BIO 168 CHEMICAL LEVEL OF ORGANIZATION CHAPTER 2

1. BIO 168 CHEMICAL LEVEL OF ORGANIZATION CHAPTER 2 created by Dr. C. Morgan

2. TOPICS Introduction Atoms, Molecules, and Bonds Chemical Notation Chemical Reactions Inorganic Compounds Organic Compounds Chemicals and Living Cells

3. Introduction Objectives Discuss the composition of matter. Learn why you need to understand some basic chemistry. Learn about the relationship between chemical reactions and living systems.

4. Introduction For all practical purposes, we may say that everything is composed of chemicals—atoms and molecules. Therefore, to understand living systems, you must understand some basic chemistry. The structure and function of living systems is a constant interplay of finely tuned chemical reactions. You will learn about the nature of chemicals, how they react, and their role in the structure and function of living things.

5. TOPICS Introduction Atoms, Molecules, and Bonds Chemical Notation Chemical Reactions Inorganic Compounds Organic Compounds Chemicals and Living Cells

6. Atoms and Molecules Objectives Define matter and know its three states Learn the structure of an atom Distinguish between atomic number, atomic weight, and molecular weight Define isotope Understand that electrons have energy and are in motion Learn the importance of electrons in chemical reactions Understand the formation of chemical bonds

7. Atoms and Molecules Matter By definition, matter is anything that occupies a space and has mass (on earth mass = weight). Matter exists in 3 states, gas, liquid, or solid. Matter is made up of materials that are known as elements which cannot be further broken down by ordinary means. Appendix II shows the Periodic Chart of the Elements (many should be familiar to you). TABLE 1 in your text lists the main elements in your body along with their abbreviation and significance. O, C, H, N, Ca are the 5 body elements in greatest %.

8. Atoms and Molecules (cont) Atomic Structure Nucleus Protons + Neutrons Protons & neutrons have mass + + + Electrons In motion Electrons have almost zero mass electron cloud Fig. 2 b

9. Atoms and Molecules (cont) The atomic number of an atom = its number of protons. The mass number = number of protons + neutrons. The atomic weight = average number of protons + neutrons in atoms of an element including isotopes. An isotope is an element that has atoms with a different number of neutrons from the most commonly occurring type of that atom under consideration. For example: carbon (C) usually has 6 neutrons but some isotopes of carbon have 7 or 8 neutrons making the atomic weight of carbon 12.01.

10. Atoms and Molecules (cont) Electrons and electron shells Remember forever, only electrons enter into chemical reactions. Atoms are electrically neutral because they have the same number of protons (+) and electrons (–). Electrons have energy and are in motion in specific orbitals or electron shells around the nucleus. Atoms” try” to become stable but can do so only if they have a full outermost electron shell. It is the outermost shell electrons that react and determine the chemical properties of an atom.

11. Atoms and Molecules (cont) Electrons and electron shells (cont) Fig. 2

12. Atoms and Molecules (cont) Electrons and electron shells (cont) The first shell holds 2 electrons, the second 8, and the outermost shell holds 8. Atoms with full outer shells are inert (do not react). Atoms lose, gain, or share electrons in order to become stable with a full outermost electron shell. This process of atoms losing, gaining, or sharing electrons causes chemical reactions. When atoms lose or gain electrons, their electrical charge balance is upset causing an atom to have more positive or negative charge.

13. Atoms and Molecules (cont) Electrons and electron shells (cont) + Is this atom stable? +

14. Atoms and Molecules (cont) Electrons and electron shells (cont) Is this atom stable? Fig. 2 d

15. Atoms and Molecules (cont) Chemical bonding The energy and electrical charges associated with electrons that participate in chemical reactions produces relationships between atoms known as chemical bonds. Chemical bonds contain energy. A molecule consists of of a chemical structure containing more than one atom. Its molecular weight = its atomic weight of all atoms expressed in grams. A compound consists of a molecule with more than one kind of atom and new properties (i.e., water).

16. Atoms and Molecules (cont) Ionic chemical bonds Atoms that have a net positive or negative charge are called ions which are highly reactive. Cations have a net positive charge. Anions have a net negative charge. Ions present in body fluids are very important in cell function and water balance. Atoms (or molecules) with positive and negative charges are attracted to each other and will stay together to form an ionic bond which is strong. For example: table salt is sodium chloride formed by ionic bonds between adjacent sodium and chloride atoms (ions).

17. Atoms and Molecules (cont) Ionic chemical bonds (cont) ? To become stable, Na must ____ one electron. ? To become stable, Cl must ____ one electron. NaCl Fig. 3 a

18. Atoms and Molecules (cont) Ionic chemical bonds (cont) NaCl Fig. 3 b

19. Atoms and Molecules (cont) Chemical covalent bonds Sharing electrons is another option for atoms to complete their outermost electron shell. At any moment in time, each atom may “claim” the electron(s) belonging to the other atom because shared electrons spend time orbiting around both nuclei. If sharing is equal, this forms a nonpolarcovalent bond between participating atoms. If only one electron pair is shared between two atoms, it is a single covalent bond; two pairs shared = double covalent bond; three pairs shared = triple bond. Covalent bonds are strong bonds.

20. Atoms and Molecules (cont) Covalent bonds (cont) free radicals are highly reactive free radical Fig. 4

21. Atoms and Molecules (cont) Polar covalent bonds Sometimes shared electrons spend more time around one atom’s nucleus than around the other one(s) nucleus (unequal sharing). This causes a slight charge to be established on the atoms participating in the covalent bonds. The atom where shared electrons spend relatively more time becomes slightly negative; the atom(s) deprived of their electrons for relatively more time become slightly positive. This produces a polar covalent bond. There are positive and negative poles on the “polar” molecule.

22. Atoms and Molecules (cont) Polar covalent bonds (cont) WATER the most famous polar molecule Fig. 5

23. Atoms and Molecules (cont) Hydrogen bonds There are several weaker chemical bonds that help hold adjacent molecules together. Hydrogen bonds are the most important weak bonds. To test the strength of hydrogen bonds, you may see a needle float horizontally on the surface of water. However, the needle tip may easily pierce the surface. The unique properties of water are associated with the hydrogen bonds between adjacent water molecules. Water is the most abundant molecule in the body.

24. Atoms and Molecules (cont) Hydrogen bonds (cont) surface tension needle Try this! Fig. 6

25. TOPICS Introduction Atoms, Molecules, and Bonds Chemical Notation Chemical Reactions Inorganic Compounds Organic Compounds Chemicals and Living Cells

26. Chemical Notation Objectives Learn the rules pertaining to chemical notation Learn how to write formulae in chemical notation Recognize a balanced chemical equation Distinguish between reactants and products of a chemical reaction written in chemical notation Recognize ionic forms of atoms written in chemical notation

27. Chemical Notation • TABLE 2 (focus) gives the rules of chemical notation. • Abbreviations: H = one atom of hydrogen • 2 H = two individual atoms of hydrogen • H2 = a molecule of hydrogen (H–H) • Reactants 2H + O  H2O Products Atoms on the left = atoms on the right A Balanced Chemical Equation • Na+ = sodium ion that lost one electron Cl– = chlorine ion that gained one electron Ca2+ = calcium ion that lost two electrons

28. TOPICS Introduction Atoms, Molecules, and Bonds Chemical Notation Chemical Reactions Inorganic Compounds Organic Compounds Chemicals and Living Cells

29. Chemical Reactions Objectives Relate chemical reactions with metabolism Define work and define energy Distinguish between kinetic and potential energy Recognize the types of chemical reactions Distinguish between catabolism and anabolism Learn the importance of reversible reactions Discuss the role of enzymes in metabolic reactions Distinguish between acids and bases Define pH; learn the pH scale and normal blood pH Learn about the role of buffers in maintaining pH

30. Chemical Reactions Every living cell has thousands of chemical reactions occurring simultaneously at all times. Some reactions are breaking molecules while others are building molecules. In chemical reactions, atoms are rearranged. The sum of all chemical reactions that sustain life is called metabolism. Because energy is associated with electrons which form chemical bonds, metabolism involves releasing, storing, and using energy.

31. Chemical Reactions (cont) Energy concepts Work is movement or events that cause a change in the physical structure of matter. Energy is the capacity to do work. Kinetic energy is the energy associated with motion. Potential energy is stored (i.e., water behind a dam). Energy may be changed from potential to kinetic as when chemical energy is used to contract muscle fibers. Conversions are not 100% efficient so some energy is lost as heat.

32. Chemical Reactions (cont) Types of Chemical Reactions Decomposition reactions: AB  A + B Catabolic reactions are metabolic reactions that breakdown molecules to harvest the potential energy in their chemical bonds. Synthesis reactions: A + B  AB Anabolic reactions are metabolic reactions that make new complex molecules from small molecular units such as assembling hair protein from individual amino acids. Exchange reactions: AB + CD  AD + BC Exergonic reactions release energy; endergonic reactions require an input of energy to make them happen.

33. Chemical Reactions (cont) Types of Chemical Reactions (cont) Reversible reactions: A + B  AB Notice that both decomposition and synthesis occur. Usually these reactions occur at rates that represent an equilibrium or balance. However, if the product is continuously used up by a cell, in which direction will the reaction proceed? Many important reactions in the body are reversible such as hemoglobin loading oxygen in the lungs and then giving it up for cellular use.

34. Chemical Reactions (cont) Enzymes and Chemical Reactions Atoms and molecules are in constant motion in a liquid. In order to react, atoms or molecules must make contact. In living systems, without the help of special proteins called enzymes, reactions would proceed too slowly to sustain life. An enzyme decreases the amount of energy (= activation energy) that is needed to get a reaction to occur. Enzymes cause reactions to proceed faster. Metabolic pathways utilize a specific enzyme for each step (chemical reaction) in the pathway. A B C D enzyme 3 enzyme 1 enzyme 2

35. Chemical Reactions (cont) Enzymes and Chemical Reactions (cont) activation energy decreases in presence of enzyme A + B AB enzyme Fig. 7

36. TOPICS Introduction Atoms, Molecules, and Bonds Chemical Notation Chemical Reactions Inorganic Compounds Organic Compounds Chemicals and Living Cells

37. Inorganic Compounds Objectives Distinguish between inorganic and organic compounds. Describe nutrients and metabolites List the three most important inorganic compounds in the body. Learn why water is important in the human body. Define a solution and the ionization process. Discuss pH, the pH scale, and buffering. Learn some inorganic acids found in the body. Define a salt and an electrolyte; learn about importance of electrolytes in body fluids.

38. Inorganic Compounds Nutrients are the essential chemical materials that you normally obtain from your diet. Metabolites include all molecules synthesized or broken down during the chemical reactions in your body. Nutrients and metabolites fall into two broad categories, inorganic and organic compounds. The minerals your body needs are inorganic compounds. The energy sources and vitamins your body needs are organic compounds.

39. Inorganic Compounds (cont) Inorganic compounds are small molecules that do not contain C and H atoms as the main ones with one exception, carbon dioxide (CO2) which is considered to be inorganic. CO2 is plentiful in the body because it is a waste product of cellular respiration, a process that makes a widely utilizable form of energy for cellular work. You get rid of CO2 when you exhale air from your lungs. The most plentiful inorganic substances in the body besides CO2 are oxygen, water, some acids and bases, and some salts.

40. Inorganic Compounds (cont) In contrast to inorganic compounds, organic compounds have carbon as their main atom, often occurring as chains of carbon atoms. Organic compounds are usually larger and more complex than inorganic compounds. Carbon dioxide and oxygen are inorganic substances that exist as gases in the body. What kind of chemical bonds hold the atoms of these molecules together?

41. Inorganic Compounds (cont) Water Water, the most important inorganic substance in your body, makes up about 2/3 of your weight and its balance is critically important. The polar covalent bond of water makes each molecule have a slight negative charge on the oxygen side and a slight positive charge on the hydrogen side. Water is a polar molecule and will react with other molecules that are polar or charged. Ionic compounds often break apart when placed in water, a process called ionization because ions are formed (like dissolving table salt in water).

42. Inorganic Compounds (cont) Water (cont) Table salt releases Na+ and Cl– which represent the largest number of ion types in body fluids bathing cells. Also, when ionized, salts will conduct an electrical current so they are called electrolytes. Every heart beat, every nerve impulse, and every muscle contraction in your body depends on the presence of certain electrolytes, especially K+ and Na+. TABLE 3 lists the most important electrolytes in the body.

43. Inorganic Compounds (cont) Water (cont) Many organic substances have polar covalent bonds so they will also dissolve in water. Substances that readily react with water are hydrophilic. Substances that do not react with water are hydrophobic. Oil and water do not mix because oil is hydrophobic. Oils and fats are nonpolar (lack polar covalent bonds) so hydration spheres do not form to dissolve them. Several more characteristics of water are due to its polarity and hydrogen bonding.

44. Inorganic Compounds (cont) Water (cont) (1) Water is an excellent solvent because it dissolves many kinds of inorganic and organic substances. Hydration Many substances release ions when they dissolve. Ions form bonds with water molecules. Fig. 8

45. Inorganic Compounds (cont) Water (cont) (2) Metabolic reactions occur in water as water is added during catabolic reactions (hydrolysis) and is removed during dehydration synthesis. (3) Water also resists changes in temperature or in other words, it has a high heat capacity. Body temperature may be maintained at minimal energy costs and chemical reactions will occur at predictable rates in the cells and body fluids. (4) Water is a good lubricant.

46. Inorganic Compounds (cont) Water (cont) A solution consists of a solvent (such as water) and solute(s) which are molecules or atoms of substances that are dissolved in the solvent. Solute concentrations of important electrolytes are closely followed in ill patients. Concentrations are usually reported in moles per liter (m / l) or millimoles per liter (mm / l) of solution. Other concentration expressions are also used. A mole is a sample that has the weight in grams equal to the elements atomic or molecular weight of a substance. g/l, g/dl, mg/l, mg/dl are used to express concentration.

47. Inorganic Compounds (cont) Water (cont) Body fluids are mostly water. Fluids in tissues, blood, lymph, and within cells contain large amounts of protein or other large molecules. This solution is called a colloid. Liquid gelatin is a colloid. A suspension consists of particles large enough to settle out due to gravity. Blood is a suspension because red blood cells will settle out of the plasma (liquid portion) if the clotting factors are removed.

48. Inorganic Compounds (cont) Hydrogen ions and pH Because H+ are so reactive and we have many of them in our body fluids, their concentration is of special concern and must be regulated. The concentration of H+ is measured in pH units, each a 10X difference in concentration. The pH values range from 0 to14 with 0 being the most acidic and 14 the least acidic (most basic). pH 7 is considered neutral (blood is about 7.4) pHs above 7 are basic and those below are acidic. If the pH of body fluids is not maintained within a narrow range, cells will not function properly and will die which may eventually lead to organismic death.

49. Inorganic Compounds (cont) pH scale basic or alkaline acidic Fig. 9 49

50. Inorganic Compounds (cont) Buffers and pH control The body maintains pH by the use of buffers which are substances that may donate or remove H+ from fluids. All body fluids contains some buffers. Most body buffers participate in reversible reactions. They may take up or supply H+ to solution. You may take an antacid tablet or liquid to settle an overly acidic stomach to relieve “heartburn”. The antacids remove excess H+ from stomach fluid so they are acting as a buffer.