Basic Biochemistry Notes PDF

**1. Basic Concepts** **Matter:**\ Matter is anything that has mass and occupies space. In the human body, matter includes all physical substances, such as bones, muscles, and bodily fluids. Matter exists in three states: solid (e.g., bones), liquid (e.g., blood), and gas (e.g., oxygen in the lungs...

**1. Basic Concepts** **Matter:**\ Matter is anything that has mass and occupies space. In the human body, matter includes all physical substances, such as bones, muscles, and bodily fluids. Matter exists in three states: solid (e.g., bones), liquid (e.g., blood), and gas (e.g., oxygen in the lungs). **Atom:**\ The atom is the fundamental unit of matter. It consists of a central nucleus, made up of protons and neutrons, surrounded by electrons that orbit the nucleus in energy levels or shells. The arrangement of these subatomic particles determines the chemical properties of the element. - **Example:** A carbon atom, which is the building block of all organic molecules, has 6 protons, 6 neutrons, and 6 electrons. **Proton:**\ Protons are positively charged particles located in the nucleus of an atom. The number of protons in an atom determines the element\'s identity and is referred to as the atomic number. - **Example:** Hydrogen has one proton, making its atomic number 1. **Electron:**\ Electrons are negatively charged particles that orbit the nucleus of an atom. The number and arrangement of electrons determine how an atom will interact with other atoms. - **Example:** In a sodium atom (Na), there is one electron in the outermost shell, which makes it highly reactive and prone to forming ionic bonds. **Neutron:**\ Neutrons are neutral particles found in the nucleus of an atom. They contribute to the atom\'s mass and can influence the stability of the nucleus. - **Example:** Carbon-12, a common isotope of carbon, has 6 neutrons, while carbon-14, a radioactive isotope, has 8 neutrons. **Ion:**\ An ion is an atom or molecule that has gained or lost one or more electrons, resulting in a net electrical charge. Ions are critical in many physiological processes, including nerve impulse transmission and muscle contraction. - **Cation:** A positively charged ion, formed when an atom loses electrons. - **Example:** Sodium (Na⁺) is a cation that plays a crucial role in generating electrical impulses in nerves. - **Anion:** A negatively charged ion, formed when an atom gains electrons. - **Example:** Chloride (Cl⁻) is an anion involved in maintaining osmotic balance and pH regulation in the body. **Atomic Number:**\ The atomic number is the number of protons in the nucleus of an atom. It defines the element and its position in the periodic table. - **Example:** Oxygen has an atomic number of 8, meaning it has 8 protons. **Mass Number:**\ The mass number is the total number of protons and neutrons in an atom\'s nucleus. It gives an approximation of the atom\'s mass. - **Example:** The mass number of carbon-12 is 12 (6 protons + 6 neutrons). **Mole:**\ A mole is a unit used to express the amount of a substance. One mole contains 6.022 × 10²³ particles (Avogadro\'s number), which could be atoms, molecules, or ions. - **Example:** One mole of glucose (C₆H₁₂O₆) contains 6.022 × 10²³ molecules and weighs approximately 180 grams. **Melting, Evaporation, Boiling, Condensation, Freezing:**\ These are phase changes that describe the transition of matter from one state to another. - **Melting:** Solid to liquid (e.g., ice melting into water). - **Evaporation:** Liquid to gas (e.g., sweat evaporating from the skin to cool the body). - **Boiling:** Rapid transition from liquid to gas at the boiling point (e.g., water boiling at 100°C at sea level). - **Condensation:** Gas to liquid (e.g., water vapor condensing into droplets on the skin during humid conditions). - **Freezing:** Liquid to solid (e.g., water freezing into ice). **2. Chemical Bonds** Chemical bonds are forces that hold atoms together, allowing the formation of molecules. The type of bond between atoms determines the stability and properties of the resulting compound. **Ionic Bonds:**\ Ionic bonds form when one atom donates an electron to another, resulting in the formation of positively charged cations and negatively charged anions. These opposite charges attract, holding the atoms together in an ionic bond. - **Example:** Sodium chloride (NaCl) is formed when a sodium atom (Na) donates an electron to a chlorine atom (Cl), resulting in a stable ionic compound. In the human body, sodium chloride is essential for maintaining electrolyte balance and conducting nerve impulses. **Covalent Bonds:**\ Covalent bonds occur when two atoms share one or more pairs of electrons. The shared electrons hold the atoms together, forming a stable molecule. - **Non-polar Covalent Bonds:** In a non-polar covalent bond, electrons are shared equally between the atoms, resulting in a molecule with no charge distribution. - **Example:** In a molecule of oxygen (O₂), the two oxygen atoms share electrons equally. - **Polar Covalent Bonds:** In a polar covalent bond, electrons are shared unequally, leading to a molecule with partial positive and negative charges. - **Example:** Water (H₂O) is a polar molecule because the oxygen atom has a stronger attraction for electrons than the hydrogen atoms, creating a partial negative charge on the oxygen and a partial positive charge on the hydrogens. **Intermolecular Bonds:**\ Intermolecular bonds are weak forces that occur between molecules, influencing the physical properties of substances. - **Example:** Van der Waals forces contribute to the weak attraction between molecules, affecting the boiling and melting points of substances. **Hydrogen Bonds:**\ Hydrogen bonds are a specific type of intermolecular bond that occurs when a hydrogen atom covalently bonded to a highly electronegative atom (such as oxygen or nitrogen) is attracted to another electronegative atom in a different molecule. - **Example:** Hydrogen bonds between water molecules give water its unique properties, such as high surface tension and the ability to act as a solvent for many biological molecules. **3. Inorganic Chemistry** **Water and Its Properties:**\ Water is the most abundant molecule in the human body, making up about 60-70% of body weight. Its unique properties are critical to life: - **Solvent:** Water's polarity allows it to dissolve a wide range of substances, making it an ideal medium for biochemical reactions. - **High Specific Heat:** Water can absorb and release a significant amount of heat without a large change in temperature, helping to regulate body temperature. - **Cohesion and Adhesion:** Water molecules stick to each other (cohesion) and to other substances (adhesion), which aids in processes like capillary action in blood vessels. - **Example:** Water is essential in the digestive system for breaking down food and absorbing nutrients. **pH:**\ The pH scale measures the concentration of hydrogen ions (H⁺) in a solution, indicating its acidity or alkalinity. - **pH 7:** Neutral (e.g., pure water). - **pH \< 7:** Acidic (e.g., gastric acid in the stomach has a pH of about 1.5-3.5, which helps in digestion). - **pH \> 7:** Alkaline (e.g., blood has a slightly alkaline pH of 7.35-7.45, essential for proper cellular function). **4. Organic Chemistry** Organic molecules contain carbon and are the basis of all living organisms. They include carbohydrates, lipids, proteins, and nucleic acids, each of which plays a vital role in the structure and function of the body. **Carbohydrates:**\ Carbohydrates are organic compounds composed of carbon, hydrogen, and oxygen, usually in a ratio of 1:2:1. They are the body\'s primary source of energy. - **Monosaccharides:** The simplest form of carbohydrates, consisting of a single sugar molecule. - **Example:** Glucose (C₆H₁₂O₆) is a monosaccharide that serves as a primary energy source for cells. - **Disaccharides:** Formed by the combination of two monosaccharides. - **Example:** Sucrose (table sugar) is a disaccharide composed of glucose and fructose. - **Polysaccharides:** Long chains of monosaccharides linked together. - **Example:** Glycogen is a polysaccharide stored in the liver and muscles, which can be broken down into glucose when energy is needed. **Lipids:**\ Lipids are a diverse group of hydrophobic organic molecules, including fats, oils, and cholesterol, that store energy, form cell membranes, and act as signaling molecules. - **Triglycerides:** Composed of glycerol and three fatty acids, they are the main form of stored fat in the body. - **Example:** Adipose tissue stores triglycerides, which can be broken down into fatty acids and glycerol for energy during fasting. - **Phospholipids:** A major component of cell membranes, consisting of two fatty acids, a glycerol, and a phosphate group. - **Example:** The phospholipid bilayer forms the structural foundation of cell membranes, providing a barrier and environment for cellular processes. - **Fatty Acids:** Long chains of carbon atoms with hydrogen atoms attached, can be saturated (no double bonds) or unsaturated (one or more double bonds). - **Example:** Omega-3 fatty acids are unsaturated fats found in fish oils, beneficial for cardiovascular health. - **Steroids:** A type of lipid with a structure of four fused carbon rings. - **Example:** Cholesterol is a steroid that is a precursor to important hormones like estrogen and testosterone and is also a component of cell membranes. **Proteins:**\ Proteins are large, complex molecules made up of amino acids, which perform a wide range of functions in the body. - **Amino Acids:** The building blocks of proteins, each containing an amino group, a carboxyl group, and a unique side chain. - **Example:** Glycine is the simplest amino acid, with just a hydrogen atom as its side chain. - **Enzymes:** Proteins that catalyze biochemical reactions, increasing the rate at which they occur. - **Example:** Amylase is an enzyme in saliva that breaks down starch into simpler sugars. - **Structural Proteins:** Provide support and shape to cells and tissues. - **Example:** Collagen is a structural protein in connective tissue, providing strength and elasticity to skin, tendons, and ligaments. - **Contractile Proteins:** Involved in muscle contraction. - **Example:** Actin and myosin are contractile proteins that interact to produce muscle contraction. - **Transport Proteins:** Carry substances throughout the body. - **Example:** Hemoglobin is a transport protein in red blood cells that carries oxygen from the lungs to tissues. - **Hormones:** Some proteins act as hormones, which are chemical messengers that regulate physiological processes. - **Example:** Insulin is a hormone that regulates blood glucose levels. **Nucleic Acids:**\ Nucleic acids, including DNA and RNA, are molecules that store and transmit genetic information. - **DNA (Deoxyribonucleic Acid):** The molecule that carries the genetic instructions for the development, functioning, growth, and reproduction of all living organisms. - **Structure:** DNA is a double helix, consisting of two strands of nucleotides held together by hydrogen bonds between complementary bases (adenine pairs with thymine, and guanine pairs with cytosine). - **RNA (Ribonucleic Acid):** A single-stranded molecule involved in protein synthesis and the transmission of genetic information. - **Structure:** RNA is similar to DNA but has a ribose sugar instead of deoxyribose and uracil instead of thymine. **Similarities and Differences between DNA and RNA:** - **Similarity:** Both DNA and RNA are composed of nucleotides, which include a sugar, a phosphate group, and a nitrogenous base. - **Difference:** DNA is double-stranded and stable under normal cellular conditions, while RNA is single-stranded and more prone to degradation. **Multiple Choice Questions (MCQs)** 1. **Which of the following is the primary energy source for cells?** - a\) Glycogen - b\) Fatty acids - c\) Glucose - d\) Cholesterol 2. **Which type of bond is formed by the sharing of electrons between atoms?** - a\) Ionic bond - b\) Covalent bond - c\) Hydrogen bond - d\) Van der Waals bond 3. **Which of the following is a function of hemoglobin?** - a\) Catalyzing biochemical reactions - b\) Providing structural support - c\) Transporting oxygen - d\) Storing genetic information **Short Answer Questions** 1. **Explain the role of water in maintaining homeostasis in the human body.** 2. **Describe the differences between saturated and unsaturated fatty acids and provide examples of each.** 3. **How do enzymes facilitate biochemical reactions in the body? Provide an example.** **Clinical Case Example: Diabetic Foot Ulcer** **Case:**\ A 55-year-old male with a history of poorly controlled type 2 diabetes presents with a non-healing ulcer on the plantar surface of his right foot. The ulcer has been present for three weeks and has shown minimal improvement despite basic wound care. On examination, the ulcer is deep with surrounding erythema and signs of infection. **Discussion:** - **Relevance of Biochemistry:**\ Diabetic foot ulcers are a common complication of diabetes, related to poor glucose control, which affects protein function (e.g., collagen in the skin), immune response, and overall wound healing. High blood glucose levels can lead to the glycation of proteins, impairing their function and contributing to delayed wound healing. - **Biochemical Considerations:**\ The patient\'s hyperglycemia has likely resulted in the formation of advanced glycation end-products (AGEs), which disrupt the normal repair processes in the skin and underlying tissues. Additionally, a deficiency in essential fatty acids and proteins might impair the structural integrity of the skin and its ability to resist infection. - **Clinical Management:**\ Effective management requires strict glucose control to reduce further glycation and improve wound healing. Nutritional support, including adequate protein intake, is essential to provide the necessary building blocks for tissue repair. Topical and systemic antibiotics may be required to treat the infection, and specialized wound care, potentially including debridement and advanced dressings, will support healing.