The Chemical Basis of Life Notes PDF

The Chemical Basis of Life Romel M. Durante, RN, MAN ( C ) Clinical Instructor  LEARNING OUTCOMES At the end of this lecture, you should be able to: 1. Define chemistry and state its relevance to anatomy and physiology. 2. Define matter, mass, and weight. 3. Disti...

The Chemical Basis of Life Romel M. Durante, RN, MAN ( C ) Clinical Instructor  LEARNING OUTCOMES At the end of this lecture, you should be able to: 1. Define chemistry and state its relevance to anatomy and physiology. 2. Define matter, mass, and weight. 3. Distinguish between an element and an atom. 4. Define atomic number and mass number. 5. Name the subatomic particles of an atom, and indicate their location. 6. Compare and contrast ionic and covalent bonds. 7. Describe the pH scale and its relationship to acidic and basic solutions. 8. Distinguish between inorganic and organic molecules. 9. Describe the structural organization and major functions of carbohydrates, lipids, proteins, and nucleic acids  Chemistry ❑Chemistry is the scientific discipline concerned with the atomic composition and structure of substances and the reactions they undergo. Composition of Matter Matter: anything that occupies space and has mass (solid, liquid, or gas) Mass: amount of matter in an object Weight: gravitational force acting on object of a given mass. 3 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Elements and Atoms Element: - simplest type of matter having unique chemical properties - Ex. C, H, O, N, Ca, K, Na, Cl Atom: - smallest particle of an element that has the chemical characteristics of that element. - contains protons, electrons, and neutrons 4 Copyright © McGraw-Hill Education. Permission required for reproduction or display. Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Three major types of subatomic particles Proton: ▪ + charge, inside nucleus Electron: ▪ - charge, outside nucleus Neutron: ▪ neutral or have no electrical charge, inside nucleus ❖ The number of protons and number of electrons in each atom are equal ❖ Protons and neutrons form the nucleus at the center of the atom ❖ electrons move around the nucleus 6 Copyright © McGraw-Hill Education. Permission required for reproduction or display. Copyright © McGraw-Hill Education. Permission required for reproduction or display. Atomic Number: number of protons in each atom because the number of electrons and number of protons are equal, the atomic number is also the number of electrons. Mass Number: number of protons plus the number neutrons in each atom. Ex. mass number for carbon is 12 because it has 6 protons and 6 neutrons. 8 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Chemical Bonds Chemical bonds occurs when outermost electrons are transferred or shared between atoms Two major types: 1. Ionic bonding ▪ occurs when electrons are transferred between atoms, creating oppositely charged ions ▪ attraction between two oppositely charged ions ▪ Ex. NaCl (table salt ) ❖Ion - charged particle ( Ex. Na+ ) If an atom loses or gains electrons, the numbers of protons and electrons are no longer equal, and a charged particle called an ion is formed 9 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Figure 2.3a Copyright © McGraw-Hill Education. Permission required for reproduction or display. 2. Covalent bonding ▪ atoms share one or more pairs of electrons ▪ the resulting combination of atoms is called a molecule ▪ Ex. Hydrogen molecule Polar covalent bonds: ✓ unequal sharing of electrons ✓ Ex. Water (H2O) Polar molecules: ✓ molecules with asymmetrical electrical charge Nonpolar covalent bond ✓ equal sharing of electrons between atoms Nonpolar molecules: ✓ molecules with symmetrical electrical charge 11 Copyright © McGraw-Hill Education. Permission required for reproduction or display. Copyright © McGraw-Hill Education. Permission required for reproduction or display. Polar Covalent Bonds (a) A water molecule forms when two hydrogen atoms form covalent bonds with an oxygen atom. (b) The hydrogen atoms and oxygen atoms are sharing electron pairs (indicated by the black dots), but the sharing is unequal. The dashed outline shows the expected location of the electron cloud if the electrons are shared equally. But as the yellow area indicates, the actual electron cloud (yellow) is shifted toward the oxygen. Consequently, the oxygen side of the molecule has a slight negative charge (indicated by δ−), and the hydrogen side of the molecule has a slight positive charge (indicated by δ+). Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Hydrogen Bonds Polar molecules have a positive end and a negative end Hydrogen bond forms when positive end of one polar molecule is weakly attracted to negative end of another polar molecule attraction between molecules resulting from hydrogen bonds is much weaker bond than ionic or covalent 14 Copyright © McGraw-Hill Education. Permission required for reproduction or display. Hydrogen Bonds The positive hydrogen part of one water molecule (δ+) forms a hydrogen bond (red dotted line) with the negative oxygen part of another water molecule (δ−). As a result, hydrogen bonds hold separate water molecules together Copyright © McGraw-Hill Education. Permission required for reproduction or display. Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Molecules and Compounds Molecule 2 or more atoms chemically combine Ex. Water (H2O) Compound substance resulting from the chemical combination of 2 or more different types of atoms Ex. NaCl ❖ Water is an example of a substance that is a compound and a molecule ❖ Not all molecules are compounds. For example, a hydrogen molecule is not a compound because it does not consist of different types of atoms. 17 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Chemical Reactions What are they? ❑ atoms, ions, molecules, or compounds interact either to form or to break chemical bonds Reactants ✓ substances that enter into a chemical reaction or what is put into reaction Products ✓ substances that result from the chemical reaction ✓ end result of reaction A+B → C+D Reactants Product 18 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Types of Chemical Reactions Synthesis reaction ✓ When two or more reactants combine to form a larger, more complex product ✓ build a new molecule; energy-requiring ✓ A + B → AB ✓ Ex. ADP + P → ATP ✓ anabolism - synthesis reactions that occur in the body Decomposition reaction ✓ reactants are broken down into smaller, less complex products ✓ break down molecule ; reverse of a synthesis reaction ✓ energy-releasing ✓ AB → A + B ✓ Ex. ATP → ADP + P ✓ catabolism - decomposition reactions that occur in the body metabolism - all of the anabolic and catabolic reactions in the body 19 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Copyright © McGraw-Hill Education. Permission required for reproduction or display. REACTANT PRODUCTS ATP ADP + Pi + Energy More potential Less potential energy energy (a) REACTANTS PRODUCT ADP + Pi + Energy ATP Less potential More potential energy energy 20 (b) Copyright © McGraw-Hill Education. Permission required for reproduction or display. Exchange reaction ✓ combination of synthesis and decomposition reactions ✓ AB + CD → AC + BD ✓ Ex. HCl + NaOH → NaCl + H2O ✓ hydrochloric acid (HCl) with sodium hydroxide (NaOH) to form table salt (NaCl) and water (H2O) Enzymes: ✓ proteins that speed up reactions 21 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Copyright © McGraw-Hill Education. Permission required for reproduction or display. Molecule A Molecule B Enzyme New molecule AB 22 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Energy What is it? ✓ capacity / ability to do work - that is, to move matter. Subdivisions: Kinetic energy: energy caused by the movement of an object and is the form of energy that actually does work energy in motion Ex. uncoiling spring pushing an object and causing it to move Potential energy: stored energy that could do work but is not doing so. Ex. coiled spring has potential energy When potential energy is released, it becomes kinetic energy, thus doing work. 23 Copyright © McGraw-Hill Education. Permission required for reproduction or display. Chemical energy ✓ form of potential energy stored in chemical bonds (food) Glucose ✓ sugar found in food ✓ glucose is used to make ATP (energy) Glycogen ✓ stored glucose ✓ stored in liver, skeletal muscle, and fat 24 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  ATP What does it stand for? ✓ adenosine triphosphate What is it? ✓ stored energy ✓ the “energy currency of cells” - capable of both storing and providing energy ❑ When ATP is broken down (ATP → ADP + P) energy is released. 25 Copyright © McGraw-Hill Education. Permission required for reproduction or display. Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Acids and Bases The body has many molecules and compounds, called acids and bases, that can alter body functions Acids ✓ proton donor or donate H+ (proton) ✓ Because a hydrogen atom without its electron is a proton, any substance that releases hydrogen ions (H+) in water is an acid ✓ pH below 7 ✓ Ex. HCl (hydrochloric acid) in the stomach Bases ✓ Proton acceptor or accept H+ (proton) ✓ pH above 7 ✓ Ex. NaOH (sodium hydroxide) forms sodium ions (Na+) and hydroxide ions (OH−). It is a base because the OH− is a proton acceptor that binds with a H+ to form water. 27 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Acids and Bases pH scale ✓ indicates the H+ concentration of a solution ✓ The scale ranges from 0 to 14 ✓ neutral solution - has an equal number of H+ and OH− and thus a pH of 7.0 ✓ acidic solution - has a greater concentration of H+ than of OH− and thus a pH less than 7.0 ✓ basic or alkaline solution - has fewer H+ than OH− and thus a pH greater than 7.0. the pH number and the actual H+ concentration are inversely related ( the lower the pH number, the higher the H+ concentration ) ❑ normal pH range for human blood is 7.35 to 7.45 ❑ Acidosis - blood pH below 7.35 ❑ Alkalosis - blood pH above 7.45 28 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  29 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Organic and Inorganic Chemistry ❑ inorganic chemistry ✓ deals with those substances that do not contain carbon ✓Ex. O2 , CO2 , calcium phosphate, iron in hemoglobin, zinc in alcohol dehydrogenase. ❑ organic chemistry ✓ is the study of carbon-containing substances. These definitions have a few exceptions. For example, CO2 and carbon monoxide (CO) are classified as inorganic molecules, even though they contain carbon. 30 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Organic and Inorganic Chemistry ❑ Oxygen (O2) ✓ small, nonpolar, inorganic molecule consisting of two oxygen atoms bound together by a double covalent bond ✓ 21% of the gas in the atmosphere is O2 ✓ Humans require O2 in the final step of a series of chemical reactions in which energy is extracted from food molecules ❑ Carbon dioxide (CO2 ) ✓ consists of one carbon atom bound to two oxygen atoms ✓ produced when food molecules, such as glucose, are metabolized within the cells of the body ✓ Once produced, it is eliminated from the cell as a metabolic by-product, transferred to the lungs by the blood, and exhaled during respiration. ✓ If it is allowed to accumulate within cells, it becomes toxic. 31 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Organic Molecules A. CARBOHYDRATES ❑ composed of carbon ( C ), hydrogen ( H ), and oxygen ( O ) atoms ❑ In most carbohydrates, for each carbon atom there are two hydrogen atoms and one oxygen atom ❑ H:O is a 2:1 ratio ❑ Ex. Glucose - C6H12O6 ❑ Monosaccharides ( simple sugar ) ✓ smallest carbohydrates; are the building blocks of carbohydrates ✓ Ex. Glucose ( blood sugar ) and fructose ( fruit sugar ) ❑ Disaccharide ( two sugars ) ✓ formed when two monosaccharides are joined by a covalent bond ✓ Ex. glucose + fructose = sucrose (table sugar) ; Glucose + galactose = lactose 32 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Figure 2.11a Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Organic Molecules A. CARBOHYDRATES ❑ Polysaccharide ( many sugars ) ✓ consist of many monosaccharides bound in long chains ✓ Ex. Glycogen ( animal starch , is a polysaccharide of glucose ), Plant starch, Cellulose 34 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Functions of Carbohydrates Short-term energy storage Converted to glucose quickly Glucose is used to make ATP (energy) Brain cells require glucose 35 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Organic Molecules B. LIPIDS ❑ are substances that dissolve in nonpolar solvents, such as alcohol or acetone, but not in polar solvents, such as water - insoluble in water ❑ composed mainly of carbon, hydrogen, and oxygen, but other elements, such as phosphorus and nitrogen, are minor components of some lipids ❑ contain a lower proportion of oxygen to carbon than do carbohydrates ❑ Ex. Fats, phospholipids, eicosanoids, and steroids ❑ 1. Fats ✓ important energy-storage molecules; they also pad and insulate the body ✓ building blocks: glycerol and fatty acids ✓ Triglycerides - most common type of fat molecules 36 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Types of Lipids Saturated ❑ it contains only single covalent bonds between the carbon atoms ❑ Sources: beef, pork, whole milk, cheese, butter, eggs, coconut oil, and palm oil Unsaturated ❑ it has one or more double covalent bonds ❑ Monounsaturated fats: olive and peanut oils ( have one double covalent bond between carbon atoms ) ❑ Polyunsaturated fats: safflower, sunflower, corn, and fish oils ( have two or more double covalent bonds between carbon atoms ) Unsaturated fats are the best type of fats in the diet because, unlike saturated fats, they do not contribute to the development of cardiovascular disease. 37 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Organic Molecules B. LIPIDS ❑ 2. Phospholipids ✓ similar to triglycerides, except that one of the fatty acids bound to the glycerol is replaced by a molecule containing phosphorus ✓ is polar at the end of the molecule to which the phosphate is bound and nonpolar at the other end ✓ are important structural components of cell membranes ▪ hydrophilic (water-loving) - polar end of the molecule is attracted to water ▪ hydrophobic (water-fearing) - nonpolar end is repelled by water ❑ 3. eicosanoids ✓ a group of important chemicals derived from fatty acids ✓ are made in most cells and are important regulatory molecules - role in the response of tissues to injuries ✓ Ex. Prostaglandins - regulates the secretion of some hormones, blood clotting, some reproductive functions 38 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Organic Molecules B. LIPIDS ❑ 4. Steroids ✓ composed of carbon atoms bound together into four ringlike structures ✓ Cholesterol - important steroid because other steroid molecules are synthesized from it ✓ For example, bile salts, which increase fat absorption in the intestines, are derived from cholesterol, as are the reproductive hormones estrogen, progesterone, and testosterone 39 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Functions of Lipids Long term energy storage Insulates against heat loss Protective cushion for organs Cholesterol is part of the cell membrane structure 40 Copyright © McGraw-Hill Education. Permission required for reproduction or display. Triglyceride: one glycerol molecule and three fatty acids are combined to produce a triglyceride. Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Figure 2.13 Fatty Acids (a) Palmitic acid is a saturated fatty acid; it contains no double bonds between the carbons. (b) Linolenic acid is an unsaturated fatty acid; note the three double bonds between the carbons, which cause the molecule to have a bent shape. Copyright © McGraw-Hill Education. Permission required for reproduction or display. Phospholipids (a) Molecular model of a phospholipid. Note that one of the fatty acid tails is bent, indicating that it is unsaturated. (b) A simplified depiction of a phospholipid. Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Organic Molecules C. PROTEIN ❑ contain carbon, hydrogen, oxygen, and nitrogen, and most have some sulfur ❑ building blocks: Amino acids. ✓ There are 20 basic types of amino acids ✓ Humans can synthesize 12 of them from simple organic molecules, but the remaining 8 so-called essential amino acids must be obtained in the diet [ Quinoa (grain), eggs, turkey, cottage cheese, mushroom, fish like salmon ] ✓ denaturation - change in shape of protein caused by abnormally high temperatures or changes in pH, hence protein becomes nonfunctional. ❑ Proteins perform many important functions: ▪ enzymes are proteins that regulate the rate of chemical reactions, ▪ structural proteins provide the framework for many of the body’s tissues ▪ muscles contain proteins that are responsible for muscle contraction. ❑ Enzyme - a protein catalyst that increases the rate at which a chemical reaction proceeds without the enzyme being permanently changed 44 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Figure 2.16c Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Figure 2.16ab Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Functions of Proteins Used to make skin, hair, nails, muscles Hemoglobin = oxygen transport protein, ("globin") Act as enzymes Immune system functions Muscle contractions (actin and myosin) Part of cell membrane 47 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  Organic Molecules Nucleic Acids D. Nucleic Acids ❑ are large molecules composed of carbon, hydrogen, oxygen, nitrogen, and phosphorus (C, H, O, N, P ) ❑ basic building blocks : Nucleotides ❑ Deoxyribonucleic acid (DNA) ✓ is the genetic material of cells, and copies of DNA are transferred from one generation of cells to the next. ✓ contains the information that determines the structure of proteins ❑ Ribonucleic acid (RNA) is structurally related to DNA, and three types of RNA also play important roles in gene expression or protein synthesis 48 Copyright © McGraw-Hill Education. Permission required for reproduction or display. Copyright © McGraw-Hill Education. Permission required for reproduction or display.