Small Molecules and the Chemistry of Life

1. Small Molecules and the Chemistry of Life

2. 2 Small Molecules and the Chemistry of Life • 2.1 How Does Atomic Structure Explain the Properties of Matter? • 2.2 How Do Atoms Bond to Form Molecules? • 2.3 How Do Atoms Change Partners in Chemical Reactions? • 2.4 What Makes Water So Important for Life?

3. 2 Small Molecules and the Chemistry of Life Elements have naturally occurring variants called isotopes, which have slightly different weights. Opening Question: Can isotope analysis of water be used to detect climate change?

4. Figure 2.1 The Helium Atom • All matter is composed of atoms.

5. 2.1 How Does Atomic Structure Explain the Properties of Matter? • Electrons—negligible mass; negative charge • In the nucleus: • Protons—have mass; positive charge • Neutrons—have mass; no charge

6. 2.1 How Does Atomic Structure Explain the Properties of Matter? • Atoms have volume and mass. • Mass of one proton or one neutron = • 1 atomic mass unit (amu),or 1 dalton, • or 1.7 × 10–24 grams. • Mass of one electron = 9 × 10–28 • (usually ignored).

7. 2.1 How Does Atomic Structure Explain the Properties of Matter? • Element: pure substance containing only one kind of atom. • The number of protons identifies an element. • Number of protons = atomic number.

8. 2.1 How Does Atomic Structure Explain the Properties of Matter? • The number of protons and electrons determines how an element behaves in chemical reactions. • Elements are arranged in the periodic table.

9. Figure 2.2 The Periodic Table (Part 1)

10. Figure 2.2 The Periodic Table (Part 2)

11. 2.1 How Does Atomic Structure Explain the Properties of Matter? • All elements except hydrogen have one or more neutrons. • Mass number = number of protons + number of neutrons. • Mass number = mass of atom in daltons.

12. 2.1 How Does Atomic Structure Explain the Properties of Matter? • Isotopes: forms of an element with different numbers of neutrons, and thus different mass numbers. • Example: • 12C has 6 neutrons • 13C has 7 neutrons • 14C has 8 neutrons

13. 2.1 How Does Atomic Structure Explain the Properties of Matter? • The isotopes of some elements have special names:

14. 2.1 How Does Atomic Structure Explain the Properties of Matter? • Atomic weight (relative atomic mass): average of mass numbers of isotopes in their normally occurring proportions. • Atomic weight of hydrogen = 1.0079 • Given as a range = 1.00784 – 1.00811

15. 2.1 How Does Atomic Structure Explain the Properties of Matter? • Some isotopes are unstable: • Radioisotopes give off energy in the form of alpha, beta, and gamma radiation from the nucleus. • This radioactive decay transforms the atom, sometimes resulting in a change in the number of protons.

16. 2.1 How Does Atomic Structure Explain the Properties of Matter? • The radiation can be used to detect the presence of radioisotopes. • Radioisotopes can be incorporated into molecules to act as a tag or label. • Molecule: stable association of atoms.

17. Figure 2.3 Tagging the Brain

18. 2.1 How Does Atomic Structure Explain the Properties of Matter? • Radioisotopes are useful in research and in medicine, but radiation can damage cells and tissues. • Radiation is sometimes used to treat cancer.

19. 2.1 How Does Atomic Structure Explain the Properties of Matter? • The number of electrons determines how atoms will interact. • Chemical reactions involve changes in the distribution of electrons between atoms.

20. 2.1 How Does Atomic Structure Explain the Properties of Matter? • Locations of electrons are described by orbitals. • Orbital: region where an electron is found at least 90% of the time. • Orbitals have characteristic shapes and orientations and can be occupied by two electrons. • Orbitals are filled in a specific sequence.

21. Figure 2.4 Electron Shells and Orbitals

22. 2.1 How Does Atomic Structure Explain the Properties of Matter? • Orbitals occur in a series called electron shells, or energy levels. • First shell: one s orbital (holds 2 electrons). • Second shell: 1 s and 3 p orbitals (holds 8 electrons). • Additional shells: 4 orbitals (each holds 8 electrons).

23. 2.1 How Does Atomic Structure Explain the Properties of Matter? • The outermost electron shell (valence shell) determines how the atom behaves. • If the outermost shell is full, the atom is stable; it won’t react with other atoms. • Reactive atoms have unpaired electrons in their outermost shell.

24. Figure 2.5 Electron Shells Determine the Reactivity of Atoms

25. 2.1 How Does Atomic Structure Explain the Properties of Matter? • Reactive atoms can share electrons, or lose or gain electrons, resulting in atoms being bonded together to form molecules. • Octet rule: tendency of atoms to form stable molecules resulting in 8 electrons in their outermost shells.

26. 2.2 How Do Atoms Bond to Form Molecules? • Chemical bond: the attractive force that links atoms together to form molecules. • There are several kinds of chemical bonds.

27. Table 2.1

28. 2.2 How Do Atoms Bond to Form Molecules? • Covalent bonds: atoms share one or more pairs of electrons so that the outer shells are filled.

29. Figure 2.6 Electrons Are Shared in Covalent Bonds

30. 2.2 How Do Atoms Bond to Form Molecules? • Compound: a molecule made up of two or more elements bonded together in a fixed ratio. • Example: H2O • The molecular weight of a compound is the sum of the atomic weights of all atoms in the molecule.

31. Table 2.2

32. 2.2 How Do Atoms Bond to Form Molecules? • Covalent bonds are very strong—a lot of energy is required to break them. • At temperatures in which life exists, the covalent bonds of biological molecules are very stable (although changes can still occur).

33. 2.2 How Do Atoms Bond to Form Molecules? • Orientation of bonds: • The length, angle, and direction of bonds between any two elements are always the same. • Example: Methane always forms a tetrahedron.

34. Figure 2.7 Covalent Bonding Can Form Compounds

35. 2.2 How Do Atoms Bond to Form Molecules? • The shape of molecules can change as atoms rotate around a covalent bond: • In-text art, pg 7, bottom

36. 2.2 How Do Atoms Bond to Form Molecules? N N C H C C • Covalent bonds can be: • Single, sharing 1 pair of electrons • Double, sharing 2 pairs of electrons • Triple, sharing 3 pairs of electrons

37. 2.2 How Do Atoms Bond to Form Molecules? • Sharing of electrons in a covalent bond is not always equal. • Electronegativity: the attractive force that an atomic nucleus exerts on electrons. • Electronegativity depends on the number of protons and the distance between the nucleus and electrons.

38. Table 2.3

39. 2.2 How Do Atoms Bond to Form Molecules? • Polar covalent bond: electrons are drawn to one nucleus more than the other because that atom has greater electronegativity. • Nonpolar covalent bond: electrons are shared equally (atoms have similar electronegativity).

40. Figure 2.8 Water’s Covalent Bonds Are Polar

41. 2.2 How Do Atoms Bond to Form Molecules? • Because of unequal sharing, a molecule with a polar bond has a slightly negative charge on one end and a slightly positive charge on the other. • The partial charges result in polar molecules or polar regions of large molecules.

42. 2.2 How Do Atoms Bond to Form Molecules? • When one atom is much more electronegative than the other, a complete transfer of electrons may occur. • This results in two ions with full outer shells.

43. Figure 2.9 Formation of Sodium and Chloride Ions

44. 2.2 How Do Atoms Bond to Form Molecules? • Ions: electrically charged particles formed when atoms lose or gain electrons. • Cations—positive • Anions—negative • Complex ions: groups of covalently bonded atoms that carry a charge, e.g., NH4+ and SO42–.

45. 2.2 How Do Atoms Bond to Form Molecules? • Ionic attractions:bonds formed by the electrical attraction of positive and negative ions. • Salts are ionically bonded compounds.

46. 2.2 How Do Atoms Bond to Form Molecules? • In a solid, ions are close together and the ionic attractions are strong. • In water, the ions are far apart and the attraction is much weaker. • Ions can interact with polar molecules (e.g., salts dissolve in water).

47. Figure 2.10 Water Molecules Surround Ions

48. 2.2 How Do Atoms Bond to Form Molecules? • Hydrogen bonds: attraction between the δ–end of one molecule and the δ+ hydrogen end of another molecule. • Hydrogen bonds form between water molecules and are important in the structure of DNA and proteins.

49. Figure 2.11 Hydrogen Bonds Can Form between or within Molecules

50. 2.2 How Do Atoms Bond to Form Molecules? • Polar molecules that form hydrogen bonds with water are hydrophilic (“water-loving”). • Nonpolar molecules, such as hydrocarbons that interact with each other but not with water, are hydrophobic (“water-hating”).