1. Life’s Chemical Basis
Atoms and Molecules

2. Matter and Energy Matter - the physical material of the universe
Energy - the capacity to do work (usually manifested as the moving of matter from place to place)
Technically - are interchangeable
E=mc2
Haemmerle - Bio160 Chapter 2

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ATOMIC THEORY
Matter is composed of tiny, fundamental paricles called ATOMS
Atoms of the same element are identical but differ from atoms of other elements.
Atoms enter into combinations to form COMPOUNDS.
Haemmerle - Bio160 Chapter 2

4. Forms of Energy Kinetic - energy of movement
movement of atoms and molecules influenced by temperature
electrical energy
Potential - energy of position; stored energy
rock on a hill
chemical bonds
Haemmerle - Bio160 Chapter 2

5. 1/1/2019
ATOMIC THEORY
Matter is composed of tiny, fundamental paricles called ATOMS
Atoms of the same element are identical but differ from atoms of other elements.
Atoms enter into combinations to form COMPOUNDS.
Haemmerle - Bio160 Chapter 2

6. Atoms
The behavior of elements, which make up all living things, starts with the structure of individual atoms
The number of protons in the atomic nucleus defines the element, and the number of neutrons defines the isotope

7. Structure of Atoms Atoms are the building blocks of all substances
Made up of electrons, protons and neutrons
Charge is an electrical property
Attracts or repels other subatomic particles

8. Characteristics of Atoms
Electrons (e-) have a negative charge
Move around the nucleus
The nucleus contains protons and neutrons
Protons (p+) have a positive charge
Neutrons (n) have no charge

9. Living and nonliving matter is composed of atoms.

10. Characteristics of Atoms
Atoms differ in number of subatomic particles
Atomic number (number of protons) determines the element
Elements consist only of atoms with the same atomic number
Mass number
Total protons and neutrons in a nucleus
Used to identify isotopes

11. Atoms proton neutron electron
Figure 2.2 Atoms consist of electrons moving around a core, or nucleus, of protons and neutrons. Models such as this diagram cannot show what atoms really look like. Electrons zoom around in fuzzy, three-dimensional spaces about 10,000 times bigger than the nucleus.
electron

12. The Periodic Table Periodic table of the elements
An arrangement of the elements based on their atomic number and chemical properties
Created by Dmitry Mendeleev

13. Haemmerle - Bio160 Chapter 2

14. Periodic Table Song

15. Isotopes and Radioisotopes
Different forms of the same element, with different numbers of neutrons
Some radioactive isotopes – radioisotopes – are used in research and medical applications

16. Atom
Def. - the fundamental unit of matter that can enter into chemical reactions
Protons +
Electrons -
Neutrons 0
All atoms are alike in that they are composed of protons, electrons, and neutrons
They are different from each other in their number of protons, electrons, and neutrons
Haemmerle - Bio160 Chapter 2

17. The basic building blocks of all matter
All matter consists of atoms, tiny particles that in turn consist of electrons moving around a nucleus of protons and neutrons
An element is a pure substance that consists only of atoms with the same number of protons. Isotopes are forms of an element that have different numbers of neutrons
Unstable nuclei of radioisotopes disintegrate spontaneously (decay) at a predictable rate to form predictable products

18. Why Electrons Matter Atoms acquire, share, and donate electrons
Whether an atom will interact with other atoms depends on how many electrons it has

19. About Vacancies Electrons move around nuclei in orbitals
Each orbital holds two electrons
Each orbital corresponds to an energy level
An electron can move in only if there is a vacancy
free radical
Atom with an unpaired electron

20. Orbital
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Def. - the volume of space surrounding an atoms nucleus in which the greatest probability of finding specific electron(s) occurs.
Orbitals have specific shapes, contain up to 2 electrons, and have unique energy levels.
Orbital nomenclature - s, p, d, f, and g.
Haemmerle - Bio160 Chapter 2

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Shells
Def. - layer or layers of electrons or orbitals surrounding an atoms nucleus.
Shells can consists of one to many orbitals.
Haemmerle - Bio160 Chapter 2

23. Why Atoms Interact
The shell model of electron orbitals diagrams electron vacancies; filled from inside out
First shell: one orbital (2 electrons)
Second shell: four orbitals (8 electrons)
Third shell: four orbitals (8 electrons)
Atoms with vacancies in their outer shell tend to give up, acquire, or share electrons

24. Orbitals and Shells Shell 1 Shell 2 Shell 3 Shell 4 Shell 5
1s -- 2 electrons
Shell 2
2s -- 2 electrons
2p -- 6 electrons
Shell 3
3s -- 2 electrons
3p -- 6 electrons
3d - 10 electrons
Shell 4
4s -- 2 electrons
4p -- 6 electrons
4d - 10 electrons
4f electrons
Shell 5
5s -- 2 electrons
5p -- 6 electrons
5d electrons
5f electrons
5g electrons
Haemmerle - Bio160 Chapter 2

25. Haemmerle - Bio160 Chapter 2

26. Electron Shells

27. Different Ways to Represent the Same Molecule

28. A The first shell corresponds to the first energy level, and it can hold up to 2 electrons. Hydrogen has one proton, so it has 1 electron and 1 vacancy. A helium atom has 2 protons, 2 electrons, and no vacancies. The number of protons in each model is shown.
first shell
hydrogen (H)
helium (He) 1
1 proton
1 electron 2 6
B The second shell corresponds to the second energy level, and it can hold up to 8 electrons. Carbon has 6 protons, so its first shell is full. Its second shell has 4 electrons, and four vacancies. Oxygen has 8 protons and two vacancies. Neon has 10 protons and no vacancies.
neon (Ne)
second shell
carbon (C)
oxygen (O) 8 10
C The third shell, which corresponds to the third energy level, can hold up to 8 electrons. A sodium atom has 11 protons, so its first two shells are full; the third shell has one electron. Thus, sodium has seven vacancies. Chlorine has 17 pro tons and one vacancy. Argon has 18 protons and no vacancies.
third shell
argon (Ar)
chlorine (Cl)
sodium (Na) 18 17 11
Figure 2.5 Animated Shell models. Each circle (shell) represents all orbitals at one energy level. A model is filled with electrons from the innermost shell out, until there are as many electrons as protons. Atoms with vacancies (room for additional electrons) in their outermost shell tend to get rid of them.
A The first shell corresponds to the first energy level, and it can hold up to 2 electrons. Hydrogen has one proton, so it has 1 electron and 1 vacancy. A helium atom has 2 protons, 2 electrons, and no vacancies. The number of protons in each model is shown.
B The second shell corresponds to the second energy level, and it can hold up to 8 electrons. Carbon has 6 protons, so its first shell is full. Its second shell has 4 electrons, and four vacancies. Oxygen has 8 protons and two vacancies. Neon has 10 protons and no vacancies.
Stepped Art
Figure 2-5 p26

29. Atoms and Ions
Ion
An atom with a positive or negative charge due to loss or gain of electrons in its outer shell
Examples: Na+ (cation), Cl- (anion)
Electronegativity
A measure of an atom’s ability to pull electrons from another atom

30. Electronegativities

31. If two atoms have similar electronegativities, they share electrons equally, in what is called a nonpolar covalent bond.
If atoms have different electronegativities, electrons tend to be near the most attractive atom, in what is called a polar covalent bond

32. Octet rule—atoms with at least two electron shells form stable molecules so they have eight electrons in their outermost shells.
Haemmerle - Bio160 Chapter 2

33. electron loss electron gain Sodium atom Chlorine atom 11p+ 11e–
charge: 0
charge: 0
Sodium ion
Chloride ion
Figure 2.6 Animated Ion formation
A A sodium atom (Na) becomes a positively charged sodium ion (Na+) when it loses the electron in its third shell. The atom’s full second shell is now its outermost, so it has no vacancies.
B A chlorine atom (Cl) becomes a negatively charged chloride ion (Cl–) when it gains an electron and fills the vacancy in its third, outermost shell.
11p+ 10e–
17p+ 18e–
charge: +1
charge: –1
Figure 2-6 p27

34. There are several kinds of chemical bonds.
When Atoms Interact
Chemical bond is an attractive force that links atoms together to form molecules.
There are several kinds of chemical bonds.
ANIMATED TUTORIAL 2.1 Chemical Bond Formation

35. When Atoms Interact
The characteristics of a bond arise from the properties of the atoms that participate in it
The three most common types of bonds in biological molecules are ionic, covalent, and hydrogen bonds

36. Types of Chemical Bonds

37. Basic Principle of Chemical Reactions
An atom is stable when its outermost electron shell is either completely full or completely empty
An atom is reactive when its outermost electron shell is only partially full
1st shell = 2 electrons
2nd shell = 8 electrons
3rd shell = 8 electrons
Haemmerle - Bio160 Chapter 2

38. Why do atoms interact?
An atom’s electrons are the basis of its chemical behavior
Shells represent all electron orbitals at one energy level in an atom; when the outermost shell is not full of electrons, the atom has a vacancy
Atoms with vacancies tend to interact with other atoms

39. Chemical Bonds: From Atoms to Molecules
Chemical bonds link atoms into molecules
The characteristics of a chemical bond arise from the properties of the atoms taking part in it

40. Chemical Bonds Chemical bond
An attractive force existing between two atoms when their electrons interact
Molecule
Two or more atoms joined in chemical bonds

41. Combining Substances Compounds
Molecules consisting of two or more elements whose proportions do not vary
Example: Water (H2O)
Mixture
Two or more substances that intermingle but do not bond; proportions of each can vary

42. The Water Molecule one oxygen atom two hydrogen atoms
Figure 2.7 The water molecule. Each water molecule has two hydrogen atoms bonded to the same oxygen atom.

43. Bonds and Electrons
Whether one atom will bond with others depends on the element, and the number and arrangement of its electrons
electronegativity
Measure of the ability of an atom to pull electrons away from other atoms

44. Three Types of Bonds
The characteristics of a bond arise from the properties of the atoms that participate in it
The three most common types of bonds in biological molecules are ionic, covalent, and hydrogen bonds

45. Ionic Bonds
Ionic bond
A strong mutual attraction between two oppositely charges ions with a large difference in electronegativity (no electron transferred)
Example: NaCl (table salt)

46. Ionic Bond: Sodium Chloride11 17
Figure 2.8 Animated An example of ionic bonding: table salt, or NaCl.
Ions taking part in an ionic bond retain their charge, so the molecule is polar. One side is positively charged (here represented by a blue overlay); the other side is negatively charged (red overlay).
Sodium ion
11p+, 10e–
Chloride ion
17p+, 18e–

47. Ionic Bond: Sodium Chloride
Cl–
Na+
Figure 2.8 Animated An example of ionic bonding: table salt, or NaCl.
Ions taking part in an ionic bond retain their charge, so the molecule is polar. One side is positively charged (here represented by a blue overlay); the other side is negatively charged (red overlay).

48. Ionic Bond: Sodium Chloride
Figure 2.8 Animated An example of ionic bonding: table salt, or NaCl.
Ions taking part in an ionic bond retain their charge, so the molecule is polar. One side is positively charged (here represented by a blue overlay); the other side is negatively charged (red overlay).
positive charge
negative charge

49. Covalent Bonds Covalent bond
Two atoms with similar electronegativity and unpaired electrons sharing a pair of electrons
Can be stronger than ionic bonds
Atoms can share one, two, or three pairs of electrons (single, double, or triple covalent bonds)

50. Ionic and Covalent Bonding

51. Characteristics of Covalent Bonds
Nonpolar covalent bond
Atoms sharing electrons equally; formed between atoms with identical electronegativity
Polar covalent bond
Atoms with different electronegativity do not share electrons equally; one atom has a more negative charge, the other is more positive

52. Polarity
Polarity
Separation of charge into distinct positive and negative regions in a polar covalent molecule
Example: Water (H2O)

53. molecular hydrogen (H2)
molecular oxygen (O2)
Figure 2.9 Animated Covalent bonds, in which atoms fill vacancies by sharing electrons. Two electrons are shared in each covalent bond. When sharing is equal, the bond is nonpolar. When one atom exerts a greater pull on the electrons, the bond is polar.
water (H2O)
Figure 2-9 p29

54. Table 2-1 p29

55. How do atoms interact in chemical bonds?
A chemical bond forms between atoms when their electrons interact
A chemical bond may be ionic or covalent depending on the atoms taking part in it
An ionic bond is a strong mutual attraction between two ions of opposite charge
Atoms share a pair of electrons in a covalent bond; when the atoms share electrons unequally, the bond is polar

56. Haemmerle - Bio160 Chapter 2
Figure :2-T3
Title:
Bonding Patterns of Atoms Commonly Found in Biological Molecules
Caption:

57. Strength and stability—covalent bonds are very strong; it takes a lot of energy to break them.
Multiple bonds
Single—sharing 1 pair of electrons
Double—sharing 2 pairs of electrons
Triple—sharing 3 pairs of electrons
C H
C C
N N

58. Hydrogen Bonding Hydrogen bond
A weak attraction between a highly electronegative atom and a hydrogen atom taking part in a separate polar covalent bond
Hydrogen bonds do not form molecules and are not by definition chemical bonds
Hydrogen bonds stabilize the structures of large biological molecules

59. Hydrogen Bonds and Water
The unique properties of liquid water arise because of the water molecule's polarity
Extensive hydrogen bonds form among water molecules

60. Polarity of the Water Molecule
Overall, water (H2O) has no charge
The water molecule is polar
Oxygen atom is slightly negative
Hydrogen atoms are slightly positive
Hydrogen bonds form between water molecules
Gives water unique properties

61. Polarity of the Water Molecule
negative charge
Figure 2.10 Polarity of the water molecule. Each of the hydrogen atoms in a water molecule bears a slight positive charge (represented by a blue overlay). The electronegative oxygen atom carries a slight negative charge (red overlay).
positive charge

62. Figure 2.9
Hydrogen bonds. Hydrogen bonds form at a hydrogen atom taking part in a polar covalent bond. The hydrogen atom’s slight positive charge weakly attracts an electronegative atom. As shown here, hydrogen (H) bonds can form between molecules or between different parts of the same molecule.
Fig. 2-9a, p. 27

63. Water’s Special Properties
Living organisms are mostly water; all the chemical reactions of life are carried out in water
Water is essential to life because of its unique properties
The properties of water are a result of extensive hydrogen bonding among water molecules

64. Water Has Cohesion Hydrogen bonds give water cohesion
Provides surface tension
Draws water up from roots of plants
Cohesion
Molecules resist separation from one another

65. Water Cohesion and Surface Tension

66. Water Stabilizes Temperature
Compared with other molecules, water absorbs more heat before it becomes measurably hotter
Temperature
A way to measure the energy of molecular motion
Molecules move faster as they absorb heat

67. Water Stabilizes Temperature
The surface temperature of water decreases during evaporation
Evaporation
Conversion of a liquid to a gas by heat energy
Ice is less dense than liquid water
Hydrogen bonds form a lattice during freezing

68. Water is a Solvent Solvent
A substance (usually liquid) that can dissolve other substances (solutes)
Water is a solvent
The collective strength of many hydrogen bonds pulls ions apart and keeps them dissolved

69. Water is a Solvent Water dissolves polar molecules
Hydrogen bonds form between water molecules and other polar molecules
Polar molecules dissolved by water are hydrophilic (water-loving)
Nonpolar (hydrophobic) molecules are not dissolved by water

70. Water Molecules Surrounding an Ionic Solid

71. Take-Home Message: What gives water the special properties that make life possible?
The polarity of a water molecule gives rise to extensive hydrogen bonding among water molecules
Hydrogen bonding among water molecules imparts cohesion to liquid water, and the ability to stabilize temperature and dissolve many substances

72. 2.6 Acids and Bases
pH is a measure of the number of hydrogen ions in a solution
The more hydrogen ions, the lower the pH
pH 7 is neutral (pure water)
Most biological processes occur within a narrow range of pH, typically around pH 7
Concentration refers to the amount of a particular solute that is dissolved in a given volume of fluid

73. — 0
battery acid
— 1
gastric fluid
acid rain
— 2
lemon juice
cola
more acidic
vinegar
— 3
orange juice
tomatoes, wine
bananas
— 4
beer
bread
black coffee
— 5
urine, tea, typical rain
corn
— 6
butter
milk
pure water
— 7
blood, tears
egg white
— 8
seawater
baking soda
— 9
detergents
Figure 2.12 A pH scale. Here, red dots signify hydrogen ions (H+) and blue dots signify hydroxyl ions (OH–). Also shown are approximate pH values for some common solutions. This pH scale ranges from 0 (most acidic) to 14 (most basic). A change of one unit on the scale corresponds to a tenfold change in the amount of H+ ions.
Tums
toothpaste
— 10
hand soap
milk of magnesia
— 11
household ammonia
more basic
hair remover
— 12
bleach
— 13
oven cleaner
— 14
drain cleaner
Figure 2-12 p32

74. Biological Reactions Occur In Water
Molecules in water (H2O) can separate into hydrogen ions (H+) and hydroxide ions (OH-)
H20 ↔ H+ + OH-

75. Acids and Bases Acids donate hydrogen ions in a water solution
pH below 7
Bases accept hydrogen ions in a water solution
pH above 7

76. Acids: Weak or Strong Acids and bases can be weak or strong
Gastric fluid, pH 2-3
Acid rain
Example: Hydrochloric acid is a strong acid
HCl ↔ H+ + Cl-

77. Salts
Salt
A compound that dissolves easily in water and releases ions other than H+ and OH-
HCl (acid) + NaOH (base) → NaCl (salt) + H20

78. Buffers Against Shifts in pH
A set of chemicals (a weak acid or base and its salt) that can keep the pH of a solution stable
OH- + H2CO3 (carbonic acid) →
HCO3- (bicarbonate) + H20
H+ + HCO3- (bicarbonate) →
H2CO3 (carbonic acid)

79. Buffering Carbon Dioxide in Blood
Carbon dioxide in blood forms carbonic acid, which separates into H+ and bicarbonate
H2O + CO2 (carbon dioxide) →
H2CO3 (carbonic acid) →
H+ + HCO3- (bicarbonate)

80. Take Home Message: Why is hydrogen important in biological systems?
pH reflects the number of hydrogen ions in a fluid. Most biological systems function properly only within a narrow range of pH
Acids release hydrogen ions in water; bases accept them
Salts release ions other than H+ and OH–
Buffers help keep pH stable. Inside organisms, they are part of homeostasis

81. Table 2-1 p34