CHAPTERS 2 & 3:
THE CHEMISTRY
OF LIFE
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WHY ARE WE STUDYING CHEMISTRY…AGAIN?
Chemistry is the
foundation of Biology
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CHEMISTRY LEADS TO…
Biomolecules
lead to…
Cells
lead to…
Organisms…
Populations…
Communities…
Ecosystems…
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 Everything is made of matter
 Matter is made of atoms
Hydrogen
Proton
+
Neutron
0
1 proton
1 electron
Electron –
Oxygen
8 protons
8 neutrons
8 electrons
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THE WORLD OF ELEMENTS
H
C N O
Na Mg
P S
K Ca
Different kinds of atoms = elements
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LIFE REQUIRES ~25 CHEMICAL
ELEMENTS
About 25 elements are essential for life
 Four elements make up 96% of living matter:
• carbon (C)
• hydrogen (H)
• oxygen (O)
• nitrogen (N)
 Four elements make up most of remaining 4%:
• phosphorus (P)
• calcium (Ca)
• sulfur (S)
• potassium (K)
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Bonding…what’s up buddy?
= Effect of electrons (they’re at the center of it all…har har!)
 electrons determine chemical behavior of atom
 depends on number of electrons in atom’s
outermost shell
= valence shell
How does this
atom behave?
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Bonding properties
How does this atom behave?
How does this atom behave?
The most important parts of an atom
interms of BIOLOGY are its…???
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Electrons!!!!
WHY?
Electrons are on the OUTSIDE
They are the parts that BUMP
INTO other atoms
= the parts that REACT with and
BOND to other atoms
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CHEMICAL REACTIVITY DEPENDS ON
BONDING!
Atoms “want” 8 electrons in
their outer shell!
Atoms tend to:
complete a partially filled valence shell (take or share) =
strong (non-metals)
or
empty a partially filled valence shell (give) = weak (metals)
This tendency drives chemical reactions…
and creates bonds
–
–
–
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ELEMENTS & THEIR VALENCE SHELLS
Elements in the same row have
the same number of shells
Generally, knowing how many SHELLS an atom has
Is not very useful to us (at least in ap bio)
Moving from left to right, each element has a
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sequential addition of electrons (& protons)
Why do you think the only
atom other than oxygen
used in
food chains on
planet Earth is SULFUR?
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Solid @ RT
Liquid or Gas @ RT
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WHAT TYPES OF BONDS
SHOULD YOU KNOW FOR
BIOLOGY?
Hydrogen bond
H2O
Weak bonds
hydrogen bonds
VIDEO
H2O
attraction between + and –
hydrophobic & hydrophilic interactions
interaction with H2O
Covalent bond
van derWaals forces
 disulfide bridges
–
Strong bonds
covalent bonds
Ionic bonds
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–
H2 (hydrogen gas)
COVALENT BONDS
Why are covalent bonds strong bonds?
 two atoms share a pair of electrons
 both atoms holding onto the electrons
 very stable
 not always equal sharing
Forms molecules
H
–
H
H—H
O
Oxygen
H
–
H
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H2 (hydrogen
gas)
H2O (water)
NONPOLAR COVALENT BOND
Pair of electrons shared equally by 2 atoms
example: hydrocarbons = CxHx
methane (CH4 )
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balanced, stable,
good building block
POLAR COVALENT BONDS
= Pair of electrons shared unequally
by 2 atoms
example: water = H2O
+
oxygen has stronger “attraction” for H
the electrons than hydrogen
 oxygen has higher electronegativity
 + vs – poles
 leads to many interesting
H
properties of water…
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+
–
–
Oxygen
–
–
HYDROGEN BONDING
Polar water creates external molecular
attractions
 between positive H in one H2O molecule to
negative O in another
H
 also can occur wherever
H
O
an -OH exists in a larger
molecule
= Weak bond
Hydrogen bonding of water has
PROFOUND importance for LIFE
ON EARTH!
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KEY CONCEPTS OF CHAPTER 2 FOR AP
BIO EXAM:
1. Chemical rxns are the basis of speciesspecific communication strategies (BIG
IDEA 3)
2. Biochemistry is vital to natural selection
and evolution (BIG IDEA 1)
3. Biochemistry can serve as the
mechanisms by which populations
interact (BIG IDEA 4)
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THE PERCENTAGES OF NATURALLY OCCURRING
ELEMENTS MAKING UP THE HUMAN BODY ARE
SIMILAR TO THE PERCENTAGES OF THESE
ELEMENTS FOUND IN OTHER ORGANISMS.
HOW COULD YOU ACCOUNT FOR THIS
SIMILARITY AMONG ORGANISMS? EXPLAIN
YOUR THINKING.
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DRAW LEWIS DOT STRUCTURES FOR EACH
HYPOTHETICAL MOLECULE SHOWN BELOW,
USING THE CORRECT NUMBER OF VALENCE
ELECTRONS FOR EACH ATOM. DETERMINE
WHICH MOLECULE MAKES SENSE BECAUSE
EACH ATOM HAS A COMPLETE VALENCE SHELL
& EACH BOND HAS THE CORRECT NUMBER OF
ELECTRONS. EXPLAIN WHAT MAKES THE
OTHER MOLECULES NONSENSICAL,
CONSIDERING THE NUMBER OF BONDS EACH
TYPE OF ATOM CAN MAKE.
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CHEMISTRY OF LIFE
P R O P E R T I E S O F W AT E R :
CHAPTER 3
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WHY ARE WE STUDYING WATER???
ITS
POLARITY
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All life occurs in water &
needs water for life
processes
inside & outside the cell
CHEMISTRY OF WATER
H2O molecules form H-bonds with each other
 +H attracted to –O (SLIGHT)
 creates a sticky molecule
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REMEMBER…
Covalent bonds are
WITHIN the water
molecule
Hydrogen bonds are
BETWEEN water
molecules
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THE ELIXIR OF LIFE
Special properties of water:
1. cohesion & adhesion
surface tension, capillary action
2. good solvent
many molecules dissolve in H2O
hydrophilic vs. hydrophobic
3. lower density as a solid
ice floats!
4. high specific heat
water stores heat
5. high heat of vaporization
heats & cools slowly
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1. COHESION & 2. ADHESION
Cohesion
H bonding between H2O molecules
water is “sticky”
surface tension
drinking straw
Adhesion
H bonding between H2O & other substances
capillary action
meniscus
water climbs up
paper towel or cloth
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TRANSPIRATION IS BUILT UPON THE CONCEPTS
OF COHESION & ADHESION
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3. WATER IS THE SOLVENT OF LIFE
Polarity makes H2O a good solvent
polar H2O molecules surround + & – ions
solvents dissolve solutes creating solutions
Hydration
shells
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WHAT DISSOLVES IN WATER?
Hydrophilic
substances have attraction to H2O
polar or non-polar?
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4. WATER IS AN ORGANIZER OF NON
POLAR MOLECULES
Water is attracted to things that are also polar or
charged in some way.
Molecules that LACK polarity / charge cannot attract
water…much like a magnet will not stick to plastic.
However, water WILL push these non polar molecules
out of the way and thus organize them as it is drawn
toward other polar things
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WHY IS THIS IMPORTANT?
WATER’S ABILITY TO ORGANIZE NON
POLAR MOLECULES IS CRITICAL TO THE
FORMATION OF CELLULAR MEMBRANES…
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WHAT DOESN’T DISSOLVE IN WATER?
Hydrophobic
substances that don’t have
an attraction to H2O
polar or non-polar?
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fat (triglycerol)
SOLID WATER FLOATS?!?!...HUH??
Oceans & lakes don’t freeze solid
Water is MOST
surface ice insulates water below
allowing life to survive the winter dense at 4 deg. C
if ice sank…
ponds, lakes & even oceans would freeze solid
in summer, only upper few inches would thaw
seasonal turnover of lakes
sinking cold H2O cycles nutrients in autumn
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5. SPECIFIC HEAT
H2O resists changes in temperature
 specific heat HIGH OR LOW ??
H2O moderates temperatures on Earth
& homeostasis in living things!!!
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6. Water has a high heat of vaporization
= the amount of energy it takes to cause 1g of a liquid to
become a gas
**It takes a lot of energy to cause water to vaporize
**Why is this important?
When water leaves the body, it takes a
LOT of heat energy with it
= Sweat cools us down!
Back to homeostasis
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7. IONIZATION OF WATER & PH
Water ionizes
H+ splits off from H2O, leaving OH–
if [H+] = [-OH], water is neutral
if [H+] > [-OH], water is acidic
if [H+] < [-OH], water is basic
H2O  H+ + OH–
pH scale
how acid or basic solution is
1  7 acidic
7  14 basic 7 neutral
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PH
H+ Ion
SCALE Concentration
pH
Examples of Solutions
100
0
10–1
1
tenfold change
in H+ ions
10–2
2
Stomach acid, Lemon juice
10–3
3
Vinegar, cola, beer
10–4
4
Tomatoes
pH1  pH2
10-1  10-2
10–5
5
Black coffee, Rainwater
10–6
6
Urine, Saliva
10 times less H+
10–7
7
Pure water, Blood
pH8  pH7
10-8  10-7
10–8
8
Seawater
10–9
9
Baking soda
10 times more H+
10–10
10
Great Salt Lake
pH10  pH8
10-10  10-8
10–11
11
Household ammonia
10–12
12
Household bleach
10–13
13
Oven cleaner
10–14
14
Sodium hydroxide
100 times more H+
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Hydrochloric acid
BUFFERS & CELLULAR REGULATION
pH of cells must be kept ~7
 affects shape of molecules
shape affects function
= pH affects cellular function
Control pH by buffers
= reservoir of H+
7
6
pH
donate H+ when
[H+] falls
absorb H+ when
[H+] rises
9
8
Buffering
range
5
4
3
2
1
0
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0
1
2
3
4
5
Amount of base added
REMEMBER ALL THESE
PROPERTIES EXIST BECAUSE…
…Water hydrogen bonds with itself
Which happens because…
…Water molecules are polar
Which happens because…
…Oxygen is Elelctronegative
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