1. Life and Chemistry: Small Molecules

2. Life and Chemistry: Small Molecules
Water and the Origin of Life’s Chemistry
Atoms: The Constituents of Matter
Chemical Bonds: Linking Atoms Together
Chemical Reactions: Atoms Change Partners
Water: Structure and Properties
Acids, Bases, and the pH Scale
Properties of Molecules

3. Water and the Origin of Life’s Chemistry
The earliest chemical signatures of life on Earth are about 4 billion years old.
The presence of water, possibly brought by comets striking the Earth, was critical in making conditions suitable for life.
Environmental conditions conducive to life evolved during the Hadean period.

4. Figure 2.1 A Geological Time Scale

5. Atoms: The Constituents of Matter
All matter is composed of atoms.
Each atom consists of at least one proton and one electron.
Atoms have mass. The mass comes mostly from the proton and a neutrally charged body called a neutron.

6. Figure 2.2 The Helium Atom

7. Atoms: The Constituents of Matter
Each element contains only one type of atom.
Information on elements is arranged in logical order in a table called the periodic table.
The periodic table arranges elements left to right based on their atomic number, and in columns based on similarities in their properties.

8. Figure 2.3 The Periodic Table (Part 1)

9. Figure 2.3 The Periodic Table (Part 2)

10. Atoms: The Constituents of Matter
Each element has a unique atomic number which is the number of protons found in an atom of the element.
The mass number is the number of protons plus the number of neutrons.
The mass number is used as the weight of the atom, in units called daltons.
Each element has a unique symbol: H is hydrogen, C is carbon, Na is sodium, and Fe is iron.

11. Atoms: The Constituents of Matter
All atoms of an element have the same number of protons, but not necessarily the same number of neutrons.
Atoms of the same element that have different atomic weights are called isotopes.

12. Figure 2.4 Isotopes Have Different Numbers of Neutrons

13. Atoms: The Constituents of Matter
Some isotopes are radioisotopes, which emit energy as alpha, beta, and gamma radiation from their nuclei.
Radioactive decay transforms the original atom into another atom, usually of another element.

14. Atoms: The Constituents of Matter
The region in which an electron travels is called the electron’s orbital.
The orbitals constitute a series of electron shells, or energy levels, around the nucleus.
Two electrons at most can occupy each orbital.

15. Atoms: The Constituents of Matter
The first shell is the innermost shell and has just one orbital, called the s orbital.
The s orbital fills first and its electrons have the lowest energy.
The second shell is next closest to the nucleus and has one s and three p orbitals.
The second shell can accommodate eight electrons, two per orbital.

16. Figure 2.6 Electron Orbitals

17. Atoms: The Constituents of Matter
The outermost shell of an atom determines how it reacts with other atoms.
Generally, if eight electrons are in the outer shell, the atom is stable and does not tend to react.
Atoms which do not have eight electrons in the outermost shell will share, gain, or lose electrons to arrive at a stable state.

18. Atoms: The Constituents of Matter
The tendency of atoms to be stable when they have eight electrons in their outermost shells is called the rule of eight, or the octet rule.
Hydrogen and phosphorus are exceptions to the octet rule.

19. Chemical Bonds: Linking Atoms Together
A molecule is two or more atoms bonded together.
A chemical bond is an attractive force that links two atoms together.

20. Chemical Bonds: Linking Atoms Together
A covalent bond is formed by sharing of a pair of electrons between two atoms.
In hydrogen molecules (H2), a pair of electrons share a common orbital and spend equal amounts of time around each of the two nuclei.
The nuclei stay some distance from each other due to mutually repelling positive charges.

21. Properties of Molecules
Figure 2.8 Electrons Are Shared in Covalent Bonds
Properties of Molecules

22. Chemical Bonds: Linking Atoms Together
Molecules made up of more than one type of atoms are called compounds.
Every compound has a molecular weight that is the sum of all atoms in the molecule.

23. Chemical Bonds: Linking Atoms Together
Covalent bonds are very strong.
Each covalent bond has a predictable length, angle, and direction, which makes it possible to predict the three-dimensional structures of molecules.
A double covalent bond occurs when atoms share two pairs of electrons; in triple covalent bonds atoms share three electron pairs.

24. Properties of Molecules
Figure Covalent Bonding With Carbon
Properties of Molecules

25. Chemical Bonds: Linking Atoms Together
Electrons are not always shared equally between covalently bonded atoms.
The attractive force that an atom exerts on electrons is called electronegativity.
When a molecule has nuclei with different electronegativities, an electron spends most of its time around the nucleus with the greater electronegativity.

26. Chemical Bonds: Linking Atoms Together
Unequal sharing of electrons causes a partial negative charge around the more electronegative atom, and a partial positive charge around the less electronegative atom, resulting in a polar covalent bond.
Molecules that have polar covalent bonds are called polar molecules.

27. Properties of Molecules
Figure The Polar Covalent Bond in the Water Molecule
Properties of Molecules

28. Chemical Bonds: Linking Atoms Together
Hydrogen bonds may form within or between atoms with polar covalent bonds.
The d– portion of one molecule has a weak attraction to the d+ portion of another molecule. Each of these attractions is called a hydrogen bond.
Hydrogen bonds do not share electrons.
Although hydrogen bonds are weak, they tend to be additive, and they are of profound biological importance.

29. Properties of Molecules
Figure Hydrogen Bonds Can Form between or within Molecules
Properties of Molecules

30. Chemical Bonds: Linking Atoms Together
Ionic bonds involve a complete transfer of one or more electrons.
Ions are formed when an atom loses or gains electrons.
Positively charged ions are called cations.
Negatively charged ions are called anions.

31. Properties of Molecules
Figure Formation of Sodium and Chloride Ions
Properties of Molecules

32. Chemical Bonds: Linking Atoms Together
Ionic bonds are formed by the electrical attraction between ions with opposite charges.
Table salt has chloride and sodium ions, held together by ionic bonds.
When salt is introduced into water, the partial charges of the water molecules can easily interfere with the ionic bonds.

33. Properties of Molecules
Figure Water Molecules Surround Ions
Properties of Molecules

34. Chemical Bonds: Linking Atoms Together
Polar molecules tend to be hydrophilic. Substances that are ionic or polar often dissolve in water due to hydrogen bonds.
Nonpolar molecules are called hydrophobic because they tend to aggregate with other nonpolar molecules.
Nonpolar molecules are also attracted to each other via relatively weak attractions called van der Waals forces.

35. Chemical Reactions: Atoms Change Partners
Chemical reactions occur when atoms combine or change partners.
In a chemical reaction, reactants are converted to products.
A chemical reaction can be written as an equation. The equation must balance because matter is neither created nor destroyed.

36. Properties of Molecules
Figure Bonding Partners and Energy May Change in a Chemical Reaction
Properties of Molecules

37. Chemical Reactions: Atoms Change Partners
Changes in energy usually accompany chemical reactions.
Stored energy, such as that in chemical bonds, is called potential energy and is available for future use.
We can measure the potential energy of molecules and express it in units of heat called calories.
A calorie is the amount of heat required to raise the temperature of one gram of pure water from 14.5°C to 15.5°C.

38. Water: Structure and Properties
Due to its shape, polarity, and ability to form hydrogen bonds, water has some unusual properties.

39. Water: Structure and Properties
Ice is held in a crystalline structure by the orientation of water molecules’ hydrogen bonds.
Each molecule forms hydrogen bonds with four other molecules.
These four hydrogen bonds increase the space the water molecules take up, so water expands as it freezes, and ice is less dense than liquid water.
For these reasons, ice floats in liquid water.

40. Properties of Molecules
Figure Hydrogen Bonds Hold Water Molecules Together (Part 1)
Properties of Molecules

41. Properties of Molecules
Figure Hydrogen Bonds Hold Water Molecules Together (Part 2)
Properties of Molecules

42. Water: Structure and Properties
Compared to other nonmetallic substances, ice requires a lot of heat to melt because hydrogen bonds must be broken.
The opposite process, freezing, requires water to lose a great deal of heat.

43. Water: Structure and Properties
A great deal of heat energy is required to change the temperature of liquid water because the hydrogen bonds must be broken.
Specific heat is the number of calories needed to raise one gram of a substance 1oC. The specific heat of liquid water is 1.
Liquid water has a higher specific heat than most other small molecules in liquid form.

44. Water: Structure and Properties
The heat of vaporization is the amount of heat needed to change a substance from its liquid state to its gaseous state.
A lot of heat is required to change water to a gaseous state because the hydrogen bonds of the liquid water must be broken.
Evaporation has a cooling effect by absorbing calories.
Condensing has the opposite effect, releasing heat.

45. Water: Structure and Properties
Water has a cohesive strength because of hydrogen bonds.
The cohesive strength of water molecules allows the transport of water from the roots to the tops of trees.
Water has high surface tension, which means that the surface of liquid water is relatively difficult to puncture.

46. Water: Structure and Properties
Water is the solvent of life.
Living organisms are over 70 percent water by weight and many reactions take place in this watery environment.
A solution is a substance (the solute) dissolved in a liquid (the solvent).

47. Water: Structure and Properties
Reactions that take place in aqueous solutions may be studied in two ways:
Qualitative analysis is the study of substances dissolved in a solvent and their reactions.
Quantitative analysis measures the amounts of substances and solvents.

48. Water: Structure and Properties
The mole concept is fundamental to quantitative analysis. A mole is the amount of a substance in grams whose weight is equal to its molecular weight.
One mole of any given compound contains approximately 6.03 x 1023 molecules of that compound (Avogadro’s number).

49. Water: Structure and Properties
A 1 molar (1 M) solution is one mole of a compound dissolved in water to make one liter.
Example: One mole of NaCl is the atomic weight of Na (23) plus the atomic weight of Cl (35.5), or 58.5, in grams. When 58.5 grams of NaCl are dissolved in water to make one liter, the solution is 1 molar.

50. Acids, Bases, and the pH Scale
Some substances dissolve in water and release hydrogen ions (H+); these are called acids. Their release is called ionization.
Other substances dissolve in water and release hydroxide ions (OH–); these are called bases.
Acids donate H+; bases accept H+.

51. Acids, Bases, and the pH Scale
Acids release H+ ions in solution.
If the reaction is complete, it is a strong acid, such as HCl.
The carboxyl group (—COOH) is common in biological compounds. It functions as an acid because
—COOH ® —COO– + H+

52. Acids, Bases, and the pH Scale
Bases accept H+ in solution.
NaOH ionizes completely to Na+ and OH–. The OH– absorbs H+ to form water. It is a strong base.
The amino group (—NH2) is an important part of many biological compounds; it functions as a weak base by accepting H+:
—NH2 + H+ ® —(NH3)+

53. Acids, Bases, and the pH Scale
Ionization of strong acids is virtually irreversible.
Ionization of weak acids and bases is somewhat reversible.
Many large molecules in biological systems contain weak acid or base groups.

54. Acids, Bases, and the pH Scale
Water is really a weak acid and has a slight tendency to ionize into H+ and OH–.
This ionization is very important for living creatures and the chemical reactions they must perform because the H+ ion is so reactive.

55. Acids, Bases, and the pH Scale
pH is the measure of hydrogen ion concentration.
It is defined as the negative logarithm of the hydrogen ion concentration in moles per liter.
The pH scale indicates the strength of a solution of an acid or base. The scale values range from 1 through 14.
A pH 7 means the concentration of hydrogen ions is 1 x 10–7 moles per liter of water.

56. Properties of Molecules
Figure pH Values of Some Familiar Substances
Properties of Molecules

57. Acids, Bases, and the pH Scale
A buffer is a mixture of a weak acid and its corresponding base.
Because buffers can react with both added bases and acids, they make the overall solution resistant to pH change.
Buffers illustrate the law of mass action:
Addition of reactants to one side of a reaction drives the reaction in the direction that uses that component.

58. Properties of Molecules
Figure Buffers Minimize Changes in pH
Properties of Molecules

59. Properties of Molecules
Chemists use the characteristics of composition, structure, reactivity, and solubility to help classify molecules.
Two other properties that influence the behavior of molecules are the presence of recognizable functional groups, and the existence of isomers of molecules.

60. Properties of Molecules
Functional groups give specific properties to molecules.
Functional groups are covalently bonded to organic molecules.
Amino acids are biological molecules that contain both a carboxyl group and an amino group.

61. Properties of Molecules
Figure Some Functional Groups Important to Living Systems (Part 1)
Properties of Molecules

62. Properties of Molecules
Figure Some Functional Groups Important to Living Systems (Part 2)
Properties of Molecules

63. Properties of Molecules
Figure Some Functional Groups Important to Living Systems (Part 3)
Properties of Molecules

64. Properties of Molecules
Isomers are molecules that have the same chemical formula but different arrangements of the atoms.
Structural isomers differ in terms of how atoms are joined together.
Optical isomers are mirror images of each other.
Optical isomers can occur whenever a carbon has four different atoms or groups attached to it.

65. Properties of Molecules
Figure Optical Isomers
Properties of Molecules