Basic chemistry review used for Anatomy and Physiology Students

1. Anatomy & Physiology
Chemistry Review
Atomic Theory and Periodic Table Review
SPDF orbital electron configuration
Ions and Ionic Bonding
Covalent Bonding
Important Biological Reactions
Acid / Base and pH
Buffers and buffering mechanism

2. Matter is anything that has mass and takes up space…
Made up of….
Atoms are the basic building blocks of matter
All Things Are Made of Matter
Chemistry can be thought of as the study of matter, which is
“Anything that is.”

3. Elements are substances made up of 1 kind of atom
6 different elements make up 97% of the mass of compounds that are found in
living things
There are more than 100 known elements today
Elements

4. The periodic table describes all the different types of
known elements; all the different kinds of atoms
Elements

5. Atoms
Recall that atoms are comprised of three subatomic
particles:
Protons (p+) = atomic number; 1 proton = 1 AMU
Neutrons (n0) = mass number-atomic number
Electrons (e-) = (1/2000 amu)
When # of (e-) = # of (P+) atom is neutral.
When # of (e-) ≠ # of (P+) an ion
When # of (e-) > # of (P+) = anion
When # of (e-) < # of (P+) = cation

6. Element Information - Review
This (the electron
statement) is only true
if we are discussing an
atom and NOT an ion

7. Atoms of the same element that differ in
their number of neutrons
Isotopes
Useful in biological research if radioisotopes
Can be used to determine age of fossils

9. (Neutrons
would be at
nucleus too)
• 1 valence electron
• To increase stability, loses
valence electron
• Forms H+ cation

10. Bohr Model of Lithium
• Lithium
• 1 valence electron
• Loses valence electron
– Forms Li+ cation

11. Bohr Model of Sodium
• Sodium
• 1 valence electron, if lost, Na+ cation

12. Bohr model of Beryllium
• 2 valence electrons
• Loses valence electrons
– Becomes Be2+ cation.

13. Bohr Model of Magnesium
• 2 valence electrons
• Loses 2 valence electrons
– Forms Mg2+ cation

14. Anions
• Fluorine – 7 valence electrons
• Chlorine – 7 valence electrons
– Both gain 1 electron
– Form -1 anions

15. SPDF Orbitals – a more modern look

17. Orbitals

22. Atoms with 3 or less valence electrons tend to
lose them and become positive cations
From Atoms to Ions

23. From Atoms to Ions
Atoms with 5 or more valence
electrons tend to gain more and
become negative anions

24. Periodic Table of the Elements
1
H
2
He
3
Li
4
Be
5
B
6
C
7
N
8
O
9
F
10
Ne
11
Na
12
Mg
13
Al
14
Si
15
P
16
S
17
Cl
18
Ar
19
K
20
Ca
21
Sc
22
Ti
23
V
24
Cr
25
Mn
26
Fe
27
Co
28
Ni
29
Cu
30
Zn
31
Ga
32
Ge
33
As
34
Se
35
Br
36
Kr
37
Rb
38
Sr
39
Y
40
Zr
41
Nb
42
Mo
43
Tc
44
Ru
45
Rh
46
Pd
47
Ag
48
Cd
49
In
50
Sn
51
Sb
52
Te
53
I
54
Xe
55
Cs
56
Ba
57
La
72
Hf
73
Ta
74
W
75
Re
76
Os
77
Ir
78
Pt
79
Au
80
Hg
81
Tl
82
Pb
83
Bi
84
Po
85
At
86
Rn
87
Fr
88
Ra
89
Ac
104 105 106 107 108 109 110 111 112
+1

25. Periodic Table of the Elements
1
H
2
He
3
Li
4
Be
5
B
6
C
7
N
8
O
9
F
10
Ne
11
Na
12
Mg
13
Al
14
Si
15
P
16
S
17
Cl
18
Ar
19
K
20
Ca
21
Sc
22
Ti
23
V
24
Cr
25
Mn
26
Fe
27
Co
28
Ni
29
Cu
30
Zn
31
Ga
32
Ge
33
As
34
Se
35
Br
36
Kr
37
Rb
38
Sr
39
Y
40
Zr
41
Nb
42
Mo
43
Tc
44
Ru
45
Rh
46
Pd
47
Ag
48
Cd
49
In
50
Sn
51
Sb
52
Te
53
I
54
Xe
55
Cs
56
Ba
57
La
72
Hf
73
Ta
74
W
75
Re
76
Os
77
Ir
78
Pt
79
Au
80
Hg
81
Tl
82
Pb
83
Bi
84
Po
85
At
86
Rn
87
Fr
88
Ra
89
Ac
104 105 106 107 108 109 110 111 112
+2

26. Periodic Table of the Elements
1
H
2
He
3
Li
4
Be
5
B
6
C
7
N
8
O
9
F
10
Ne
11
Na
12
Mg
13
Al
14
Si
15
P
16
S
17
Cl
18
Ar
19
K
20
Ca
21
Sc
22
Ti
23
V
24
Cr
25
Mn
26
Fe
27
Co
28
Ni
29
Cu
30
Zn
31
Ga
32
Ge
33
As
34
Se
35
Br
36
Kr
37
Rb
38
Sr
39
Y
40
Zr
41
Nb
42
Mo
43
Tc
44
Ru
45
Rh
46
Pd
47
Ag
48
Cd
49
In
50
Sn
51
Sb
52
Te
53
I
54
Xe
55
Cs
56
Ba
57
La
72
Hf
73
Ta
74
W
75
Re
76
Os
77
Ir
78
Pt
79
Au
80
Hg
81
Tl
82
Pb
83
Bi
84
Po
85
At
86
Rn
87
Fr
88
Ra
89
Ac
104 105 106 107 108 109 110 111 112
+2 for many; some +1,
others +3; several vary

27. Periodic Table of the Elements
1
H
2
He
3
Li
4
Be
5
B
6
C
7
N
8
O
9
F
10
Ne
11
Na
12
Mg
13
Al
14
Si
15
P
16
S
17
Cl
18
Ar
19
K
20
Ca
21
Sc
22
Ti
23
V
24
Cr
25
Mn
26
Fe
27
Co
28
Ni
29
Cu
30
Zn
31
Ga
32
Ge
33
As
34
Se
35
Br
36
Kr
37
Rb
38
Sr
39
Y
40
Zr
41
Nb
42
Mo
43
Tc
44
Ru
45
Rh
46
Pd
47
Ag
48
Cd
49
In
50
Sn
51
Sb
52
Te
53
I
54
Xe
55
Cs
56
Ba
57
La
72
Hf
73
Ta
74
W
75
Re
76
Os
77
Ir
78
Pt
79
Au
80
Hg
81
Tl
82
Pb
83
Bi
84
Po
85
At
86
Rn
87
Fr
88
Ra
89
Ac
104 105 106 107 108 109 110 111 112
-1

28. Periodic Table of the Elements
1
H
2
He
3
Li
4
Be
5
B
6
C
7
N
8
O
9
F
10
Ne
11
Na
12
Mg
13
Al
14
Si
15
P
16
S
17
Cl
18
Ar
19
K
20
Ca
21
Sc
22
Ti
23
V
24
Cr
25
Mn
26
Fe
27
Co
28
Ni
29
Cu
30
Zn
31
Ga
32
Ge
33
As
34
Se
35
Br
36
Kr
37
Rb
38
Sr
39
Y
40
Zr
41
Nb
42
Mo
43
Tc
44
Ru
45
Rh
46
Pd
47
Ag
48
Cd
49
In
50
Sn
51
Sb
52
Te
53
I
54
Xe
55
Cs
56
Ba
57
La
72
Hf
73
Ta
74
W
75
Re
76
Os
77
Ir
78
Pt
79
Au
80
Hg
81
Tl
82
Pb
83
Bi
84
Po
85
At
86
Rn
87
Fr
88
Ra
89
Ac
104 105 106 107 108 109 110 111 112
-2

29. Periodic Table of the Elements
1
H
2
He
3
Li
4
Be
5
B
6
C
7
N
8
O
9
F
10
Ne
11
Na
12
Mg
13
Al
14
Si
15
P
16
S
17
Cl
18
Ar
19
K
20
Ca
21
Sc
22
Ti
23
V
24
Cr
25
Mn
26
Fe
27
Co
28
Ni
29
Cu
30
Zn
31
Ga
32
Ge
33
As
34
Se
35
Br
36
Kr
37
Rb
38
Sr
39
Y
40
Zr
41
Nb
42
Mo
43
Tc
44
Ru
45
Rh
46
Pd
47
Ag
48
Cd
49
In
50
Sn
51
Sb
52
Te
53
I
54
Xe
55
Cs
56
Ba
57
La
72
Hf
73
Ta
74
W
75
Re
76
Os
77
Ir
78
Pt
79
Au
80
Hg
81
Tl
82
Pb
83
Bi
84
Po
85
At
86
Rn
87
Fr
88
Ra
89
Ac
104 105 106 107 108 109 110 111 112
-3

30. Periodic Table of the Elements
1
H
2
He
3
Li
4
Be
5
B
6
C
7
N
8
O
9
F
10
Ne
11
Na
12
Mg
13
Al
14
Si
15
P
16
S
17
Cl
18
Ar
19
K
20
Ca
21
Sc
22
Ti
23
V
24
Cr
25
Mn
26
Fe
27
Co
28
Ni
29
Cu
30
Zn
31
Ga
32
Ge
33
As
34
Se
35
Br
36
Kr
37
Rb
38
Sr
39
Y
40
Zr
41
Nb
42
Mo
43
Tc
44
Ru
45
Rh
46
Pd
47
Ag
48
Cd
49
In
50
Sn
51
Sb
52
Te
53
I
54
Xe
55
Cs
56
Ba
57
La
72
Hf
73
Ta
74
W
75
Re
76
Os
77
Ir
78
Pt
79
Au
80
Hg
81
Tl
82
Pb
83
Bi
84
Po
85
At
86
Rn
87
Fr
88
Ra
89
Ac
104 105 106 107 108 109 110 111 112
+3

31. Periodic Table of the Elements
1
H
2
He
3
Li
4
Be
5
B
6
C
7
N
8
O
9
F
10
Ne
11
Na
12
Mg
13
Al
14
Si
15
P
16
S
17
Cl
18
Ar
19
K
20
Ca
21
Sc
22
Ti
23
V
24
Cr
25
Mn
26
Fe
27
Co
28
Ni
29
Cu
30
Zn
31
Ga
32
Ge
33
As
34
Se
35
Br
36
Kr
37
Rb
38
Sr
39
Y
40
Zr
41
Nb
42
Mo
43
Tc
44
Ru
45
Rh
46
Pd
47
Ag
48
Cd
49
In
50
Sn
51
Sb
52
Te
53
I
54
Xe
55
Cs
56
Ba
57
La
72
Hf
73
Ta
74
W
75
Re
76
Os
77
Ir
78
Pt
79
Au
80
Hg
81
Tl
82
Pb
83
Bi
84
Po
85
At
86
Rn
87
Fr
88
Ra
89
Ac
104 105 106 107 108 109 110 111 112
No ions for
noble gases.

32. Common Cations (+) and Anions (-)
+1
+2
Transition metals – mult. oxidation states
+3 4 -3 -2 -1

33. Matter – Atoms and Combinations of Atoms
Sometimes atoms of elements combine into MOLECULES
and / or COMPOUNDS

34. Compounds are substances which contain 2 or more different types of
elements chemically combined in a fixed ratio
Compounds
H2O C2H4OH

35. Molecules are substances which contain 2 or more atoms, and are the most
basic unit of a substance
Molecules can contain atoms of the same element or different types of
elements
Molecules

36. The Point of Reactions and Bonding is….
Why Bonds Form
Types of Bonds
Reactions and Equations
Energy!
Chemical Bonds and Reactions

37. Why Do Chemical Bonds Form?
Atoms are most stable when their outermost
energy level is filled with electrons
In order to have a full valence atoms can
share or transfer electrons among their
nuclei. This results in formation of bonds.
A Bohr Model or electron configuration can
be used to determine the number of
electrons in the outer shell (valence shell) of
any atom

38. Bohr Models? Electron
configuration? How?

39. Element Information - Review
This (the electron
statement) is only true
if we are discussing an
atom and NOT an ion

41. Types of Bonds
Chemical Bonds Form When Atoms Share or Transfer Electrons
Covalent Bonds form when an electron (or
electrons) are shared between atoms
Ionic Bonds forms when an electron (or
electrons) is transferred from one atom to
another
Type of bond formed is dependent on the
relative electronegativities of atoms involved

42. Ionic Bonds
Draw a Bohr Model of Sodium (Na) and Chlorine (Cl) How does each atom
become most stable with a full outer shell of electrons?
The strong attraction
between the positive
sodium ion and the
negative chloride ion
creates an ionic bond

43. Ionic Compounds
These are compounds typically compounds of a metal element
and a nonmetal element.
– The metal loses electrons to become a + ion (Cation), and the
nonmetal gains electrons to become a – ion (Anion); the non metal
element has a significantly higher electronegativity
– The + and – ions are attracted to each other in a ratio so that the
resulting compound is neutral in charge; ionic bonds. NaCl MgF2
are examples.
– The formula unit is the simplest ratio of ions.
– These have unique names formed from naming the cation followed
by the anion with an “ide” ending.

44. Ionic Compounds - Formulas
Examples (don’t show charges in compound)
Na & F Na+1 F-1
Na & O Na+1 O-2
Ca & N Ca+2 N-3
K+1 & NO2
-1
NaF
Na2O
Ca3N2
KNO2

45. Ionic Compounds - Nomenclature
Simple Ionic Compounds
Name + then – ions and change ending to “ide.” If a polyatomic ion is
present, then name it.
Examples:
NaCl = Sodium Chloride
BaI2 = Barium Iodide
Na3P = Sodium Phosphide
Al2O3 = Aluminum Oxide
AlF3 = Aluminum Fluoride
Mg3N2 = Magnesium Nitride

46. Polyatomic Ions
Multi-atom Ions
Usually are negative
Usually contain oxygen
Names often end in -ite or -ate
Charges and formulas cannot be predicted from
Periodic Table

47. Polyatomic Ions
• Nitrate = NO3
-
– One N plus three oxygens; total charge = -1
• Carbonate = CO3
-2
– One carbon plus three oxygens; total charge = -2
• Sulfate = SO4
-2
– One S plus four oxygens; total charge = -2
• Hypochlorite = ClO-
– One Cl plus one oxygen; total charge = -1

48. Combining Ions
Rules are the same; charges add to zero.
Magnesium nitrate
Mg+2 and NO3
-1
Mg(NO3)2
+2 -1 -1
Note: where more than one polyatomic ion occurs,
it must be enclosed in parentheses. A subscript
always follows the closed parenthesis.

49. Covalent Bonds
Non-polar covalent bonds form if the electrons are shared equally
Polar covalent bonds form if the electrons are not shared equally

50. Valence
The number of chemical bonds an atom can form.
Usually calculated by subtracting the number of valence shell electrons
from 8 (or 2 in the case of H and He)
Helps to predict chemical formula
Examples:
HCl H2O NH3 CH4

51. Electronegativity
The affinity an atom has for electrons
Electronegativity and Bonding Rules
1. Extreme differences in electro- (group 1 or 2 with
group 6 or 7) results in ionic bonds.
2. C and H very little difference in electro- results in
nonpolar covalent bond.
3. 2 atoms of the same element have no difference
in electro- results in nonpolar covalent bond.
4. O or N with C or H, moderate difference in
electronegativity. Electrons pulled toward O or N,
results in polar covalent bond

53. A chemical reaction involves the making or breaking of
chemical bonds (ionic or covalent)
Chemical reactions are necessary for life:
• To establish stable atomic structures
• To form new molecules that cells need
•To manage cellular energy (energy release, usage, and storage)
Chemical Reactions and Equations

54. Chemical equations describe a chemical reaction
Chemical equations provide the following information:
The different elements involved in the reaction
The number of atoms involved in the reaction
The reactants and products of the reaction
Chemical Reactions and Equations

55. Reading a chemical reaction…..
Carbon dioxide and water react (in the presence of sunlight and
chlorophyll) to produce carbohydrate (glucose) and oxygen
Chemical Reactions and Equations

56. Other information from the equation….
Coefficient tells # of molecules of reactants and products:
6 CO2
6 H2O
1 C6H12O6
6 O2
Chemical Reactions and Equations

57. Law of Conservation of Matter
In a chemical reaction matter cannot be created or
destroyed, but it may change form

58. Five general types of reactions
1. Synthesis / Combination (Anabolism)
2. Decomposition (Catabolism)
3. Combustion
4. Single Replacement
5. Double Replacement
Exchange

59. Classify each of the following as one of your
5 from the previous slide.
Add to or adjust your list as necessary.
1. A + B  AB
2. AB  A + B
3. A + O2  CO2 + H2O
4. A + BC  AC + B
5. AB + CD  AD + CB

60. Reactions can be reversible

61. Oxidation Reduction

62. The Chemistry of Water

63. The Structure of Water
Surface tension and capillary action
Temperature moderation
Low density of ice
Water as a solvent
The Importance of Water

64. The Structure of Water
Two hydrogen atoms are each joined to an oxygen
atom by a single polar covalent bond
Hydrogen Bond
The weak attraction between the
hydrogen atom of one molecule and a
slightly negative atom within another
molecule
The Importance of Water

65. Surface Tension

66. The tendency of
molecules of the same
kind to stick to one
another is called
cohesion.
The type of attraction that
occurs between unlike
molecules is called
adhesion.
Surface Tension and Capillary Action

67. Temperature Moderation
Water has a better ability to resist temperature change than
most other substances
•Oceans and large lakes moderate
the temperatures of nearby land
areas
•Water also moderates
temperature through
evaporation, such as when you
sweat

68. Low Density of Ice

70. When NaCl dissolves in water the ionic bonds are
broken. The sodium cation is attracted to the
slightly negative part of the water molecule and
the chloride anion is attracted to the positive part
of the water molecule.
Water is an excellent solvent

71. Water is an excellent lubricant

72. Solutions
Solute A solid that dissolves in a solution
Solvent The liquid that does the dissolving
Hydrophilic Any substance that will dissolve in water.
Ionic Compounds
Molecules with polar covalent bonds
Electrical charges attract to partial charges on
water molecule
Salt, sugar, proteins
Hydrophobic Any substance that will not dissolve in water
Molecules with nonpolar covalent bonds
Majority of atoms are C and H
Oils, fats, waxes (lipids)

73. When a covalent compound
such as water is converted to
ions, there are H+ and OH-
ions in solution
The presence and abundance of these ions is critical to the
functioning of the cell in terms of its biochemistry
The relative abundance of H+ and OH- ions in solution is
measured by the….
pH Scale
Ions and Living Cells

74. A pH of 7 [H+] = [OH-] ions in solution
A pH less than 7 [H+] > [OH-] ; acid
A pH greater than 7 [H+] < [OH-] ; base
Ions and Living Cells

75. Acid Bases and Salts
HF  H+ + F-
HCl  H+ + Cl-
H2SO4  2H+ + SO4
2-
NaOH  Na+ + OH-
KOH  K+ + OH-
Mg(OH)2  Mg2+ + 2OH-
KCl  K+ + Cl-
MgF2  Mg2+ + 2F-
Acids
Donate H + + to solution
Lower pH
Bases
Donate OH- to solution
Raise pH
Salts
Donate neither H + + nor OH- to
solution; do not affect pH

76. The functioning of
living cells can be
affected by a
change in pH
Because the very
reactions of life cause
pH changes, there is a
need for cells to be
able to regulate the
pH of the intracellular
fluid
Ions and Living Cells

77. Buffers
Biological fluids resist changes to pH because of buffers
Buffers work by accepting H+ from solution when they are in
excess and donating H+ when they have been depleted
Most Buffers are weak acids and bases

78. Bicarbonate buffer system