Life, Chemistry and Water

1. Life, Chemistry and Water

2. JBS Haldane – What is Life? • I am not going to answer this question. In fact, I doubt if it will ever be possible to give a full answer, because we know what it feels like to be alive, just as we know what redness, or pain, or effort are. So we cannot describe them in terms of anything else.

3. JBS Haldane – What is Life? • …life consists of chemical processes.     This pattern has special properties. It begets a similar pattern, as a flame does, but it regulates itself as a flame does not …. So when we have said that life is a pattern of chemical processes, we have said something true and important.     But to suppose that one can describe life fully on these lines is to attempt to reduce it to mechanism, which I believe to be impossible. On the other hand, to say that life does not consist of chemical processes is to my mind as futile and untrue as to say that poetry does not consist of words.

4. Overarching theme of biology • At the molecular level, biology is based on three dimensional interactions of complementary surfaces • Structure dictates function

6. Example • There is a human version of the D crystallin protein that is known to be involved in cataract formation in the eye. Cataracts form when several proteins in the eye bond to one another and become a very large insoluble multi-protein complex.

7. Example • There is a point mutation that occurs in some children that changes the arginine normally found at position 14 to a cysteine causing them to develop cataracts. The overall 3-D structure of the protein remains the same despite this substitution. • Structure

8. 25 Key Elements in Living Organisms • 96% of the weight of living organisms = carbon, hydrogen, oxygen, and nitrogen • 4% = calcium, phosphorus, potassium, sulfur, sodium, chlorine, and magnesium • 0.01% = nine trace elementsvital to biological functions

9. Proportions of Elements Fig. 2-2, p. 23

10. Atoms and Molecules • Atoms • Smallest units of elements • Molecules • Formed from atoms • Combined in fixed numbers and ratios • Compounds • Molecules with different component atoms

11. Think/Pair/Share • What are the characteristics of the particles that compose atoms?

12. Atomic Structure • Atomic nucleus contains protons and neutrons • Electrons travel around nucleus in orbitals

13. Atomic Nucleus • Protons • Positively charged • Atomic number • Number of protons in an element • Neutrons • Uncharged

14. Atomic Mass • Atomic mass = mass of protons + neutrons (electrons have insignificant mass) • Proton = 1 dalton = 1.66 X 10-24 grams • Neutron = 1 dalton

15. Periodic table • link

16. Isotopes • Atoms of an element with differing numbers of neutrons • Differ in physical but not chemical properties Fig. 2-4, p. 24

17. Isotopes of carbon 12C 6 protons 6 neutrons atomic number = 6 mass number = 12 13C 6 protons 7 neutrons atomic number = 6 mass number = 13 14C 6 protons 8 neutrons atomic number = 6 mass number = 14 Fig. 2-4b, p. 24

18. Radiocarbon dating • The Dating Game

19. Radioisotopes • Some isotope nuclei are unstable and break down (decay) • Release particles of matter and energy (radioactivity) • Radioisotopes decay at a steady rate • Used to estimate the age of organic material, rocks, fossils • Used as tracers to label molecules in chemical reactions

20. Radioisotopes used in biological research

21. Medically useful radioisotopes • Iodine-123 • Tracer • Absorbed by the thyroid gland and used to produce thyroxine • Location in body readily detected • Short half-lives • Non-toxic

22. Medically useful radioisotopes • Idodine-131 • Used therapeutically to treat thyroid cancer and hyperthyroidishm

23. Electrons • Electron are negatively charged • Number of electrons = number of protons • Electron mass = 1/1800 dalton

24. Electron Orbitals • Electrons are found in regions of space called energy levels (shells) • Within each energy level, electrons are grouped into electron orbitals

25. Electron orbitals Animation: The shell model of electron distribution

26. Orbitals • s orbitals are spherical • p orbitals are propeller or dumbbell shaped • Each orbital can hold only 2 electrons • An atom with more than 2 electrons has more than 1 orbital

27. Atoms with progressively more electrons have orbitals within electron shells that are at greater and greater distances from the center of the nucleus • 1st shell - 1 spherical orbital (1s) - holds 2 electrons • 2nd shell - 1 spherical orbital (2s) and 3 dumbbell-shaped orbitals (2p) – can hold 4 pairs of electrons

29. Nitrogen example • A nitrogen atom has seven protons and seven electrons • 2 electrons fill 1st shell • 5 electrons in 2nd shell • 2 fill 2s orbital • 1 each in the 3p orbitals • Outer 2nd shell is not full • Electrons in the outer shell that are available to combine with other atoms are called the valence electrons

32. Periodic table • Organized by atomic number • Rows correspond to number of electron shells • Columns, from left to right, indicate the numbers of electrons in the outer shell • Similarities of elements within a column occur because they have the same number of electrons in their outer shells, and therefore they have similar chemical bonding properties

33. Electron Orbitals Fig. 2-6, p. 27

34. CHON shells Animation: Predicting the number of bonds of elements

35. Valence Electrons • If outermost energy level filled, atoms are stable and unreactive • Atoms tend to lose, gain, or share electrons to fill the outermost energy level • Leads to chemical bonds and forces that hold atoms together in a molecule

36. Atomic Bonds • Covalent Bonds • Noncovalent Bonds • Ionic • Hydrogen • Van der Waals

37. Bond types Animation: How atoms bond

38. Bond energies

39. Ions • Charged atoms • Cation: Positively charged ion • Anion: Negatively charged ion • Ionic Bond • Forms between atoms that gain or lose valence electrons completely

40. Ions • One atom loses an electron and becomes positively charged • Na+ :11 protons + 10 electrons • One atom gains an electron and becomes negatively charged • Cl– :17 protons + 18 electrons

41. Ionic interactions • Result from the attraction of a positively charged ion (cation) with a negatively charged ion (anion) • Ions surrounded by hydration shell

43. Ionic Bond Fig. 2-7, p. 28

44. Ionic Bond • Exerts attractive force over greater distance than other bonds • Attractive force extends in all directions • Varies in strength depending on presence of other charged substances

45. Covalent bonds • Pairs of electrons shared between atoms • Stable under most conditions • Bond energy C-C 83kcal/mole; double bond about twice as much energy needed to break the bonds

46. Valence for CHON

48. Covalent Bond • Two atoms share a pair of electrons • Shared orbitals occur at discrete angles and directions

49. Covalent Bonds Fig. 2-8, p. 30

50. Unequal Electron Sharing • Electronegativity • Measure of atom’s attractions for electrons shared in a chemical bond • Nonpolar covalent bond • Electrons shared equally • Polar covalent bond • Electrons shared unequally