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Chapter 2:
Atoms, Molecules & Life
What Are Atoms?
• An atom are the smallest unit of
matter.
• Atoms are composed of
Electrons = negatively charged particles.
Neutrons = particles with no charge
(neutral).
Protons = positively charged particles.
• Protons and neutrons are found in the
nucleus of an atom
• Electrons orbit the nucleus.
An atom is neutral, the # of electrons = #
protons
An example of an atom:
Remember that neutrons are neutral, so there can
be more of them than protons.
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Chapter 2: Atoms, Molecules & Life
Periodic Table of Elements:
Element = Substance that can’t be
broken down or converted to another,
simpler substance by ordinary chemical
means.
Atomic Number = Number of protons in
the nucleus
Since # of protons always equals the #
of electrons, why don’t we use the # of
electrons as the atomic number?
Atomic Mass
= Number of protons &
neutrons in nucleus
Periodic Table
Why is the mass number a decimal?
Chapter 2: Atoms, Molecules & Life
Isotope = The same element with a different
number of neutrons
• C14
• P32
• U235
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Isotopes
• Isotopes: Same element,
different number of neutrons.
• Different number of neutrons
changes the atomic mass, but
NOT the atomic number.
Atomic number remains
1 for hydrogen and its
isotopes
Isotopes
• Some isotopes, but not all, are radioactive.
Example: Carbon 14 (C14) is radioactive
Example: Hydrogen 2 (not radioactive) and hydrogen 3
(radiocative)
• Isotopes are useful in research
Nuclear experiments involved heavy water (H2)
Radiolabelling
used to be H3, but now other isotopes are used.
Radiocarbon Dating:
• Technique for determining the age of materials that contain
carbon based on C14 levels
C12O2
C14O2
Half-life ~ 5730 years
1 C14 for every
1,000,000,000,000 C12
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Crucial elements in life
• Carbon
All organic matter has carbon.
18.5% of the human body mass is carbon atoms.
• Hydrogen
All macromolecules have hydrogen as a component.
9.5% of the human body mass is hydrogen atoms.
• Oxygen
All macromolecules have oxygen as a component.
65% of the human body mass is oxygen atoms. Why so much oxygen?
• Nitrogen
All proteins have nitrogen as a component
3.3% of the human body mass is nitrogen atoms (mainly in muscle and
other proteins)
Other important elements in life
•
Calcium
Component of bones.
•
Phosphorus
A component of all cells (phospholipids).
•
Potassium
An important electrolyte, also keeps cell alive via
sodium potassium pump.
•
Sulfur
A component of some protein molecules.
•
Sodium
Another important electrolyte, sodium ion pumps.
Compounds vs. Molecules
• Compound: A substance made up of different
types of atoms.
Example: Table salt, NaCl.
• Molecule: a particle composed of one or more
atoms held together by chemical bonds.
Example: Table salt, NaCl
Also the smallest unit of a compound.
• Not all molecules are compounds.
H2, O2, and other diatomic gases are not molecules.
Why?
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How are molecules formed?
• The number of electrons in the outermost electron
shell determine whether an atom is reactive or inert.
Carbon: reactive.
4 electrons in outer shell,
needs 4 more to fill shell
Neon: inert
8 electrons in outer shell,
Does not need electrons to fill shell
How are molecules formed?
• How many electrons are
needed to fill an electron
shell?
Depends on which shell.
• First shell only needs two
hydrogen, helium.
• Second shell needs eight.
• Third shell needs eight.
Inert Atoms = Atoms with their outermost shell either
completely full or empty
Reactive Atoms = Atoms with their outermost shell only
partially filled
Hydrogen
Carbon
Oxygen
Helium
Neon
Argon
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How are molecules formed?
• Reactive atoms want to lose or gain electrons to
stabilize their outer (valence) shell.
(Figure 2.3)
Chemical bonds
• Types of chemical bonds
Covalent: the strongest of the three main types.
Ionic: weaker than covalent bonds.
Hydrogen bonds: the weakest chemical bond of the
three main types.
• Chemical bonds are crucial for chemical reactions
Chemical Reaction = making or breaking chemical
bonds.
Chemical reactions are essential for all life.
Covalent bonds: the strongest chemical bond
• Atoms share electrons in covalent bonds.
Sharing of
electrons
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Covalent bonds: the strongest
• Most biological molecules
utilize covalent bonds.
Proteins
Carbohydrates
Lipids
DNA
• Carbon atoms are always
linked by covalent bonds.
Examples of Covalent Bonds:
Share one pair of electrons (H2)
• Single covalent bond
H-H
Share two pairs of electrons (O2)
• Double covalent bond
O=O
Share three pairs of electrons (N2)
• Triple covalent bond
N N
Bonding Patterns (Table 2.3):
Carbon (C)
Oxygen (O)
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Non-polar Covalent Bonds:
Equal sharing of electrons
Polar Covalent Bonds:
Unequal sharing of electrons
Molecule is electrically neutral, but
poles are charged due to differences
in nuclear attraction for electrons
(electronegativity)
Ionic Bonds
• Attractive force between atoms that have lost or gained
electrons
Creates ions (negatively or positively charged atoms)
Transfer of
electrons
Example of ionic bonds
• Sodium chloride (table salt)
Sodium wants to lose one electron to stabilize its outer shell
Chloride needs to gain one electron to stabilize its outer shell.
Sodium Chloride (NaCl - Figure 2.3)
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Ionic bonds typically occur between atoms that are
located on opposite sides of the periodic table.
Hydrogen Bonds
• Attractive force between water
molecules due to polar covalent
bonds.
Electrons are far more attracted to
oxygen than to hydrogen atoms.
hydrogen atoms have a slight
positive charge.
Oxygen atoms have a slight
negative charge.
(Figure 2.5)
• Makes water a very special
molecule.
Water = Good Stuff!
Life most likely arose in water
Living organisms 60 - 90% water
Why is Water so Important to Life?
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Humans and water
• Human body is 65% water.
• The average human can
survive several months
without food.
But you can only survive
3 – 4 days without water.
All life depends on water
• Search for life on other planets often includes
the search for H2O
• Phoenix spacecraft will land in
one
of Martian ice caps in hopes of
finding water and microbial life.
Landed May, 2008,
found ice on
July 31st, 2008.
Why is Water so Important to Life?
Importance of Water:
1) Water is an excellent solvent:
• liquid capable of dissolving other substances in itself
Dissolving Ionic Bonds:
(Salt)
(Figure 2.6)
Polar nature of water
Solution = Fluid containing dissolved substances
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Dissolving Polar Covalent Bonds:
(e.g. glucose)
Hydrophilic Molecules:
Water-loving
+
-
• Molecules electrically
attracted to water
• Ions, polar molecules
Hydrophobic Molecules:
Water-fearing
• Molecules electrically
neutral (fats / oils)
• Molecules tend to clump
together in water
(Figure 2.7)
Hydrophilic vs hydrophobic
Hydrophilic
Hydrophobic
Importance of Water:
2) Water molecules tend to stick together (cohesion):
• Surface Tension: Tendency for a water surface to
resist breaking
• Adhesion: Tendency for water to stick to walls of
surfaces
Flow against
gravity
Walk on
water
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Importance of Water:
3) Water Can Form H+ and OH- Ions (ionization):
H+ + OH-
H2O
Pure water contains equal amounts of H+ and OH-
HCl
Acidic
H+ = OH-
H+
> OH-
Water
Basic
NaOH
H+ = OHH+ <
OH-
Water
Acids & bases disrupt the equilibrium.
Acid
A substance that increases the [H+]
in a solution
Base
A substance that decreases the
[H+] in a solution
The pH of a solution describes its degree of acidity:
(Figure 2.9)
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Importance of pH to living systems
Changes in pH disrupt life chemistry
Example: Blood
usual pH = 7.4
pH 7.0 , 7.8 lethal
So how does blood maintain a healthy pH?
Buffers
Buffers - solutes that act to resist changes to
the pH of a solution when H+ or OH- is
added.
Biological fluids use buffers to help maintain
correct pH.
Buffers maintain a solution at relatively constant pH:
• Stable pH essential for normal function
• Buffers either accept or release a H+ in response to
changes in pH
Example: Bicarbonate ion (HCO3-)
Too acidic?
HCO3- + H+
Bicarbonate ion
Hydrogen ion
H2CO3
Carbonic Acid
Too basic?
H2CO3 + OHCarbonic Acid
Hydroxide ion
HCO3- + H20
Bicarbonate ion
Water
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Importance of Water:
4) Water Moderates Temperature Changes:
Background:
• Temperature = Speed of molecules
• Slow molecules = Cool temperatures
• Fast molecules = Warm temperatures
A) Water Heats Slowly
• Energy first initiates breaking of hydrogen bonds…
• Specific Heat = energy needed to heat 1 gram of
a substance 1°C
• Specific HeatWater = 1 cal
• Specific HeatAlcohol = 0.6 cal
• Specific HeatGranite = 0.02 cal
Importance of Water:
4) Water Moderates Temperature Changes:
A) Water heats slowly
B) Water is an effective coolant
• Heat of Vaporization: Heat needed to convert liquid
water to water vapor
• 529 calories/gram (very high!)
By evaporating 1 g of water,
539 grams of human body cools 1°C
C) Water freezes slowly
• Moderates the effects of low temperatures
D) Water forms ice (less dense than fluid water):
• Acts as an insulator for life below
Why does ice weigh less than liquid water?
• Water is the most dense
(0.9998 g/cm3) at 40 C.
• Below 4 degrees, the water
molecules form more hydrogen
bonds, forming lattice like
crystals.
• This characteristic is very
important for aquatic
organisms.
Why??
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Because ice floats!
Any questions?
Next Class
• We will be starting Chapter 3: Biological
molecules
• Remember there are games to use as study tools
Especially useful for learning terminology.
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