BIO30S Unit 2: Biochemistry

Biochemistry is divided into two major branches: Basic Chemistry, which includes atomic structure, bonding, and chemical reactions, and Biological Chemistry, which focuses on carbohydrates, lipids, proteins, nucleic acids, and body functions. In Basic Chemistry, all elements are made of protons, electrons, and neutrons. The number of protons defines the element and is known as the atomic number, which dictates the chemical properties. In a neutral atom, the number of electrons equals the number of protons, and they occupy specific energy levels around the nucleus. Neutrons contribute to the mass of the atom, and isotopes of an element have the same number of protons but different numbers of neutrons. Everything is made up of matter, and matter is made up of atoms. Different atoms are called Elements, each with a unique symbol and set of properties. The Periodic Table contains all known elements, arranged by increasing atomic number and recurring chemical properties. Elements to the left of the staircase are metals, while those to the right are non-metals. The group number indicates the number of valence electrons, which determine the bonding properties of the element. About 25 elements are essential for life, with carbon, hydrogen, oxygen, and nitrogen making up 96% of living matter, and phosphorus, sulphur, potassium, and sodium making up most of the remaining 4%. Ionic bonding involves the transfer of electron(s) between a non-metal and metal atom and the attraction of negative and positive charges, forming ions. A cation is a positively charged ion formed when an atom loses electrons, while an anion is a negatively charged ion formed when an atom gains electrons. Covalent bonding occurs when two atoms share electrons to attain a full valence shell, typically between two non-metals. Non-polar covalent bonds involve equal sharing of electrons, while polar covalent bonds involve unequal sharing, resulting in partial charges on the atoms. Hydrogen bonds form between a slightly positive hydrogen atom and another slightly negative atom or molecule and are important in stabilizing large biological molecules. Chemical reactions occur when unstable elements combine to produce a more stable compound, involving the breaking and forming of chemical bonds, and follow the Law Conservation of Matter. Chemical reactions in the body enable essential life processes, such as converting food and oxygen into energy, facilitated by reactants, catalysts, and enzymes. Water is a polar molecule essential for transporting substances, participating in hydrolysis and dehydration reactions, and interacting with hydrophilic (polar and charged) and hydrophobic (non-polar) substances. Acids produce hydrogen ions (H+) in solution, while bases produce hydroxide ions (OH-), and salts are formed from neutralization reactions between acids and bases. Maintaining a stable pH is crucial for enzyme function and cellular health, with buffers helping to resist changes in hydrogen ion concentration, and the pH scale measuring acidity or basicity from 0 to 14. Biological macromolecules contain elements essential to life and are classified into inorganic and organic molecules. Inorganic molecules like water, salts, and minerals play major roles in living things, while organic molecules always contain carbon and hydrogen, allowing for diverse and stable structures. Monomers are simple organic molecules that link to form polymers through dehydration reactions, while polymers are broken down into monomers through hydrolysis reactions. Dehydration reactions remove water to join monomers, while hydrolysis reactions add water to break down polymers. Carbohydrates are composed of carbon, hydrogen, and oxygen, functioning as quick fuel and short-term energy storage, and include monosaccharides, disaccharides, and polysaccharides. Monosaccharides are simple sugars, disaccharides are formed from two monosaccharides through dehydration synthesis, and polysaccharides are large polymers for energy storage and structure. Lipids function in energy storage, structure, hormone regulation, and protection, and are non-polar. Fats are solid at room temperature and high in saturated fatty acids, while oils are liquid and high in unsaturated fatty acids. Lipids consist of glycerol and fatty acids, with triglycerides being the most common type. Fatty acids can be saturated or unsaturated, with saturated fats having all carbons bonded to hydrogen and unsaturated fats having C=C double bonds. Phospholipids have a glycerol, two fatty acids, and a phosphate group, forming the phospholipid bilayer in cell membranes. Steroids have four fused carbon rings and various functional groups, with cholesterol being an important cell component and precursor for other steroids. Proteins are structurally and functionally diverse, involved in enzymes, structure, transport, cell communication, defense, and movement. Enzymes catalyze biochemical reactions, with the lock and key model explaining enzyme-substrate interactions. Protein monomers are amino acids, linked by peptide bonds to form polypeptides, with protein structure having primary, secondary, tertiary, and quaternary levels. Denaturation is the unfolding of a protein, causing loss of function due to temperature, pH, or salinity. Carbohydrates consist of monosaccharides, lipids consist of glycerol, fatty acid, cholesterol, and H-C chains, proteins consist of amino acids, and nucleic acids consist of nucleotides.