Biochemistry Notes PDF

Biochemistry Chapter 2 2.1 Concepts of Matter and Energy Matter - (the “stuff” of the universe) anything that occupies space and has mass (weight). ○ Chemistry Studies the nature of matter Studies how its building blocks are put toge...

Biochemistry Chapter 2 2.1 Concepts of Matter and Energy Matter - (the “stuff” of the universe) anything that occupies space and has mass (weight). ○ Chemistry Studies the nature of matter Studies how its building blocks are put together and how they interact. ○ Matter exists as a solid, liquid, and gas Solids - bones and teeth Liquids - blood plasma and interstitial fluid Gases - air (Carbon dioxide and Oxygen)  Energy - does not have mass and does not take up space. ○ Can only measured by the effects it has on matter ○ Ability to do work kinetic energy - displayed in constant movement of particles of matter (atoms) as well as larger objects (bouncing ball) potential energy - inactive or stored energy ○ Forms of Energy Chemical energy - stored in bonds of chemical substances When bonds are broken, the potential (stored) energy is unleashed and become kinetic energy ○ Chemical energy from foods we eat “runs” all body activities Electrical energy - from movement of charge particles. In your body - an electrical current is generated when charged particles (ions) move across the cell membrane Nerve impulses Mechanical energy - directly involved in moving matter Riding a bicycle, your legs provide the mechanical energy to move the pedals ○ Muscles in your legs shorten, pulling your bones, causing your leg move Radiant energy - travels in waves, it is the energy of the electromagnetic spectrum Light energy stimulates your retinas UV waves cause sunburn, but also stimulate our bodies to produce Vit D.  Energy from conversions - energy can change from one form to another ○ Chemical energy of foods is trapped by ATP ATP (adenosine triphosphate) ATP energy can be transferred to electrical energy in a nerve impulse Or mechanical energy of shortening muscles ○ Energy is “lost” with each conversion as heat (thermal energy) ○ This release of heat in the body is what makes us “warm-blooded” and contributes to our body temperature. Common Elements Making Up the Human Body Element Atomic % of body Role in human body Symbol mass Major 96.1 % Oxygen O 65% Major component to organic and inorganic molecules; as a gas essential to the oxidation of glucose and other food fuels, required to make for efficient cellular respiration (making ATP) Carbon C 18.5% Primary element of all organic molecules, including carbohydrates, lipids, proteins and nucleic acids Hydrogen H 9.5% Part of most organic molecules; as an ion it influenced pH of body fluids Nitrogen N 3.2 % Component of proteins and nucleic acids Lesser 3.9% Calcium Ca 1.5% Found in bones and teeth, required for muscle contraction, neural transmission and blood clotting Phosphorus p 1.0 % Combines with calcium in bones and teeth, also present in nucleic acids, proteins and ATP Potassium K.4% Necessary for conduction of nerve impulses and muscle contractions Sulfur S.3% Component of proteins (muscle contraction) Sodium Na.2% Water balance, nerve impulses, and muscle contraction Magnesium Mg.1% In bones, important in metabolic reactions Iodine I.1% Needed for function of thyroid hormones Iron Fe.1% Hemoglobin, allows blood to transport oxygen Patterns of Chemical Reactions ○ Synthesis Reactions - two or more atoms or molecules combine to form one larger, more complex molecule A + B → AB Ex. amino acids are joined together → proteins Important for growth, repairing worn-out or damaged tissues ○ Decomposition Reactions - when molecules is broken down into smaller molecules AB → A + B Ex. digestion of food and the breakdown of glycogen to release glucose ○ Exchange Reactions - both synthesis and decomposition reactions AB + C → AC + B AB + CD → AD + CB ATP → ADP  Factors influencing the rate of chemical reactions ○ Increase in Temperature - increases kinetic energy of the molecules increases, which in turn move more rapidly and collide more forcefully ○ Increase in concentration of reactants - increases the number of collisions because of increased numbers of reacting particles ○ Decrease in particle size - smaller particles have more kinetic energy and move faster than larger ones. ○ Presence of catalysts - decrease the amount of energy the molecules need to interact by holding the reactants in proper positions to interact. Biochemistry Inorganic compounds - lack carbon and tend to be small ○ EX found in body - water, salts and many acids and bases (but not all) Organic compounds - carbon-containing compounds, large molecules ○ Ex. - carbohydrates, lipids, proteins, and nucleic acids  INORGANIC COMPOUNDS ○ Water is the most abundant inorganic compound in the body (66% of body weight) High heat capacity - absorbs and releases large amounts of heat before its temperature changes noticeably Prevents sudden changes in body temperature Polarity/solvent properties Because of water's polarity it is an excellent solvent (stuff easily dissolves in it) Water is the “universal solvent” salts , acids and bases dissolve easily in water. Molecules cannot react chemically unless they are in solution Nutrients, respiratory gases (CO2 and O2) and wastes can dissolve in water, water then acts as a transport and exchange medium in the body Chemical reactivity Water is an important reactant in some chemical reactions Ex. digesting food or breaking down biological molecules Hydrolysis reactions - when water molecules are added to bonds of a larger molecule Cushioning cerebrospinal fluid, water forms a cushion around the brain ○ Salts - ionic compound containing cations other than H+ and anions other than OH-. Most plentiful salts (of metal elements) in the body is calcium (Ca2+) and phosphorus (Phosphate PO43-) found mainly in the bones and teeth. Dissociation -salts dissolve in body fluids, and easily separate into their ions. Salts are vital to the human body in both ionic and in combination with other elements. EX. Sodium (Na+), potassium (K+) essential for nerve impulses Iron (Fe2+) part of hemoglobin (transports oxygen) Electrolytes - molecules that ionize and then dissociate in water and can conduct an electrical impulse. ○ Acids - Releases hydrogen ions (H+) Proton donors Sour taste Can dissolve many metals or “burn” a hole in things The release of the proton determines an acids effect on the environment EX in the body - hydrochloric acid (stomach acid), acetic acid, and carbonic acid. Strong acids - ionize completely and liberate all protons Ex. Stomach acid HCl → H+ + Cl- Weak acids - ionize incompletely Ex. acetic and carbonic acid 2H2CO3 → H+ + HCO3- + H2CO3  ○ Bases - Bitter taste Feel slippery Proton acceptors Ex. ionization of sodium hydroxide (lye) NaOH → Na+ + OH- Strong base Hydroxyl ion (OH-) Weak base Bicarbonate ion (HCO3-) found in blood Neutralization reaction - acid and base react to form water and salt HCl + NaOH → H2O + NaCl (acid) (base) (water) (salt) ○ pH - Acid-Base Concentration Buffers - balance acids and bases ○ Ex. kidneys, lungs chemicals in body fluids Blood pH 7.35-7.45 ○ Any change in blood pH can result in death ○ When it dips lower, the amount of oxygen that hemoglobin can carry begins to fall rapidly (depriving the body of oxygen)  ORGANIC COMPOUNDS ○ Contain carbon ○ Very large molecules Functional group - small reactive portion of the large molecule that interacts with other molecules. Polymers - chainlike molecules made of many similar or repeating units (monomers) Dehydration synthesis - building of polymers Hydrolysis - break down of polymers ○ Carbohydrates - include sugars and starches Contain carbon, hydrogen, and oxygen 1:2:1 ratio Glucose - C6H12O6 Ribose - C5H10O5 Classified by size and solubility in water Monosaccharides, disaccharides or polysaccharides Monosaccharides “One sugar” Simple sugars Single chain or single ring structures with 3-6 carbons Most important in humans ○ Glucose “blood sugar” is the universal cellular fuel. ○ Fructose and galactose - convert glucose for use in cells ○ Ribose and deoxyribose - part of nucleic acids (RNA and DNA)  Disaccharides Double sugars Formed when two simple sugars are joined by dehydration synthesis Some important disaccharides ○ Sucrose (glucose-fructose) - cane sugar ○ Lactose (glucose-galactose) - found in milk ○ Maltose (glucose-glucose) - malt sugar ○ Too large to pass through cell membrane, must be broken down (hydrolysis) into their monosaccharide units to be absorbed by the digestive tract into the blood Polysaccharides Long, branching chains of linked monosaccharides Large, insoluble molecules, they are ideal for storage products Due to large size, they lack the sweetness of mono- and di- saccharides Two most important ○ Starch - storage polysaccharide formed by plants Grain products and root vegetables (potatoes and carrots) ○ Glycogen - slightly smaller and found in animal tissue (large muscles and liver) ○ Lipids - Enter the body in the form of fat-marbled meats, eggs yolks, milk products and oils Contain carbon, hydrogen, and oxygen atoms, but carbon and hydrogen atoms far outnumber oxygen atoms Typical fat tristearin C57H110O6 Most are insoluble in water but readily dissolve in other lipids and organic solvents such as alcohol and acetone. Most abundant Triglycerides, phospholipids, and steroids Triglycerides “Neutral fats” Composed of two types of building blocks ○ Fatty acids ○ Glycerol Synthesis involves the attachment of three fatty acids to one glycerol through dehydration synthesis. E - shaped molecule The body's most abundant source of usable energy Stored in fat deposits under the skin and around organs  Two types of triglycerides Saturated fats ○ Only single covalent bonds between carbon atoms ○ Chains are straight ○ Solid at room temperature Unsaturated fats (monounsaturated and polyunsaturated) ○ Contain one or more double bonds between carbon atoms ○ Chains have a “kink” (not straight) ○ Oils - liquid at room temperature ○ Trans fats - “margarines” oils that are solid at room temperature Phospholipids Similar to triglycerides, except it always has a phosphate group takes the place of one of the fatty acid chains. Two fatty acid chains and one phosphate group Hydrophilic head - water loving Hydrophobic tails - repels water  Steroids Flat molecules formed of four interlocking rings Made largely of hydrogen and carbon atoms Fat soluble (does not dissolve in water) Ex. Cholesterol - single most important steroid molecule ○ Essential for human life ○ Found in cell membranes ○ Raw material of vitamin D, steroid hormones, and bile salts ○ Proteins - Account for 50% of organic matter in the body Most varied functions of the organic molecules Construction materials Vital roles in cell function Contain carbon, oxygen, hydrogen and nitrogen. Can also contain sulfur. Amino acids - building blocks of proteins 20 common amino acids Amine group (NH2) basic properties + acid group (COOH) allows them act as acids + R-group (single group of atoms that makes amino acids acids different from each other) ○ Nucleic acids - Make up genes Provide the basic blueprint for life Composed of carbon, oxygen, hydrogen, nitrogen and phosphorus Nucleotides - building blocks of nucleic acids Nitrogen containing base, 5 carbon sugar, and a phosphate group DNA - deoxyribonucleic acid RNA - Ribonucleic acid Adenosine Triphosphate (ATP) cellular energy Without ATP molecules can not be made or broken down Modified nucleotide ○ Adenine base, ribose sugar and 3 phosphate groups Adenosine Diphosphate (ADP) Formed through hydrolysis of ATP Adenine base, ribose sugar and 2 phosphate groups