction Medicine: Developing new drugs and treatments 4. Transport of substances Agriculture: Improving crop yields and pest control 5. Defense and immunity Environmental science: Understanding 6. Cell communication bioremediation and pollution control 7. Synthesis of biomolecules Cells Subcellular Organelles The smallest, basic unit of life that is responsible for all of life's processes. They provide structure for the body, take in nutrients from food, convert those nutrients into energy, and carry out specialized functions. Cell theory states that: All living things are composed of cells. Cells are the basic unit of life. New cells arise from existing cells. Nucleus: Houses DNA and is the site of Types of Cells transcription. Nucleolus: A region within the nucleus that produces ribosomes. Mitochondria: Produce ATP through cellular respiration. Endoplasmic reticulum (ER): Rough ER for protein synthesis, smooth ER for lipid synthesis. Golgi apparatus: Modifies, sorts, and packages proteins and lipids. Lysosomes and peroxisomes: Breakdown of waste Prokaryotic cells: Lack a nucleus (e.g., bacteria) materials. Eukaryotic cells: Have a nucleus and Peroxisomes: Contain enzymes that break down membrane-bound organelles (e.g., plants, animals) fatty acids and toxic substances.  Ribosomes: Sites of protein synthesis. triphosphate),which can be used by the cell to Chloroplasts (in plant cells): Site of photosynthesis. perform various functions. Microtubules: Composed of tubulin, they are 2. Anabolic reactions: Anabolic reactions are the involved in cell shape, movement, and intracellular opposite of catabolic reactions. They involve the transport. building up of complex molecules from simpler Centrosomes: Organize microtubules during cell ones, often requiring energy input. division. Vacuoles: Store and digest food particles. Cilia and flagella: Hair-like structures that aid in cell movement. Biomolecules 3. Oxidation-reduction reactions: Involve electron transfer (e.g., cellular respiration) a. Reduction: Gain of Electrons b. Oxidation: Loose of Electrons 4. Condensation reactions: Join two molecules (e.g., peptide bond formation) 5. Polymerization reactions: Form polymers from Carbohydrates: Provide energy (e.g., glucose, monomers (e.g., DNA synthesis) starch) Lipids: Store energy and form cell membranes (e.g., Biochemical Pathways fats, oils) Metabolic pathways: Linked series of reactions Proteins: Perform various functions (e.g., enzymes, (e.g., glycolysis, Krebs cycle) structural proteins) Signal transduction pathways: Transmit signals Nucleic acids: Store and transmit genetic within cells information (e.g., DNA, RNA) Feedback mechanisms: Regulate biochemical reactions Biochemical Reactions Biochemical reactions are the chemical reactions that occur Mechanisms of Biochemical Reactions within living organisms. These reactions are essential for all Enzyme Catalysis - These are biological catalysts life processes, including metabolism, growth, reproduction, that speed up chemical reactions without being and response to the environment. consumed in the process. 1. Enzymes: Catalyze biochemical reactions. Acid-Base Catalysis - These involve the transfer of 2. Metabolism: The sum of all biochemical reactions protons (H+) between molecules. in an organism. 3. Energy transfer: ATP, NADH, and FADH2 are key energy carriers. CARBOHYDRATES Types of Reactions: Carbohydrates are organic compounds composed 1. Catabolic reactions: Catabolic reactions are a type primarily of carbon, hydrogen, and oxygen atoms. of metabolic reaction that involves the breakdown They are essential nutrients for the human body, of complex molecules into simpler molecules, often providing energy and structural components. releasing energy in the process. This energy is Carbohydrates are defined as polyhydroxy typically stored in the form of ATP (adenosine aldehydes or ketones, or substances that can be  hydrolyzed to yield polyhydroxy aldehydes or Crystallinity: Many carbohydrates can form ketones. In simpler terms, they are sugars and their crystals. polymers. Viscosity: Solutions of carbohydrates can be viscous, especially polysaccharides. Polyhydroxy aldehydes: These compounds have an Chemical Properties aldehyde group at one end of the carbon chain and multiple Hydrolysis: Carbohydrates can be hydrolyzed to hydroxyl groups along the chain. yield smaller carbohydrates or monosaccharides. Oxidation: Carbohydrates can be oxidized to form Polyhydroxy ketones: These compounds have a ketone carboxylic acids. group within the carbon chain and multiple hydroxyl Reduction: Carbohydrates can be reduced to form groups. alcohols. Crystallinity: Many carbohydrates can form crystals. Glycosidic Bond Formation: Carbohydrates can form glycosidic bonds with other molecules, such as proteins or lipids. Biological Properties Energy Source: Carbohydrates are the primary source of energy for the body. Structural Components: Carbohydrates are used to build cell walls, tissues, and other structures. Cell Recognition: Carbohydrates are involved in cell recognition and communication. Storage: Carbohydrates are stored in the body as glycogen (in animals) or starch (in plants). Fiber: Indigestible carbohydrates, such as fiber, play a role in digestion and gut health. Isomerism Isomerism is a phenomenon in chemistry where two or more compounds have the same chemical formula but different arrangements of atoms, leading to distinct Sources of Carbohydrates properties. These compounds are called isomers. Grains: Rice, wheat, corn, oats, barley Stereoisomer Starchy vegetables: Potatoes, sweet ○ These isomers have the same arrangement potatoes, peas, beans, lentils of atoms but differ in their spatial Fruits: Apples, bananas, grapes, berries arrangement. Dairy products: Milk, yogurt, cheese Sugary foods and drinks: Candy, soda, honey, Constitutional syrup. ○ Also known as structural isomers, have the same molecular formula but differ in the Properties of Carbohydrates connectivity of their atoms. Physical Properties Sweet Taste: Many carbohydrates, especially Enantiomers simple sugars, have a sweet taste. ○ Enantiomers are stereoisomers that are Solubility: Most carbohydrates are soluble in water, mirror images of each other and cannot be especially simple sugars. superimposed on one another Colorlessness: Carbohydrates are generally colorless. Diastereomers  ○ Diastereomers are stereoisomers that are not mirror images of each other. Disaccharides: Sugars composed of two monosaccharide units joined by a glycosidic bond. Examples include sucrose Chirality (table sugar), lactose (milk sugar), and maltose. Chirality is a property of molecules that cannot be superimposed on their mirror image. Molecules that are chiral are said to be optically active Chiral Molecules - They are often asymmetric, meaning they lack a plane of symmetry or a center of symmetry. Achiral Molecules - They have a plane of symmetry or a center of symmetry. Polysaccharides: Sugars composed of many monosaccharide units joined together. Examples include starch, glycogen, and cellulose. Classification of Carbohydrates Based on the Number of Carbons Monosaccharides: Simple sugars with one sugar unit. Examples include glucose, fructose, and galactose. Classification of Carbohydrates Based on the Functional Group Ketoses: Ketoses are monosaccharides with a ketone functional group (C=O). Aldoses: Aldoses are monosaccharides with an aldehyde functional group (CHO). Fischer Projections The origin of Fischer Projections can be traced back to the late 19th century and the work of German chemist Emil Fischer. Fischer was studying carbohydrates, a complex group of organic molecules, and needed a way to visually represent their three dimensional structures in a two-dimensional format. He developed the Fischer projection system as a tool to simplify the depiction of these molecules, particularly their chiral centers. Haworth Projections Haworth Projections were introduced by Sir Walter Norman Haworth inthe early 20th century. He developed this system to represent the cyclic Phosphorylation structures of sugars, particularly those with Involves the addition of a phosphate group to the hydroxyl six-membered rings (pyranoses) and (-OH) group of a monosaccharide, typically catalyzed by five-membered rings (furanoses). enzymes called kinases. Haworth's innovation was to use a simplified representation of the cyclic structure, with the ring depicted as a hexagon or pentagon, and the substituents (OH groups, H atoms, etc.) Different Chemical Reactions involving Monosaccharides Oxidation Involves the loss of electrons or hydrogen atoms in the Condensation carbonyl group of the sugar molecule A chemical reaction where two or more molecules combine Mild - aldehydes can be oxidized to carboxylic acid to form a larger molecule. For monosaccharides, it is crucial to form sugar acids. for the formation of larger carbohydrate molecules. Strong - both ketone and aldehydes can be oxidized to carboxylic acids resulting in a complete breakdown of the sugar. Glycosidic Bonds Reduction A "Molecular Bridge". A covalent bond that joins a Involves the addition of electrons or hydrogen atoms to the carbohydrate to another molecule, typically another carbonyl group in the sugar molecule. Forms Sugar alcohol carbohydrate or non- carbohydrate group. Is formed between the anomeric carbon atom of a monosaccharide. Covalent Bonds  Covalent bonds take place when, rather than taking A variant of Benedict's Test. A chemical test used or giving electrons, atoms share their electrons in to test the presence of reducing sugars order to fill their energy shells. (monosaccharides). Reducing sugars react with crupric ions, causing Types of Glycocydic Bonds them to precipitate as cuprous oxide. 3. Silver Mirror Test A test conducted to detect the presence of O-Glycosidic Bond - most common; formed Aldehydes. Involves the Reduction of silver Ions between the anomeric carbon and hydroxyl group (Ag+) to metallic silver (Ag). Forms a shiny silver of another molecule mirror on the surface of the clean test tube. N-Glycosidic Bond - formed between the anomeric Uses Tollen's reagent, a solution of silver nitrate carbon and amine group. (AgNO3) and ammonia (NH3). A formation of S-Glycosidic Bond - formed between the anomeric silver mirror tubes in the inner surface of the test carbon and thiol group. tube indicates the presence of an aldehyde. The opposite if none. Types of Biochemical Tests 1. Benedict's Test 4. Molisch's Test A chemical test used to test the presence of A general test for Carbohydrates. Used to detect the reducing sugars (monosaccharides). Uses Benedict presence of any carbohydrates. solution, which is a reagent that's blue in color. Molisch's reagent contains alpha-napthol. A change in color indicates a presence of reducing Undergoes Dehydration and Condensation. sugars. Vice versa if none. A purple ring at the interface indicates the presence of carbohydrates. The opposite if none. 2. Fehling's Test