Exploring Atoms and Chemical Bonds: Understanding the Basics of Chemistry

1. Chapter 2: Chemistry Part 1 • Atoms • Chemical Bonds • Acids, Bases and the pH Scale 2-2

2. Elements • The most fundamental different types of material that things (e.g., the body) are made of are called elements. • Examples: Gold, iron, sodium, carbon, helium, potassium • Different elements have different properties (behaviors)

3. Table of known elements

5. Structure of Atoms • The smallest chemical units • Composed of 3 particles: • Protons: + charged • Neutrons: neutral • Electrons: - charged • Regions of Atoms: • Nucleus: • in center • contains protons & neutrons • Electron Cloud organized into Shells/Orbitals: • External to the nucleus 2-4

6. What makes different types of atoms different? Different numbers of protons and electrons 2-4

7. Electron Shells • Electron shells/orbitals • Surround the nucleus • 1st shell: up to 2 e- • 2nd shell: up to 8 e- • 3rd shell: up to 8 e- 2-6

8. Atoms - Electron Shells continued • Valence shell: Outermost e- shell • Valence electrons: e- in the outermost shell • participate in chemical reactions/form bonds • e- lost, gained, or shared to fill/empty the valence shell • Basis of chemical bonding 2-7

9. Atoms - Isotopes • Are different forms of same atom • Number of protons and electrons are same • Number of neutrons different • Different isotopes are detectable and sometime emit radiation and can be used in imaging, research, and treatment of disease e.g., Carbon Isotopes Carbon 12: 6 p+, 6 e-, 6 n Carbon 13: 6 p+, 6 e-, 7 n Carbon 14 : 6 p+, 6 e-, 8 n * Carbon 12 is most common stable form, carbon 13 is naturally occurring and makes up just over 1%, C14 is radioactive 2-8

10. Number of valance electrons

11. Ion Formation • Electrons are transferred • Lost & gained • e- transfer creates ions • cation (+ charged ) • anion (- charged) 11 e- 17 e- 10 e- 18 e- 2-13

12. Examples of Common ions and their Functions:

13. Relevance of Isotopes • Imaging: using radioactive (low risk) isotope (tracers/radiolabelling) injected into the body to create anatomical images • E.g.NMR: imaging using isotopes • Clearance/processing: injecting molecules with uncommon isotopes to see how the molecule is used or how fast is it is processed. • Specific isotopes connected to specific molecules can test/image specific tissues, organs, or processes • E.g. iodine for thyroid, cobalt for intestinal absorption of B vitamins • Radiopharmaceutics: using radioactive isotopes inside the body to destroy tumors or other abnormal tissue • Radioactive decay/dating: not very common in A&P but used to date very old things.

14. Chemical Bonds • Atoms join together through chemically bonding: • Creates molecules • Based on valence e- (number and shell) • Atoms “want” valence shell to be empty or full • Lose, gain, or share e- to empty of fill their valance shell 2-10

15. Chemical Bond Overview • Covalent • Non-polar • Polar • Ionic • hydrogen

16. Ionic Bonding • Ions, + cation & - anion, are attracted to one another • Opposite charges attract 2-14

17. Covalent Bonds • Valence electrons are shared • Single, double, triple 2-11

18. Type of Covalent Bonds • Nonpolar: electrons shared equally • e.g. in H2 or O2 • Polar: electrons shared unequally • Creates molecules with + and – regions (poles) • O, N, P commonly create • e.g., water/H20 2-11

19. Free Radicles • Free radicals are atoms/molecules that have single unpaired electrons in valance shells. • Highly reactive—damaging • Free radical theory of aging • The/a hypothetical reason why anti-oxidants are good for your health

20. Ions, Polar Molecules and Water • Ions dissociate (atoms unbind) when mixed in H2O • Polar molecules freely separate from one another and mix with water. • H2O forms hydration spheres around ions and polar molecules 2-14

22. Hydrophobic v. Hydrophilic • Hydrophilic : soluble in water (interact w/ water) • Polar or charged • e.g. ions, glucose, some amino acids • Form hydration spheres • Hydrophobic : not soluble in water (lipid soluble) • Nonpolar • e.g., fats, oils, cholesterol (lipids) • cannot form hydration spheres 2-15

23. Polar (and charged) Water soluble Hydrophilic nonpolar Not water soluble (i.e., lipid soluble) Hydrophobic

24. Hydrogen Bonds • Attraction between a H and a (partially) negatively charged atom • Oxygen, Nitrogen • H+ is part of a polar bond. • e.g., between adjacent H20s 2-16

25. Hydrogen Bonds Hydrogen bond can form between two different molecules: this creates an attraction between the molecules that causes them to want to “hold onto each other” does not combine the two molecules to create a new molecule Within a molecule: causes the molecule to bend and twist into a 3-dimensional shape 2-16

26. Properties of Water • Due to water molecules’ polarity and the H-bonds between water molecules • Water is an excellent solvent • Many molecules dissolve in water creating a solution • due to water’s polarity • Ability to absorb and retain heat (high heat capacity) • evaporation of water is an excellent cooler • excellent distributor of heat (via blood) • water has a high thermal inertia that stabilizes Tb • due to hydrogen bonds between water molecules • Surface tension • due to hydrogen bonds between water molecules 2-16

27. Acids and Bases • Acids release protons (H+ /hydrogen ion) in a solution • proton donor • Bases lower H+ levels of a solution (or generates OH-) • proton acceptor 2-18

28. pH Scale • pH scale runs from 0 to 14 (commonly) • Pure H2O = neutral: pH = 7 • H+ = to OH- • Acids have a pH < 7 (pH 0 - 7) • Acidic • More H+ than pure water • Bases have a pH > 7 (pH 7 - 14) • Basic/Alkaline • H+ < pure water • Acid and Basic can be used in a relative sense • E.g., 11 is more acidic then 13 even though 11 is in the basic end of the pH scale • Fill in: pH 5 is more ____ (acidic/basic) then pH 2. 2-19

29. pH Scale(technically not linear as show in diagram) 2-19

30. Neutral acidic H2CO3 + H2O  H++ HCO3- H2O H2O H2O H2O H2O H2O H2O H2O H2O H2O OH- H2O H2O H+ H2O H2O H+ OH- H2O H+ H+ H2O H+ + OH- OH- HCO3- H2O H+ HCO3- H+ OH-

31. Neutral Basic 1) NaOH + H2O  Na + OH- 2) OH- + H+ H20 H2O H2O H2O H2O H2O H2O H2O H2O H2O H2O H2O H2O H+ H+ H2O H2O H2O H+ + OH- OH- OH- H2O H2O OH- H+ H+ OH- OH- Na+ H2O

32. Blood pH • Normal range of pH is 7.35 – 7.45 • Maintained by buffering action • Acidosis occurs if pH < 7.35 • Alkalosis occurs if pH > 7.45 Loss of homeostasis 2-22

33. Buffers • Reduce changes in pH • combining with or release H+s • Buffers stabilize pH/minimize pH changes • e.g. the bicarbonate buffer system in blood: H20 + C02 H2C03 H+ + HC03- • Too acidic – too many H+ H+ + HC03- H2C03 • This removes H+, reducing acidity • Too alkaline (basic) – too few H+ H2C03 H+ + HC03- This adds H+, reducing alkalinity 2-21

34. H + H2O HO Synthesis Reactions • smaller molecules  larger molecules • creates a water molecule as it adds two other molecules together • synthesis = dehydration synthesis (condensation) = anabolism +

35. Chemical Reactions: • Synthesis = building (adding together) • Dehydration Synthesis = adds molecules and creates water Example above two monosaccharides joined this way make a disaccharide

36. Dehydration Synthesis /Condensation Splits water out of 2 monosaccharides An H+ and OH- removed H+ + OH- = H2O Example: two monosaccharides joined this way make a disaccharide

37. H + H2O HO Decomposition Reactions • large molecules  smaller molecules • a pre-existing water is split into H + OH which are added to the fragments of the original molecule • decomposition = hydrolysis = catabolism +

38. Chemical Reactions: • Hydro + Lysis Breakdown/separate Breaking water apart water

39. Hydrolysis Water and another molecule are split H2O is split, H+ added to one monosaccharide, OH- to other Example, Polysaccharide hydrolyzed into disaccharides, then to monosaccharides 2-33

40. H + H2O HO Reversible Rnx +