1. Chapter 2
Chemistry

2. __Matter_ is anything that has mass and volume.
__Mass_ is the amount of matter in an object
and __volume_ is how much space it takes up.
_Element_ = a substance that can not be broken down into other substances by chemical reactions.

3. A __compound_ is 2 or more elements combined in a certain ratio.
Ex. H2O

4. Sodium Chlorine Sodium chloride Fig. 2-3
Figure 2.3 The emergent properties of a compound
Sodium
Chlorine
Sodium
chloride

5. The four primary elements found in living things are __Carbon__,
___Hydrogen___,
__Oxygen___ and
___Nitrogen__.

6. __Trace_ elements are those that are needed only in small quantities by living things.
Ex. _iron_ is needed by all organisms
Only vertebrates need _iodine_, but without they can not make a necessary hormone and the thyroid gland grows abnormally large (goiter).

7. (b) Iodine deficiency Fig. 2-4b
Figure 2.4 The effects of essential-element deficiencies
(b) Iodine deficiency

8. (a) Nitrogen deficiency
Fig. 2-4a
Figure 2.4 The effects of essential-element deficiencies
(a) Nitrogen deficiency

9. An _atom_is the smallest part of an element that still has all the properties of that element.

10. Chemical symbols you must know:
O N
P S
Na Cl
K Mg
Ca I
Cu Zn
F Fe

11. Atomic structure: The center of the atom is called the __nucleus_
and contains the _protons__
which have a positive charge
and the _neutrons_ which have
_no__ charge.

12. Cloud of negative charge (2 electrons) Electrons Nucleus (a) (b)
Fig. 2-5
Cloud of negative
charge (2 electrons)
Electrons
Nucleus
Figure 2.5 Simplified models of a helium (He) atom
(a)
(b)

13. Around the nucleus, the __electrons__ are moving around in a space
called the __electron_ __cloud__.
Electrons have a __negative __ charge.

14. Diagram of atomic structure:

15. Protons and neutrons have a mass of 1 Atomic Mass Unit __(AMU)___ or 1 __Dalton_.
__Electrons__ have a mass of only 1/2000 of an AMU.

16. Which type of atom (element) you have is determined by its number of __protons_,
which is also called the atomic __number ___.

17. In a neutral atom, the number of protons is the same as the number of __electrons__ .
The number of protons and the number of neutrons added together gives us the __mass__ __number_ of the element.

18. 1H 2He 3Li 4Be 5B 6C 7N 8O 9F 10Ne 11Na 12Mg 13Al 14Si 15P 16S 17Cl
Fig. 2-9
Hydrogen 1H 2
Atomic number
Helium
2He He
Atomic mass
4.00
First
shell
Element symbol
Electron-
distribution
diagram
Lithium
3Li
Beryllium
4Be
Boron 5B
Carbon 6C
Nitrogen 7N
Oxygen 8O
Fluorine 9F
Neon
10Ne
Second
shell
Sodium
11Na
Magnesium
12Mg
Aluminum
13Al
Silicon
14Si
Phosphorus
15P
Sulfur
16S
Chlorine
17Cl
Argon
18Ar
Figure 2.9 Electron-distribution diagrams for the first 18 elements in the periodic table
Third
shell

19. Ex. Na has 11 protons and an atomic mass of 22.9.
How many electrons does Na have?
__11__
How many neutrons does Na have?
__12___

20. Na can be written as 2311Na_.
The upper number is the atomic _mass_
and the lower number is its atomic number.

21. _Isotopes_ are forms an atom can have that differ in their number of neutrons.
Ex. Carbon 12 and Carbon 14.
Both have 6 protons and 6 electrons,
but carbon 12 has 6 neutrons and carbon 14 has 7 neutrons.

22. The atomic __mass_ written on the periodic table is an average of the masses of the various isotopes of the element based on how common each is in nature.
Isotopes behave the same way in __chemical__ ___reactions__.

23. Some isotopes, however, are __radioactive__ isotopes
in which the nucleus decays and gives off __particles_ and __energy__.
This can change the number of protons and create a different _element__.

24. Radioactive isotopes are very useful in biology.
They can be used to:
1. __Date_ fossils and other old biological materials.

25. 2. As radioactive __tracers_ that we can follow through chemical reactions to find out how they react chemically.
Radioactive tracers are used to follow chemicals within _reactions_ or through the body.
Ex. Kidney disorders can be diagnosed by injecting radioactive tracers into the__blood_ and seeing how much is excreted in the urine.

26. PET scanners use radioactive tracers to locate __cancer_ in the body.
Ex. A patient is injected with radioactive glucose and the areas with greater cellular activity (cancerous) show up as colored areas on the PET scan.

27. Cancerous throat tissue Fig. 2-7
Figure 2.7 A PET scan, a medical use for radioactive isotopes

28. Radioactive isotopes can also release radiation that damages _cells_ such as in nuclear bombs or nuclear reactor accidents

29. Energy and electrons __Energy__ is the ability to do work.
Energy which is stored is called __potential_ energy.
The __farther_ electrons are from the nucleus, the greater their potential energy.

30. There are several energy __shells_ or energy levels around the nucleus where electrons can be found.
The first energy shell is __closest_ to the nucleus and
has the _least_ amount of energy.

31. An electron can jump to a __higher_ energy level if it absorbs energy that is equal to the amount of energy difference between the 2 shells.
Ex. When light hits a chlorophyll molecule in photosynthesis, the light excites electrons to a higher energy level.

32. But the electron can not stay in that higher energy level, and when it falls back to its original level, it gives off the extra energy, usually as _heat__.

33. (a) A ball bouncing down a flight of stairs provides an analogy
Fig. 2-8
(a) A ball bouncing down a flight
of stairs provides an analogy
for energy levels of electrons
Third shell (highest energy
level)
Second shell (higher
energy level)
Energy
absorbed
Figure 2.8 Energy levels of an atom’s electrons
First shell (lowest energy
level)
Energy
lost
Atomic
nucleus
(b)

34. Energy shell diagram

35. Each energy shell can only hold a certain number of __electrons___.
The first level can only hold _2__ electrons,
the second can hold __8___ and the
third can hold ___18__.

36. Whether or not an element will react chemically with other elements depends on the number of __electrons_ it has it in it outer energy level
(which is called its ___valence__ __shell__).
These outer electrons are called __valence_ electrons.

37. 2
An element that does not want to react with other elements is said to be __stable__.
If an element has only the first valence energy shell and it has _2_ electrons in it, then it is stable and will not react with other elements.
If an element has more than one energy shell, it needs _8__ electrons in it to be stable.

38. The path an electron travels is not like the orbit of a planet around the sun.
Each electron has an area in which it is most likely to be found, called an __orbital__.
Each shell has certain shapes of orbitals in it.

39. Neon, with two filled shells (10 electrons) (a) Electron-distribution
Fig
Neon, with two filled shells (10 electrons)
(a)
Electron-distribution
diagram
First shell
Second shell
(b)
Separate electron
orbitals x y z
1s orbital
2s orbital
Three 2p orbitals
Figure 2.10 Electron orbitals
(c)
Superimposed electron
orbitals
1s, 2s, and 2p orbitals

40. Orbital diagram

41. Each orbital can hold _2_ electrons.
Each orbital shape gets 1 electron before any get a second electron in it. (Like passengers on a bus go 1 to a seat 1st)
When elements interact to become stable, it is the _valence_ electrons that are involved.

42. We can use the periodic table to determine if an atom wants to gain or lose electrons or is already stable.
Lose 1 Lose 2 varies Lose 3
Gain 4 Gain 3 Gain 2 Gain 1 stable

43. Chemical Bonding
Atoms form chemical bonds as a way to become __stable_.
The chemical bond is the _force__ that holds the atoms together.

44. Kinds of chemical bonds:
1. Ionic
In an ionic bond, one element that wants to lose electrons __gives_ its electron(s) to another element that wants to gain electrons.

45. Ex. Na wants to __lose_ __1___ electron and Cl
wants to _gain_ 1 electron.
So Na _gives_ its electron to Cl.
When an atom loses an electron, it now has 1 more __proton__ than electrons, so it
has a __positive_ charge.

46. Sodium chloride (NaCl)
Fig Na Cl Na Cl Na Cl
Na+
Cl–
Sodium atom
Chlorine atom
Sodium ion
(a cation)
Chloride ion
(an anion)
Figure 2.14 Electron transfer and ionic bonding
Sodium chloride (NaCl)

47. An atom which has a charge from having lost or gained an electron is called an _ion__.
If it has a positive charge from having lost electrons, it is now known as a _cation_.

48. If an atom gains an electron, it now has more negative electrons than protons, so it has
a __negative__ charge
and is now called an __anion__.

49. Because of their opposite charges, cations and anions attract each other and this attraction holds them together and is called an _ionic__ __bond_.
Compounds (more than element joined together) that form this way are called _ionic_compounds
or __salts_.

50. When ionic compounds form, there may be _different_ ratios of elements, depending on how many electrons each element needed to gain or lose.
The entire ionic compound must have no charge.

51. Ex. Mg and Cl
Mg needs to _lose__ _2__ electrons
and Cl needs to _gain_ _1_.
So together they form __MgCl2__.

52. Ionic bonds can be very strong in _dry_ environments. (Ex. Salt)
They can be very easily broken in __water_, however.
So in biology we will not consider them to be strong.

53. _Polyatomic_ ions are molecules with covalent bonds between the atoms that act like ions because they have charge and are attracted to other ions.
Ex. NH4+ and OH-

54. 2. Covalent Bonds
In a covalent bond, 2 atoms __share_ one or more pairs of
_electrons_ to become stable.
Ex. H2 Each H atom needs one more electron, so they share their electrons

55. Name and Molecular Formula Electron- distribution Diagram Lewis Dot
Fig. 2-12a
Name and
Molecular
Formula
Electron-
distribution
Diagram
Lewis Dot
Structure and
Structural
Formula
Space-
filling
Model
(a) Hydrogen (H2)
Figure 2.12 Covalent bonding in four molecules

56. Diagrams of H2

57. Ex. CH4
Carbon needs _4_ electrons,
so it shares 1 with each of _4_H atoms.

58. Name and Molecular Formula Electron- distribution Diagram Lewis Dot
Fig. 2-12d
Name and
Molecular
Formula
Electron-
distribution
Diagram
Lewis Dot
Structure and
Structural
Formula
Space-
filling
Model
(d) Methane (CH4)
Figure 2.12 Covalent bonding in four molecules

59. Diagrams of CH4

60. Ex. O2
Each O needs 2 electrons more, so they form __double__ bonds and share 2 pairs of electrons.

61. Name and Molecular Formula Electron- distribution Diagram Lewis Dot
Fig. 2-12b
Name and
Molecular
Formula
Electron-
distribution
Diagram
Lewis Dot
Structure and
Structural
Formula
Space-
filling
Model
(b) Oxygen (O2)
Figure 2.12 Covalent bonding in four molecules

62. Diagram of O2

63. Ex. N2
Each N needs 3 more electrons, so they form __triple_ bonds and share 3 pairs of electrons.

64. Diagram of N2

65. Ways to write chemical formulas
__Molecular__ formulas - tell us just how many atoms of each element are involved.
Ex. CH4

66. Formulas can also be written as __structural__ formulas.
They also tell us the __shape__ of the molecule.

67. Structural formula example

68. Two or more atoms held together by a covalent bond are called a __molecule__. 
If the atoms are of 2 or more different elements, it can be called a __compound__. 
Ionic compounds are not called _molecules_.

69. Polar and nonpolar bonds
__Electronegativity___ is how strongly an atom pulls electrons toward it in a covalent bond.
If the elements pull equally on the electrons, the bond is called __nonpolar_.
Ex. H2
Ex. CH4 (C and H have equal electronegativity)

70. If the elements do not pull equally on the electrons, the bond is called _polar__.
Ex. __ O__ has the greatest electronegativity of all the elements, so it pulls electrons toward it more strongly than H in water.

71. Fig. 2-13
 – O H H + +
Figure 2.13 Polar covalent bonds in a water molecule
H2O

72. Diagram of water

73. This makes some parts of a water molecule negatively charged and the other parts somewhat positively charged.

74. Diagram of water charges

75. Bonds in biology
In biology, __covalent__ bonds are the strongest bonds
and ___ionic_ bonds are next.
__Weak___ bonds are also important in living things.

76. Weak bonds
Weak bonds occur between __molecules__ or
__compounds_,
rather than between elements like in covalent bonds.

77. 1. __Hydrogen__ bonds are especially important in living things.
Hydrogen bonds occur when a __H__ atom that is covalently bonded in one molecule is also attracted to another electronegative atom,
usually _O__ or __N___.
(N is also quite electronegative)

78. Ex. H2O and NH3 (ammonia).
There is a weak hydrogen bond between the H in water and the N in the ammonia.

79.   + Water (H2O) + Hydrogen bond   Ammonia (NH3) + + +
Fig. 2-16
  +
Water (H2O) +
Hydrogen bond
 
Ammonia (NH3)
Figure 2.16 A hydrogen bond + + +

80. Ammonia and water diagram

81. More weak bonds
2. __van__ __der_ __Waal_ interactions are weak attractions that occur in molecules because
electrons __accumulate_ in certain areas of a large molecule
such as a long __proteins__.
This can cause the molecule to bend, fold and twist.

82. Diagram of van der Waals interactions

83. Molecular shapes
A molecule’s biological function is related to its __shape__.
A molecule with only 2 atoms has a __linear_ shape.
Ex. H2 or O2

84. Diagram of linear molecule

85. Molecular shapes
A molecule with 3 atoms can have a __”V”__ shape, such as water.

86. V shape diagram

87. Molecular shapes
A molecule with 5 atoms can have a ___tetrahedral_ shape, such as methane.

88. Tetrahedron

89. Complex molecules such as __protein_ can have very irregular shapes which cause them with fit with certain other molecules like a lock and key.

90. (a) Structures of endorphin and morphine
Fig. 2-18
Key
Carbon
Nitrogen
Hydrogen
Sulfur
Natural endorphin
Oxygen
Morphine
(a) Structures of endorphin and morphine
Natural
endorphin
Figure 2.18 A molecular mimic
Morphine
Endorphin
receptors
Brain cell
(b) Binding to endorphin receptors

91. This is important for signaling molecules such as _neurotransmitters__ which carry information from one cell to another.
(Ex. Between nerve cells or in the brain)

92. Protein shape diagram

93. It is also important in __enzymes_, which act as catalysts for chemical reactions.

94. It can be represented by a chemical __equation_.
A __chemical _ ___reaction__ is when bonds are broken and formed to produce new substances.
It can be represented by a chemical __equation_.
Ex. 2 H2 + O2  2H2O2
Reactants Products

95. Fig. 2-UN2
2 H2 O2
2 H2O
Reactants
Reaction
Products

96. (Remember that the number of each kind of atom in the products must be the same as the number of each kind in the products. Atoms can not be created or destroyed.)

97. A reversible reaction can go in both directions until they go at the same _rate_,
Called _chemical_ _equilibrium__.
Ex. H2CO HCO3- + H+

98. Chemical equilibrium
The actual amount of product and reactant may __not__ be the same at that point.
The __rate__ of the reactions is what matters.