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Atoms, Molecules, and Life
Atoms
The Importance of Water
Chapter 2
• The basic structural unit of matter.
nucleus
proton
neutron
electron
electron shell
1
Hydrogen
2
1
H
3
Hydrogen
1.008
4
1 - Atomic Number
= # of protons
Helium
2 - Element
3 - Symbol
4 - Molecular Mass
~ # protons + # neutrons
Carbon
1
2
6
C
Carbon
12.01
3
4
Properties of Elements
• Element: a substance that cannot be broken
down nor converted to another substance
by ordinary chemical means.
• Isotope: atoms of an element that contain
different numbers of neutrons
–
–
12C
has 6 protons and 6 neutrons (normal)
14C has 6 protons and 8 neutrons (“heavy” carbon)
• Some isotopes are
radioactive, they
spontaneously break
apart, releasing energy
and forming new
elements.
Electrons: the key to bonding
• Negatively charged
• Repel each other
• Attracted to the
positively-charged
nucleus
• Can become excited
Excited Electrons:
Disobeying Electron Shells
• Electrons orbit through different energy levels
– 1st shell: up to 2 electrons (e-)
– 2nd shell (and each larger shell): up to 8 e-
• Always fill up the lowest energy level first
Free Radicals
• Atoms with one or more unpaired electron in
their outer shell.
• Very unstable.
• Capture electrons from neighboring
molecules, creating new free radicals.
• Can lead to cell death and a variety of
diseases.
• Antioxidants react with free
radicals, rendering them
harmless to the body.
• More stable when shells are full
Interacting Elements
• An atom whose outer electron shell is full
cannot interact with other atoms and is called
inert.
• Atoms is reactive when its outer electron shell
is only partially full and it can react with other
atoms.
Molecules
• Two or more atoms of the same or different
elements held together.
• Molecules formed from different elements
are compounds.
• Atoms can form three
main types of bonds:
– Ionic, Covalent, and
Hydrogen bonds
Ionic Bonds
Example: MgCl2
Ionic bonding, with one electron from Magnesium
donated to each Chlorine atom
• An electron is transferred, creating
positive and negative ions that attract
one another.
12
Mg
Magnesium
24.31
12 protons
12 neutrons
12 electrons
(2 e- in the outer shell)
• MgCl2:
– Total # protons:
• 12 + (17)*2 = 46
– Total # electrons:
Chlorine:
17
Cl
Chlorine
34.45
Sodium (11 p+, 11 n)
Magnesium:
• 12 + (17)*2 = 46
17 protons
18 neutrons
17 electrons
(7 e- in the outer shell)
– Combined Molecular
Mass:
• 24.31 + (34.45)*2 =
93.21 g/mol
Chlorine (17 p+, 18 n)
Covalent Bonds
Covalent Bonds, continued
• Electron pairs are shared.
• Polar covalent bonds: unequal sharing.
• Nonpolar covalent bonds: equal sharing.
– Electrons spend more time around one atom
than the other.
– Two hydrogen atoms
share electrons to form
uncharged H2.
– Electrons spend the same amount of time
around each nuclei.
-
-
Oxygen is slightly negative
Hydrogen is slightly positive
+
Water, H2O
+
Example: NH3,
Ammonia
• Polar, covalent bonding, sharing
the electrons of Hydrogen to fill
Nitrogen’s outer e- shell.
7
N
Nitrogen:
14.01
H
– Total # protons:
7 protons
7 neutrons
7 electrons
(5 e- in the outer shell)
Nitrogen
1
• NH3:
• 7 + (1)*3 = 10
– Total # electrons:
• 7 + (1)*3 = 10
Hydrogen:
– Combined Molecular
Mass:
1 proton
0 neutrons
1 electrons
(1 e- in the outer shell)
Hydrogen
1.008
• 14.01 + (1.008)*3 =
17.034 g/mol
Properties of Water
Hydrogen Bonds
• The slightly attraction between atoms
involved in polar covalent bonds from
different molecules.
+
-
+
+
-
-
+
• Life likely began underwater.
• All living organisms contain 60-90% H2O.
• All life depends on water.
– (examples: Photosynthesis and Digestion)
+
+
Covalent bonds are the most common bond
found in biologic systems.
Properties of Water
Properties of Water
1. Very good solvent.
– It is able to dissolve a wide range of
substances.
Solute: Salt
Solvent: Water
Solution:
Salt Water
• Because of its
polarity, water
attracts both
positive and
negative ions,
breaking ionic
bonds.
Properties of Water
Properties of Water
2. Hydrophobic and Hydrophilic qualities.
•Hydrophobic (water-fearing)
molecules are non-polar and
uncharged.
3. Water molecules tend to stick together.
Because of their hydrogen bonds, water
molecules have high cohesion
(stickiness).
Cohesion of water molecules at the
surface creates surface tension.
•
•Water cannot dissolve them.
•Lipids, Fats and Oils
•Hydrophilic (water-loving)
molecules are polar.
•Water dissolves the covalent bonds.
•Sugars, Salts, and Amino Acids
•
•
The tendency for the water surface to resist
breaking.
Properties of Water
4. Water can be acidic, basic, or neutral.
• Water molecules are easily ionized:
Examples of Surface
Tension and Cohesion
Acids
• Acidic solutions have a higher concentration of H+
than OH-.
• Acids release hydrogen ions when dissolved in
water.
• Many acidic solutions taste sour (vinegar, lemon
juice, etc).
Bases
• Basic solutions have a higher concentration of OH-.
• Bases combine with hydrogen ions, reducing their
number.
• Many basic solutions taste bitter, and are very
harmful if consumed (ammonia, bleach, etc).
• Pure water has equal concentrations of
hydroxide (OH-) and hydrogen (H+) ions.
pH Scale (0-14)
• Measures the ratio of H+ to OH-.
• Neutrality (equal concentrations
of H+ and OH-) is set to 7.
• Acids have a pH below 7.
• Bases have a pH above 7.
0
Acidic
7
Neutral
14
Basic
Buffers
• A complex molecule that helps maintain a
solution at a constant pH.
• Can combine with H+ to increase pH.
• Releases H+ to combine
with OH- when needed
to decrease pH.
Example: Carbonate Buffering
of Blood
CO32- <--> HCO3- <--> H2CO3
pH ~ 6
Properties of Water
•Water moderates the effects of
temperature changes.
pH ~ 9.5
Water forms an unusual solid:
Ice
• Less dense than liquid water!
• H20 heats slowly
– Takes a lot of energy to break H-bonds
• H20 moderates high and low temperatures
• H20 freezes slowly
– A large amount of energy must be removed to
form ice crystals
Liquid
Solid
Homework
Chapter 2
The lizard in the beginning of this lecture
appears to be running on water.
Aside from the speed at which the lizard runs,
what properties of water allow the lizard to
move like this? How does this property work?
(i.e. describe the arrangement of molecules that gives
water this property)
Give two other examples where these properties
of water are used in nature.