The Chemical Context of Life Chapter 2

1. The Chemical Context of LifeChapter 2

2. Chemical Foundations of Biology • Matter consists of chemical elements • These elements may be pure or in compound form • 25 of the naturally occuring elements are essential for life • Carbon, Oxygen, Hydrogen & Nitrogen make up 96% of living matter • Phosphorous, Sulfur, Calcium and Potassium make up most of the other 4%

3. Osteoporotic Spongy Bone Normal Spongy Bone

4. Iodine Deficiency- Goiter

5. (a) Nitrogen deficiency (b) Iodine deficiency The effects of essential element deficiencies Figure 2.3

7. Atoms • Atoms = Protons + Neutrons + Electrons • Atomic Number = # of protons (= electrons in a neutral atom) • Atomic Mass = mass of protons + neutrons; measured in Daltons (Da) or a.m.u.’s; 1 proton’s mass = 1 Da • 6.02 X 1023 Da of atoms = 1.0 g of atoms

8. Isotopes • Atoms of same atomic # ( # protons) but different number of neutrons. • All belong to the same element; have similar chemical properties.

9. Applications of Isotopes • ½ of the amount of 14 C radioactively decays every 5,730 years. • Used in 14 C dating of materials such as fossils and rock. • Radiation treatment of cancer.

10. Electrons • Electrons are negatively charged atomic particles with almost no mass. • If the # of electrons = the # of protons in the nucleus, then the atom is neutral. • Electrons maintain an orbit around the nucleus because of their attraction to the positively charged protons in the nucleus. • Electron orbitals are only predictions of electron position around nucleus.

11. Ions • Ions – atoms in which # electrons in not equal to # of protons. • Atoms with net positive charge - cations (lose electrons). • Atoms with net negative charge - anions (gain electrons).

12. Figure 2.7A The electrons of an atom: • Differ in the amounts of potential energy they possess.

13. Third energy level (shell) Second energy level (shell) Energy absorbed First energy level (shell) Energy lost Atomic nucleus Figure 2.7B Energy levels are represented by electron shells

14. Electrons Determine the Chemical Nature of Atoms • Electrons have potential energy because of position- more energy further from nucleus; less energy closer to nucleus. • Electron’s distance from nucleus is related to the amount of potential energy it has.

15. Electron Configuration and Chemical Properties • The chemical behavior of an atom: • Is defined by its electron configuration and distribution

16. Helium 2He Atomic number 2 He 4.00 Hydrogen 1H Element symbol Atomic mass First shell Electron-shell diagram Beryllium 4Be Carbon 6C Oxygen 8O Neon 10Ne Lithium 3Li Boron 3B Nitrogen 7N Fluorine 9F Second shell Aluminum 13Al Chlorine 17Cl Argon 18Ar Sulfur 16S Sodium 11Na Magnesium 12Mg Silicon 14Si Phosphorus 15P Third shell Figure 2.8 The periodic table of the elements: • Shows the electron distribution for all the elements ( p.37)

17. Valence electrons: • Are those in the outermost, or valence shell. • Determine the chemical behavior of an atom. An orbital: • Is the three-dimensional space where an electron is found 90% of the time

18. Electron orbitals. Each orbital holds up to two electrons. x Y 1s orbital 2s orbital Three 2p orbitals 1s, 2s, and 2p orbitals Z Electron-shell diagrams. Each shell is shown with its maximum number of electrons, grouped in pairs. (b) Second shell (maximum 8 electrons) (a) First shell (maximum 2 electrons) ( Figure 2.9 • Each electron shell: • Consists of a specific number of orbitals.

19. Chemical Reactions • Energy is transferred through the movement of electrons from one atom to another. • Oxidation – the loss of electrons. • Reduction – the gain of electrons. • Always together in REDOX reactions.

20. Chemical Bonds • Groups of atoms stably held together – molecule. • Molecules of more than one element – compound.

21. + Sodium Chloride Sodium Chloride • A compound: • Is a substance consisting of two or more elements combined in a fixed ratio. • Has characteristics different from those of its elements. Figure 2.2

22. Molecular shape: • Determines how biological molecules recognize and respond to one another with specificity.

23. Nitrogen Carbon Hydrogen Sulfur Oxygen Natural Endorphin Morphine (a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds to receptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match. Natural endorphin Morphine Endorphin receptors Brain cell (b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine. Figure 2.17

24. Types of Chemical Bonds • Ionic Bonds – form crystals through electrical attractive forces between atoms of opposite charge. Example: • NaCl  Na + + Cl-

26. Na+ Cl– Figure 2.14 Ionic compounds • Are often called salts, which may form crystals.

27. Types of Chemical Bonds 2. Covalent Bonds – when two atoms share one or more pair of valence electrons. Maybe single, double or triple covalent bonds. Most common type of bond in organic compounds.

29. Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled more toward oxygen. d– This results in a partial negative charge on the oxygen and a partial positive charge on the hydrogens. O H H d+ d+ H2O In a polar covalent bond: • Atoms have differing electronegativities. • Share the electrons unequally. Figure 2.12

30. Molecular shape: • Determines how biological molecules recognize and respond to one another with specificity.

31. Ball-and-stick model Hybrid-orbital model (with ball-and-stick model superimposed) Space-filling model Unbonded Electron pair O O H H H H 104.5° Water (H2O) H H C C H H H H (b) Molecular shape models. Three models representing molecular shape are shown for two examples; water and methane. The positions of the hybrid orbital determine the shapes of the molecules H H Methane (CH4) Figure 2.16 (b)

32. van der Waal’s Forces (London’s) • Very weak, attractive forces between nonpolar atoms or molecules. • Only temporary and weak bonds.

33. Chemical Reactions • The formation and breaking of chemical bonds. ReactantsProducts A-B + C-D A-C + B + D

34. Rate of Chemical Reactions Influenced by: • Temperature – heating up reactions increases the rate. • Concentration of reactants and products – more reactants usually favor the forward and more products the reverse reaction. • Catalysts – most important in living cells; enzymes.

35. Atoms of Life • Only 11 of the 92 naturally occurring elements on earth are found in any major amounts in living organisms. • All 11 have atomic numbers less than 21; low atomic masses. • Is this an accident?

36. Element Oxygen Carbon Hydrogen Nitrogen Calcium Phosphorus Potassium Sulfur % of Human Body by Weight 65.0 18.5 9.5 3.3 1.5 1.0 0.4 0.3 Most Common Atoms in Human Body

37. Why HONC? • They all share electrons by making covalent bonds. • These bonds are weak enough to be broken at temperatures compatible with life. • 90% are O and H atoms; predominant role of water. • Many of the molecules they form are gases that are soluble in water