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3
I. Chemistry Review
A. ELEMENTS (CHAPTER 2)
Element - a substance that cannot be separated into simpler substances by physical or
chemical means,

106 named chemicals (92 naturally occurring) 25 are necessary for life.
Four make up 96% of all living matter: COHN·
Other 4% {Ca, P, K, S, Na, CI, Mg, and trace elements} Trace elements -living
organisms need these but in smaller amounts: B, Cr, Co, Cu, F, I, Fe, Mn, Mo, se, Si,
Sn, VandZn.

Atom - smallest particle ofanelement that has the characteristics of that element. '
Two or more atoms can combine chemically and form a molecule.

Compound - any pure substance that contains two or more different atoms.

Atom = H Molecule = H2 Compound = H2O

B. FORMS OF MATTER
Solid - has definite shape and definite volume
Liquid ~ has no definite shape but has definite. volume
Gas - has no ·definite shape and no definite volume

C. SUBATOMIC PARTICLES
Atoms have a dense nucleus (protons & neutrons) with a very low density electron cloud
surrounding it.

Neutron (n") - neutral subatomic particle in the nucleus of an atom that has a mass of 1
amu or 1 dalton.

amu - Atomic mass unit. A unit used to measure the mass of very small particles such as
atoms, protons, and neutrons.

Proton (p+) - positively charged subatomic particle in the nucleus that has a mass of 1 .
amu.

Electron(e-) - negatively charged andhasa small mass (112000 ofaproton) .. This small
mass is considered to be negligible (0) in atomic mass calculations.

Strong nuclear forces hold the protons and neutrons together, while the electrons are
attracted to the positive charge of the protons. Protons and neutrons can be broken down
into small particles called quarks.

Atomic number - the number of protons in an atom; distinguishes atoms of different

elements.
 ,.

Atomic mass - mass of an atom.

Mass number - protons + neutrons in an atom of a given isotope.

Isotope - atoms of the same element having a different number of neutrons and therefore
have different atomic masses.

Hydrogen: 1p, 1e- Deuterium: lp, In, Ie- Tritium: 1p, 2n, 1e-
·1 amu 2amu 3amu

Some combinations of protons and neutrons are stable, but other combinations are
internally unstable and break down spontaneously. When this happens, the atoms release
various subatomic particles and radiation. These isotopes are called radioactive isotopes.

D. ELECTRON ORBITALS

» The first energy level (closest to nucleus) can hold up to 2 electrons (1s)
» The second energy level can hold up to eight electrons (2s, 2p)
» The third energy level can hold up to eight electrons (3s, 3p)
There are more than three energy levels, but biologists are concerned with 18 total
electrons. Atoms are most stable when their outer energy level is filled with electrons.
Of the three subatomic particles, only the electrons are directly involved in the chemical
reactions between atoms.

Not every electron has the same amount of energy (the ability to do work). Potential
energy, the amount of energy that matter stores, is due to the position or location of the
matter. Electrons have potential energy in relation to the nucleus.

To move to a shell farther out from the nucleus; the electron must absorb energy (ex:
Light energy can excite an electron to a higher energy level). To move to a shell closer
in, an electron must lose energy, which is usually released to the environment in the form
of heat.

E. HOW ATOMS FILL THEIR OUTER SHELL

An atom with its outer shell filled with electrons is a stable atom. Outer electrons are
valence electrons. Outermost electron shell is the valence shell. The valence of'H is I;
0,2;. nitrogen, 3; and carbon, 4. An atom with a completed valence shell is unreactive.

The noble gases: He, Ne, Ar have full valence shells and are called inert elements.

One slightly more complicated case is phosphorus (P). It can have a valence of3 as we
predict. In biologically important molecules, however, it generally has a valence of 5,
forming three single bonds and one double bond.

Atoms react with other atoms chemically by:filling their outer shells in one of three ways:
 ":' ;~. 1-"

,," ••• t

1. Ionic Bonds
a. Gain electrons.from another atom
b. Lose electrons from its outer shell to another atom
2. Covalent-Bonds
a. Share one or more pairs of electrons with another atom

F. BONDS
1. Ionic bonds and Ions
When two atoms are so unequal in their attraction for valence electrons that the
more electronegative atom strips an electron completely away from its partner.

Electronegativity is the attraction of electrons to an atom.

Sodium has 11 electrons: Is2, 2S2,2p6, 3s1

(Na needs to gain 7 more electrons or lose 1 electron.)

Chlorine has 17 electrons; 1s2,2s2; 2p6, 3s2,.3ps

(Clhas to lose seven electrons or gain one electron.)

Na donates one electron to Cl, these two atoms combine to form a compound,
sodium chloride salt. Ionic compounds are called salts. An ion is any charged atom.
Sodium donates an electron, which is negatively charged and becomes a positively
charged ion. The chlorine receives an electron and becomes a negatively charged ion.
The two ions are Na+ and CI-. When the two atoms give and receive electrons, they form
ions and ionic bonds.

Cation - positively charged ion

Anion - negatively charged ion

2. Covalent Bonds
. Electrons between atoms are shared. Covalent bonds occur when the
electronegativities of the atoms are similar.

A. Nonpolar covalent bonds form when the electrons are shared equally, such as in
02, theelectronegativities are identical and both atoms pull equally on the
electrons.
B. Polar covalent bonds form when electrons are shared unequally~ The atom with
the greater electro negativity will be slightly negative due to the fact that a
negative electron spends more time around its nucleus. The other atom has a
slightly positive charge. In a molecule of water (HiO), for example, electrons are
shared between the oxygen atom and each hydrogen atom. Oxygen, with a
greater electronegativity exerts a stronger pull on the shared electrons than does
the hydrogen atom. This unequal distribution of electrons creates a negative pole
near the oxygen and positive poles near each hydrogen atom.
~ Single covalent, double covalent, and triple covalent bonds form when, two, four,
and six electrons are shared, respectively ..
 C. Hydrogen Bonds are weak bonds between molecules. They form when a
positively charged hydrogen atom in one covalently bonded molecule is attracted
to a negatively charged area of another covalently bonded molecule. Hydrogen
bonds are 20 times weaker than covalent bonds;

nonpolar polar covalent ionic

covalent bonds bonds bonds

e- shared e- shared e-
equally unequally transferred
( )

increasing difference of
electro negativity )

between bonding atoms

Note: Covalent bonds form when electronegativities of the atoms are similar. Ionic bonds occur
when the electronegativity of the atoms are very different and one atom has a stronger pull on the
electron.

Structural Fonnula 0=0

Molecular formula 02

Electron configuration for the element 0

Chemical reactions make and break chemical bonds .. Matter is conserved in a chemical
reaction: reactions cannot create or destroy matter but can only rearrange it.

Photosynthesis:
6C02 + 6H20 --~) C6H1206 + 6 02
reactants yields products

¢:> opposite arrow heads indicate that the reaction is reversible. Most chemical reactions
are reversible.

Chemical equilibrium - equilibrium established when the rate ofthe forward reaction
equals the rate of the reverse reaction.

A molecule's biological function is related to its shape. Shape is determined by the

positions of it's atoms' valence orbitals. Shape is often the basis of the recognition of
one biological molecule by another.
 5

II. CHEMISTRY OF WATER (CHAPTER 3)

1. Water Properties
A. Powerful Solvent
Water is able to dissolve anything polar due to its polarity. Water separates ionic
substances. Covalent compounds dissolve in water are called hydrophilic. Nonpolar.
substances that do not dissolve in water are called hydrophobic;
B. Capillary Action
1. Adhesion: the attraction between water and other substances
2. Cohesion: the attraction of water molecules to other water molecules
These two properties allow capillary action. The meniscus, in a column of water,
is formed because gravity pulls down on the water ..molecules in the center while water
molecules at the sides of the container "climb" .' ..' .. .
C. High Surface Tension .
Water is attracted to itself, and this attraction, due to hydrogen bonds; is stronger than the .
attraction to the air above it. Strong cohesion between water molecules creates a surface that
is firm enough to allowmanyinsect to walk upon without sinking.' " ' ..

D. High Specific Heat

The amount of heat that must be absorbed or lost for 1 g of that' substance to change its
temperature by 1°C. Water changes temperature very slowly, therefore, the temperatures of
large bodies of water are very stable in response to the temperature changes of the
surrounding air. Water heats up as the hydrogen atoms vibrate (molecular kinetic energy-
energy of molecular motion). 1. Water covers % of the earth, keeps temp fluctuation
within a range suitable for life 2. Coastal areas have milder climates than inland 3.
Marine environments are relatively stable

E. High Boiling Point

A great deal of energy must be present in order to break the hydrogen bonds to
change water from a liquid to a gas. .

F. Good Evaporative Coolant

When humans sweat, water absorbs heat from the body. When the water turns into water
vapor, it takes that energy (heat) with it.

G. High Freezing Point & Lower Density As A Solid ThanA Liquid

Water's maximum density is 4°C, while freezing is O°C. This is why ice floats, this.
allows for aeration of still ponds in Spring and Fall and the reason that ponds don't freeze
from the bottom up. Expands when freezes. Lakes don't freeze because ice floats.
As water freezes it releases heat to the water below and insulates it, Water freezes,
hydrogen bonds form releasing heat.
heat.·'··
As ice melts, hydrogen bonds break absorbing
. '. .

H. Dissociation and pH Scale'

Many substances come apart (dissociate) in water. Some dissociate completely, while
others dissociate only partly. In a solution, some molecules are intact while others are
ionized{gain-or losee-). Water dissociates into Wand Off equally (hydrogen ion
and hydroxide ion)." .'
 6

A mole (mol) is equal in number to the molecular weight of a substance, but upscaled from
Daltons to units of grams. Sucrose (C 12H220 11) molecular wt = 342g .
Molecular weight = sum of the weight of all atoms in a molecule (expressed in
Daltons)
C = 12 dal 12 dal x 12 = 144
H= 1 dal 1 dal x 22 = 22
0= 16 dal 16dalxl1= 176
342 g
1. Acids
Substances that yield rr
when they dissociate in water are called acids. Acids add ir to
the solution, increasing the tr
concentration.
HCI ) W and cr
Molarity = number ofmoles of solute per liter of solution
·2. Bases
Substances that yield OfI' when they dissociate in water are called bases
(e.g. NaOH ) Na + and aIr). Bases also accept W. Bases reduce the
amount of W in a solution.
Off + W ~H20 or NIb + W ~ NH4+
3. Salts
A salt is a substance in which the W of an acid is replaced by another positively
charged ion. HCI + Na ~ NaCI and W

4. pH The acidity or alkalinity (base) is known as pH.

pH formula: pH = -log [Hl

IfpH = 6 then the concentration ofW per liter is 10~ in a solution.

PH Scale

o 1 2 3 4 5 6 ~ 8 9 10 11 12 13 14
acidic ( neutral ---7) basic

A pH of 5 is 10 times more acidic than a pH of 6. The more ir, t

the the [HJ and the
more acidic. Acid precipitation is rain, snow, or fog with a pH below 5.6.
Overhead 3.9: The pH of some aqueous solutions
5. Buffers
.Buffers are substances that takes up and releases rr
or OH to prevent swings in pH.
An important buffer is H2C03 (carbonic acid). H2C03 dissociates to and HC03-. ir
The H" is a base acceptor, and the RC03- is an acid acceptor. A buffer consists of an
acid-base pair that combines reversibly with hydrogen ions.
\' \) carbonic acid bicarbonate hydrogen ion
~()..S -7 H2C03 <=> HC03 - + W
4: '.
\ \ St'. S Bicarbonate acts a base to accept excess W ions when the pH starts to fall; the
reaction moves to the left
When pH rises, W ions are donated by carbonic acid, the reaction shifts to the
right
 Nobl,
1.00794
H
I
Periodic Table of the Elements gose:
1 VIII
1 METALS
/, II
,....
,,~ IV
NONMETALS

V" VI VIi"
4.00260
He
2
1 "1 2 .
6.9~1
Li
~ 9.01218
Be
1 10.81 3 12.011 ~ 140067 ~ 15.9994 6 18.998403 3 20.179
2 B C N 0 F Ne
3 4 5 6 7 8 9 10
1
1->2.9897 ~ 24.305 8 2698154 ~ 280855 i30.9737( 2
8 32.06 ~ 35.453 ~ 39.948
3 Na I Mg 2
TRANSITION ELEMENTS AI 3 Si 4 P 5 S 6 CI 7 Ar
11 12 13 14 15 16 17 18
390983
1
8 4008 ~ 449559
1
8 4788 ~ 509415 ~ 51996 ~ 54.9380 ~ 55.847 i 58.9332 2
8 58.69 i 63.546 "1
8 65.38
"1
8 69.72
"1
8 72.59 i 74.9216 "1
8 78.96 .~ 79.904
"1
8380
4 K 8
I
Ca 8
2
Sc 9
1
Ti 10
2
V II
2
Cr 13 Mn 13 Fe 14 Co 15
"1 Ni 16
2
Cu 18 Zn 18 Ga 18' Ge 18 As 18 Se IB Br
8
\8 Kr I
19 20 21 22 23 24 I 25 2 26 "1 27 28 29
I 2
32 4 5 4 7
30 31 3 33 34 35 36
85.4678
2
8 87.62 ~ 88.9059
2
8 91.22 ~ 92.9064
2
8 95.94
2
8 (981
2
8 101.07 i102.9055 ~ 106.42 ~107.8682
2
8 112.41 2
8 1\4.82
2
8 1\8.69 i 121.75 ~ 127.60 i 126.9045 2 131.29
5 Rb 18
8 Sr 18
8 Y 18
9
Zr 1.8
10
Nb 18
11 Mo 18
13
Tc 18
13 Ru 18 Rh 18
16
Pd 18
18
Ag 18 Cd 18 In 18 Sn \8 Sb 18 Te 18 I 8
18 Xe I
18 18 18
37 I 38 2 39 2 40 1 41 I 42 I 43 2 44 I~ 45 1 46 0 47 I 48 2 49 3 50 I~ 51 I~ 52 I: 53 18 I
7 54
132.9054 ~ 13733
I:2 Lontho-
178.49
2
8 180.9479 ~ 18385
2
8 186.207 8
2
190.2
2
8 192.22 i 195.08 i196.9665
"1
200,59
"1
8 20083
2
207.2 ~ 208.980.
2 2 2
Cs 18 Ba nide
Hf 18 Ta 18 W .18 Re 18 Os 18 Ir 18 Pt l~ Au ..32188 Hg 18 TI
8
.18 Pb B'I 8 12091
Po
8 12101
At
8 (2221

55
18
8 56
18
8
Series
72
32
10 73 n 74
32
12 75 13
32
1
76
32
14 77
32
15 78 17 79 18 80
32
18 81
31
18 82
18
32
18 83
18
31
18 84
18
31
18 85
18
31
18
Rn
86
I
3
I
6 I 1 174 967
Lu
~
18
"1 "1 2 1 1 I I 1 3 4 5 6 7
32
71 9
1
1 1 "1 2 2 2
.. . .. .-
~ 226.0254 . 8 Actinide (2631 2
12231 12611 8 12621 8 8 126UI 8 (2651 8 1266il 8
SIlrill,
Fr 18
32 Ro
18
32 2
Unq 18
32
Unp 18
32 Unh 18
32
Uns 18
J1 Uno 18
32
Une 18
32
87 18 88 18 (2601 8 104 31 105 31 106 32 107 32 108 32 109 32
7 8
I
8
1 Lr 18
31
10
2
II
1
12
1
13
2
14
2
15
2
103 32
9
2

RARE EARTH ELEMENTS

1389055
2
8 140.12 ~ 140.9077 ~ 144.24
2
8 (1451 ~ 150.36
2 151.96
8 i 157.25
"1 .
8 158.9254 i162.50 i 164.9304 i 167.26 ~ 1689342
2
8 17304
2
8
lanlhanide La 18
18 Ce 18 Pr 18 Nd 18
12
Pm 18
23
Sm 18
24 Eu 18.
25
Gd 18 Tb 18 Dy 18 Ho 18 Er 18
30
Tm 18 Yb 18
32
Series 57 9 58 2~ 59 2~ 60 8 61 8 62 8 63 8 64 "1~ 65 278 66 2~ 67 2~ 68 8 69 3~ 70 8
2 2 "1 2 2 2 "1 2 "1 1 1 2 1 2

I2no27E ~ 232.0381 ~ 231.0359 ~ 238.D28S 2 2 2 1 2 2 2 2 1 2 2

8 ~J70482 a 12441 8 12431 B (2471 B (2471 B (2511 B 12521 8 (2571 8 12581 8 (2591 8
Actinide Ac 18 Th 18 Pa ia U 18 Np 18 Pu 18 Am 18 Cm 18 Ok 18 Cf 18 Es 18 Fm 18 Md 18 No 18
Series 89 t~
9
90 n
10
91 ~6
9
92
32
21
9
93
J2
12
9
94
31
24
8
95
31
25
8
96
32
25
9
97
32
27
8
98
32
2B
8
99
31
29
8
100
32
30
8
101
32
31
8
102
J1
32
8
2 2 2 2 2 2 2 2 1. 2 2 2 2 2

,•
.- A value given in brackets denotes the moss number
. of the isotope of longesl known half-life.
4.,

·C C C
~.
I -~

3 "
r.
-