Chapter 2

1. Chapter 2 0 Essential Chemistry for Biology Modified by Dr. Par Mohammadian and Dr. Diane Livio

2. BASIC CHEMISTRY To understand biology, we have to know basic chemistry… why?

3. Matter: Elements and Compounds Matter is anything that occupies space and has mass. 3 physical states: solid, liquid, and gas. Composed of chemical elements Are you a matter?

4. Element: A substance that cannot be broken down into other substances by chemical reactions. Of the 92 naturally occurring elements, can you name at least 5? Where do we find all these elements written altogether?

5. Atomic number (number of protons) 6 C Element symbol Answer: periodic table 12 Mass number (number of protons plus neutrons) H He Be Li B N F Ne C O Na Si Mg Al P Cl Ar S Co K Cr Zn Ge Se Br V Fe Ni Ca Sc Ti Mn Cu Ga As Kr Ag Rb Y Zr Nb Mo Tc Ru Rh Pd Cd In Sn Sb Te I Xe Sr Ba La Re TI Pb Bi Rn Hf Ta Os Pt Au At Cs W Ir Hg Po Fr Bh Ds Ra Db Mt Rg Cn Ac Rf Hs Sg Nd Pm Dy Er Lu Pr Tb Ho Tm Yb Ce Sm Eu Gd Pa U Np Pu Cm Es Md No Th Am Bk Cf Fm Lr

6. In Chemistry, we learn about most of these elements but in Biology we focus on four elements Oxygen O Carbon C Hydrogen H Nitrogen N Why are these 4 elements important in Biology? What do you think?

7. Carbon (C): 18.5% Oxygen (O): 65.0% Calcium (Ca): 1.5% Phosphorus (P): 1.0% Potassium (K): 0.4% Sulfur (S): 0.3% Sodium (Na): 0.2% Chlorine (Cl): 0.2% Magnesium (Mg): 0.1% Hydrogen (H): 9.5% Trace elements: less than 0.01% Boron (B) Manganese (Mn) Chromium (Cr) Molybdenum (Mo) Nitrogen (N): 3.3% Cobalt (Co) Selenium (Se) Copper (Cu) Silicon (Si) Fluorine (F) Tin (Sn) Iodine (I) Vanadium (V) Iron (Fe) Zinc (Zn)

8. Iodine (I) Iodine deficiency causes goiter. Fluorine (F) -added to dental products and drinking water & helps to maintain healthy bones and teeth.

9. Elements can combine to form compounds. NaCl (sodium chloride, table salt) H2O (water)

10. Each element consists of one kind of atom. Atom: The smallest unit of matter • Atoms are composed of subatomic particles: • -protonis positively charged. • -electronis negatively charged. • -neutronis electrically neutral. Protons Nucleus Neutrons Electrons Nucleus 2e– Electron cloud protons and neutrons packed tightly into the nucleus.

11. Atomic number 6 Check out Appendix B C Element symbol 12 Mass number Elements differ in the number of subatomic particles in their atoms. • Atomic number (p): • # of protons - determines which element it is. • Atomicmass number (p+n): • Sum of the # of protons and neutrons in its nucleus

12. Isotopes have the same number of p & e but differ in their number of n.

13. Uses in research and medicine: Used in PET scans to diagnose heart disorders and some cancers Therapy to treat cancer and Graves’ disease Radioactive isotopes: Their nucleus decays spontaneously, giving off particles and energy.

14. Determine age of Earth, different strata, igneous rock around fossils: radiometric dating • Radioactive decay: loss of atomic particles from nucleus at a regular rate that is isotope-specific. Half-life: interval for half of particles to decay

15. 1986 Chernobyl nuclear accident Naturally occurring radon gas • Uncontrolled exposure to radioactive isotopes can harm living organisms by damaging DNA. 2011 Japan nuclear accident

16. Chemical Properties of Atoms Only electrons are directly involved in the chemical activity of an atom. Electrons orbit the nucleus of an atom in specific electron shells. First electron shell (can hold 2 electrons) Outer electron shell (can hold 8 electrons) Electron Carbon (C) Atomic number  6 Nitrogen (N) Atomic number  7 Oxygen (O) Atomic number  8 Hydrogen (H) Atomic number  1 • The number of electrons in the outermost shell determines the chemical properties of an atom.

17. First (innermost) shell = up to 2 electrons Second shell = up to 8 electrons. (Third shell = up to 8 electrons too…) Complete shells = the most stable Using a periodic table which elements are the most stable and why? How many electrons does each need to be stable? • O • C • N

18. Protons Electrons • Positive charge • Negative charge • Determine element • Participate in chemicalreactions • Outer-shell electronsdetermine chemicalbehavior Neutrons Nucleus • No charge • Consists of neutronsand protons Atom • Determine isotope

19. Chemical Bonding Atoms lose or gain electrons / share to complete their outer shells to turn stable. • When atoms lose and gain / share electrons in a chemical reaction they form chemical bonds. • In our class, we will focus on three chemical bonds: • Ionic • Covalent • Hydrogen

20. Ionic Bonds: When an atom loses or gains electrons atoms become electrically chargedcharged atoms are called ions Complete outer shells Na Cl– Cl Na Cl Chlorine atom Na Sodium atom Na Sodium ion Cl– Chloride ion Sodium chloride (NaCl)

21. Covalent bond: Two atoms shareone or more pairs of outer shell electrons; the strongest compared to ionic and hydrogen Electron configuration Space-filling model Structural formula Ball-and-stick model H H Hydrogen gas (H2) Covalent bonds hold atoms together in a molecule. O O Oxygen gas (O2) # of covalent bonds = # of additional e needed to fill its outer shell H C H H H Methane (CH4)

22. Hydrogen Bonds: Weak bonds between hydrogen and certain atoms, such as oxygen Example: Water (H2O) is a compound in which the electrons in its covalent bonds are not shared equally. => water is polar molecule – uneven distribution of charge (slightly ) (slightly ) H H O (slightly −)

23. The polarity of water => weak electrical attractions between neighboring water molecules. Hydrogen bond H H Slightly positive charge Slightly negative charge Covalent Bonds O

24. Chemical Reactions Cells constantly rearrange molecules by breaking chemical bonds & forming new ones in chemical reactions. + 2 H2 2 H2O O2 Hydrogen gas Oxygen gas Water Reactants Products

25. Water’s Life-Supporting Properties Life began in water 3.5bya (and stayed there 3by) The polarity of water and the hydrogen bonds explain most of water’s life-supporting properties: • Water molecules stick together. • Water has a strong resistance to change in temperature. • Frozen water floats. • Water is a common solvent for life.

26. Water molecules stick together: Cohesion • Cohesion due to H-bonds • Important for transporting water from roots to leaves Evaporation from the leaves What is the difference between adhesion and cohesion? Microscopic water-conducting tubes Cohesion due to hydrogen bonds between water molecules Flow of water Colorized SEM

27. The Cohesion of Water results in high surface tension. Surface tension: how difficult it is to stretch/break surface of a liquid

28. Water has a strong resistance to change in temperature because of hydrogen bonds. Water Moderates Temperature Water can store or release large amounts of heat while only changing a few degrees in temperature. Evaporative cooling occurs when a substance evaporates and the surface of the liquid remaining behind cools down. Why do you sweat after you run? Why is it worse to be sweating in a humid area?

29. Ice floats because it is less dense than liquid water. Frozen water floats Which is more dense: ice or liquid water? What is density? Hydrogen bond Liquid water Ice Hydrogen bonds constantly break and re-form. Stable hydrogen bonds hold molecules apart, making ice less dense than water. Why is it important in biology (for example, our environment) that the ice floats?

30. Definition: Solution is a liquid consisting of a mixture of two or more substances. The dissolving agent is the solvent. The dissolved substance is the solute. • Water is a common solvent for life Sodium ion in solution Chloride ion in solution Cl– Na • When water is the solvent, the result is an aqueoussolution. Na Cl– Salt crystal

31. Acids, Bases, and pH 14 Oven cleaner 13 OH− Household bleach OH− OH− OH− H What is an acid? How about a base? OH− 12 OH− H Household ammonia 11 Basic solution Lower H concentration Milk of magnesia 10 9 Seawater 8 H OH− Human blood H OH− What is the range of the pH scale? What pH range makes a solution acidic, neutral, or basic? 7 OH− Pure water [H]  [OH−] H H OH− Urine 6 Neutral solution 5 Black coffee Tomato juice 4 Greater H concentration Grapefruit juice, soft drink 3 H H Lemon juice, stomach acid 2 H OH− H OH− H H Battery acid 1 Acidic solution 0 pH scale

32. Definitions: • Acid: A chemical compound that releases H+ to a solution. • Base: A compound that accepts H+ and removes them from solution. • How do we know if something is acidic or basic? To describe the acidity of a solution, chemists use the pH scale. OH− H OH− OH− OH− H H H OH− OH− H H OH− OH− H OH− OH− OH− H H H H OH− H Acidic solution Neutral solution Basic solution What is the difference between the glasses shown above? Explain!

33. Do you know how to calculate pH, [H+], and [OH-]? pH means power of Hydrogen pH = - log [H+] pH + pOH = 14 Example: If pH=3 => [H+]=1 x 10-3 [OH-] = 1 x 10-11 OR If [H+]=0.01 = 1 x 10-2 => pH=2 & pOH=12 Practice at home: Come up with three different pH values and calculate [H+] & [OH-] and then come up with a number for [H+] and calculate pH & [OH-]!

34. What are Buffers? Substances that resist pH change. How do they do it? accept H+when they are in excess donate H+ ions when they are depleted (decreased). Think about it: Why do we need buffers?

35. About 25% the CO2 released by people is absorbed in the ocean ocean acidification!

36. Review • Define elements, compounds & trace elements & examples • Describe the structure of an atom (e, p, n). • Define atomic number & mass & examples – calculations • Define & know applications of isotopes • Distinguish between ionic, hydrogen, and covalent bonds (polar & non-polar) & examples • Define a chemical reaction & reactants & products & examples • Define properties of water (adhesion, cohesion, surface tension, regulation of temperature, density) • Define solution, solute, solvent • Explain the pH scale & define acid and base & buffer & examples • Define ocean acidification