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Basic chemistry review used for Anatomy and Physiology Students
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Anatomy & PhysiologyChemistry Review
Atomic Theory and Periodic Table ReviewSPDF orbital electron configuration
Ions and Ionic BondingCovalent Bonding
Important Biological ReactionsAcid / Base and pH
Buffers and buffering mechanism
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 MatterChemistry can be thought of as the study of matter, which is “Anything that is.”
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
The periodic table describes all the different types of known elements; all the different kinds of atoms
Elements
AtomsRecall 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
Element Information - Review
This (the electron statement) is only true if we are discussing an atom and NOT an ion
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
(Neutrons would be at nucleus too)
• 1 valence electron• To increase stability, loses
valence electron• Forms H+ cation
Bohr Model of Lithium• Lithium• 1 valence electron• Loses valence electron
– Forms Li+ cation
Bohr Model of Sodium• Sodium• 1 valence electron, if lost, Na+ cation
Bohr model of Beryllium• 2 valence electrons• Loses valence electrons
– Becomes Be2+ cation.
Bohr Model of Magnesium• 2 valence electrons• Loses 2 valence electrons
– Forms Mg2+ cation
Anions• Fluorine – 7 valence electrons
• Chlorine – 7 valence electrons
– Both gain 1 electron – Form -1 anions
SPDF Orbitals – a more modern look
Orbitals
Atoms with 3 or less valence electrons tend to lose them and become positive cations
From Atoms to Ions
From Atoms to Ions
Atoms with 5 or more valence electrons tend to gain more and become negative anions
Periodic Table of the Elements1H
2He
3Li
4Be
5B
6C
7N
8O
9F
10Ne
11Na
12Mg
13Al
14Si
15P
16S
17Cl
18Ar
19K
20Ca
21Sc
22Ti
23V
24Cr
25Mn
26Fe
27Co
28Ni
29Cu
30Zn
31Ga
32Ge
33As
34Se
35Br
36Kr
37Rb
38Sr
39Y
40Zr
41Nb
42Mo
43Tc
44Ru
45Rh
46Pd
47Ag
48Cd
49In
50Sn
51Sb
52Te
53I
54Xe
55Cs
56Ba
57La
72Hf
73Ta
74W
75Re
76Os
77Ir
78Pt
79Au
80Hg
81Tl
82Pb
83Bi
84Po
85At
86Rn
87Fr
88Ra
89Ac
104 105 106 107 108 109 110 111 112
+1
Periodic Table of the Elements1H
2He
3Li
4Be
5B
6C
7N
8O
9F
10Ne
11Na
12Mg
13Al
14Si
15P
16S
17Cl
18Ar
19K
20Ca
21Sc
22Ti
23V
24Cr
25Mn
26Fe
27Co
28Ni
29Cu
30Zn
31Ga
32Ge
33As
34Se
35Br
36Kr
37Rb
38Sr
39Y
40Zr
41Nb
42Mo
43Tc
44Ru
45Rh
46Pd
47Ag
48Cd
49In
50Sn
51Sb
52Te
53I
54Xe
55Cs
56Ba
57La
72Hf
73Ta
74W
75Re
76Os
77Ir
78Pt
79Au
80Hg
81Tl
82Pb
83Bi
84Po
85At
86Rn
87Fr
88Ra
89Ac
104 105 106 107 108 109 110 111 112
+2
Periodic Table of the Elements1H
2He
3Li
4Be
5B
6C
7N
8O
9F
10Ne
11Na
12Mg
13Al
14Si
15P
16S
17Cl
18Ar
19K
20Ca
21Sc
22Ti
23V
24Cr
25Mn
26Fe
27Co
28Ni
29Cu
30Zn
31Ga
32Ge
33As
34Se
35Br
36Kr
37Rb
38Sr
39Y
40Zr
41Nb
42Mo
43Tc
44Ru
45Rh
46Pd
47Ag
48Cd
49In
50Sn
51Sb
52Te
53I
54Xe
55Cs
56Ba
57La
72Hf
73Ta
74W
75Re
76Os
77Ir
78Pt
79Au
80Hg
81Tl
82Pb
83Bi
84Po
85At
86Rn
87Fr
88Ra
89Ac
104 105 106 107 108 109 110 111 112
+2 for many; some +1, others +3; several vary
Periodic Table of the Elements1H
2He
3Li
4Be
5B
6C
7N
8O
9F
10Ne
11Na
12Mg
13Al
14Si
15P
16S
17Cl
18Ar
19K
20Ca
21Sc
22Ti
23V
24Cr
25Mn
26Fe
27Co
28Ni
29Cu
30Zn
31Ga
32Ge
33As
34Se
35Br
36Kr
37Rb
38Sr
39Y
40Zr
41Nb
42Mo
43Tc
44Ru
45Rh
46Pd
47Ag
48Cd
49In
50Sn
51Sb
52Te
53I
54Xe
55Cs
56Ba
57La
72Hf
73Ta
74W
75Re
76Os
77Ir
78Pt
79Au
80Hg
81Tl
82Pb
83Bi
84Po
85At
86Rn
87Fr
88Ra
89Ac
104 105 106 107 108 109 110 111 112
-1
Periodic Table of the Elements1H
2He
3Li
4Be
5B
6C
7N
8O
9F
10Ne
11Na
12Mg
13Al
14Si
15P
16S
17Cl
18Ar
19K
20Ca
21Sc
22Ti
23V
24Cr
25Mn
26Fe
27Co
28Ni
29Cu
30Zn
31Ga
32Ge
33As
34Se
35Br
36Kr
37Rb
38Sr
39Y
40Zr
41Nb
42Mo
43Tc
44Ru
45Rh
46Pd
47Ag
48Cd
49In
50Sn
51Sb
52Te
53I
54Xe
55Cs
56Ba
57La
72Hf
73Ta
74W
75Re
76Os
77Ir
78Pt
79Au
80Hg
81Tl
82Pb
83Bi
84Po
85At
86Rn
87Fr
88Ra
89Ac
104 105 106 107 108 109 110 111 112
-2
Periodic Table of the Elements1H
2He
3Li
4Be
5B
6C
7N
8O
9F
10Ne
11Na
12Mg
13Al
14Si
15P
16S
17Cl
18Ar
19K
20Ca
21Sc
22Ti
23V
24Cr
25Mn
26Fe
27Co
28Ni
29Cu
30Zn
31Ga
32Ge
33As
34Se
35Br
36Kr
37Rb
38Sr
39Y
40Zr
41Nb
42Mo
43Tc
44Ru
45Rh
46Pd
47Ag
48Cd
49In
50Sn
51Sb
52Te
53I
54Xe
55Cs
56Ba
57La
72Hf
73Ta
74W
75Re
76Os
77Ir
78Pt
79Au
80Hg
81Tl
82Pb
83Bi
84Po
85At
86Rn
87Fr
88Ra
89Ac
104 105 106 107 108 109 110 111 112
-3
Periodic Table of the Elements1H
2He
3Li
4Be
5B
6C
7N
8O
9F
10Ne
11Na
12Mg
13Al
14Si
15P
16S
17Cl
18Ar
19K
20Ca
21Sc
22Ti
23V
24Cr
25Mn
26Fe
27Co
28Ni
29Cu
30Zn
31Ga
32Ge
33As
34Se
35Br
36Kr
37Rb
38Sr
39Y
40Zr
41Nb
42Mo
43Tc
44Ru
45Rh
46Pd
47Ag
48Cd
49In
50Sn
51Sb
52Te
53I
54Xe
55Cs
56Ba
57La
72Hf
73Ta
74W
75Re
76Os
77Ir
78Pt
79Au
80Hg
81Tl
82Pb
83Bi
84Po
85At
86Rn
87Fr
88Ra
89Ac
104 105 106 107 108 109 110 111 112
+3
Periodic Table of the Elements1H
2He
3Li
4Be
5B
6C
7N
8O
9F
10Ne
11Na
12Mg
13Al
14Si
15P
16S
17Cl
18Ar
19K
20Ca
21Sc
22Ti
23V
24Cr
25Mn
26Fe
27Co
28Ni
29Cu
30Zn
31Ga
32Ge
33As
34Se
35Br
36Kr
37Rb
38Sr
39Y
40Zr
41Nb
42Mo
43Tc
44Ru
45Rh
46Pd
47Ag
48Cd
49In
50Sn
51Sb
52Te
53I
54Xe
55Cs
56Ba
57La
72Hf
73Ta
74W
75Re
76Os
77Ir
78Pt
79Au
80Hg
81Tl
82Pb
83Bi
84Po
85At
86Rn
87Fr
88Ra
89Ac
104 105 106 107 108 109 110 111 112
No ions for noble gases.
Common Cations (+) and Anions (-)+1
+2
Transition metals – mult. oxidation states
+3 ±4 -3 -2 -1
Matter – Atoms and Combinations of Atoms
Sometimes atoms of elements combine into MOLECULES and / or COMPOUNDS
Compounds are substances which contain 2 or more different types of elements chemically combined in a fixed ratio
Compounds
H2O C2H4OH
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
The Point of Reactions and Bonding is….
Why Bonds Form
Types of Bonds
Reactions and Equations
Energy!
Chemical Bonds and Reactions
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
Bohr Models? Electron configuration? How?
Element Information - Review
This (the electron statement) is only true if we are discussing an atom and NOT an ion
Types of BondsChemical 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
Ionic BondsDraw 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
Ionic CompoundsThese 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.
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
Ba+2 & OH-1
NaF
Na2O
Ca3N2
KNO2
Ba(OH)2
Ionic Compounds - NomenclatureSimple 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
Polyatomic IonsMulti-atom Ions
Usually are negative
Usually contain oxygen
Names often end in -ite or -ate
Charges and formulas cannot be predicted from Periodic Table
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
Combining Ions
Rules are the same; charges add to zero.
Magnesium nitrate
Mg+2 and NO3-1
Mg(NO3)2+2 -1 -1Note: where more than one polyatomic ion occurs, it must be enclosed in parentheses. A subscript always follows the closed parenthesis.
Covalent BondsNon-polar covalent bonds form if the electrons are shared equally
Polar covalent bonds form if the electrons are not shared equally
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
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
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
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
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
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
Law of Conservation of Matter
In a chemical reaction matter cannot be created or destroyed, but it may change form
Five general types of reactions
1. Synthesis / Combination (Anabolism)
2. Decomposition (Catabolism)
3. Combustion
4. Single Replacement
5. Double Replacement Exchange
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
Reactions can be reversible
Oxidation Reduction
The Chemistry of Water
The Structure of Water
Surface tension and capillary action
Temperature moderation
Low density of ice
Water as a solvent
The Importance of Water
The Structure of WaterTwo 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
Surface Tension
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
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
Low Density of Ice
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
Water is an excellent lubricant
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 CompoundsMolecules with polar covalent bondsElectrical charges attract to partial charges on water moleculeSalt, 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)
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
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
Acid Bases and Salts
HF H+ + F-
HCl H+ + Cl-
H2SO4 2H+ + SO42-
NaOH Na+ + OH-
KOH K+ + OH-
Mg(OH)2 Mg2+ + 2OH-
KCl K+ + Cl-
MgF2 Mg2+ + 2F-
AcidsDonate H + + to solutionLower pH
BasesDonate OH- to solutionRaise pH
SaltsDonate neither H + + nor OH- to solution; do not affect pH
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
BuffersBiological 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
Bicarbonate buffer system
