CH 2: Life Chemistry &
Energy
(10/29) Bellringer: chemistry?
1. Why are we studying chemistry in AP Biology???
2. Draw a model of a Carbon atom containing 6 protons, 6
neutrons, and 6 electrons. Use +, -, or 0 to represent the
3 types of subatomic particles based on their charge or
lack thereof.
3. Estimate: how many molecules are in 1 cm3 of air?
2.1 Atomic Structure Is the Basis for Life’s Chemistry
Bohr model
2.1 Atomic Structure Is the Basis for Life’s Chemistry
• Living and nonliving matter is composed of atoms.
• Element—pure substance that contains only one kind of
atom
– Living things are mostly composed of 6 elements: C,
H, N, O, P, S (96.3% of humans are C, H, O, & N).
• Number of protons = atomic number
• Mass number—total number of protons + neutrons
• Atoms with unfilled outer shells tend to undergo
chemical reactions to fill their outer shells (octet rule)
– The atoms are then bonded together into molecules
Bohr model
Bohr model
2.2 Atoms Interact and Form Molecules
• Ionic bonds are formed when atoms gain/lose electrons
– Form salts that dissolve easily in water because ionic
bonds are weak
– Produce ions (charged atoms/molecules)
• Cations are positive
• Anions are negative
Ionic bonds result from a TRANSFER of electrons from one
atom to another to fill each atom’s valence shells
2.2 Atoms Interact and Form Molecules
• Covalent bonds form
when 2 atoms share pairs
of electrons
– Each bond is a pair of
shared electrons
– Much stronger than
ionic bonds
2.2 Atoms Interact and Form Molecules
– Carbon has 4 valence electrons that can be shared
with up to 4 other atoms
Carbon has 4 valence electrons that can each form a
covalent bond with another atom
2.2 Atoms Interact and Form Molecules
– In a covalent bond, there is often unequal sharing of
electrons due to differences in electronegativity—
the attractive force that an atomic nucleus exerts on
electrons
• If 2 atoms have similar electronegativities, they
share electrons equally (nonpolar covalent bond)
• If 2 atoms have different electronegativities,
electrons tend to be near the most attractive atom
(polar covalent bond)
Draw a water molecule
in your notes that shows
its polarity!
2.2 Atoms Interact and Form Molecules
*If 2 atoms have
electronegativities
less than .5 apart,
they will form a
NONPOLAR
covalent bond
2.2 Atoms Interact and Form Molecules
• Hydrogen bonds may occur between polar molecules
– Formed by the attraction of the δ– end of one molecule
and the δ+ hydrogen end of another
– Weaker than covalent & ionic bonds
– Water molecules form H bonds with each other, giving
it unique properties significant to life on Earth
Fig 2-5: Hydrogen bonds can form between molecules (e.g.,
water) and within molecules (e.g., proteins and DNA)
(10/29) Exit
We discussed three types of bonds today. List them
in order of relative strength from strongest to
weakest.
(11/2) Partner Bellringer: WATER!
1. What roles does water play in living things? Why is
water essential to life on Earth?
2. Draw 3 molecules of water that show their polarity and
where bonds would form between them as a result of
their polarity. Then label the type of bond that would
form.
Reasons for importance
• Water molecules participate in chemical
reactions that sustain life
– Photosynthesis, respiration
• Most cells are surrounded by water
• ¾ of Earth’s surface submerged in water
• Only common substance to exist naturally
in all three states: solid, liquid, gas
2.2 Atoms Interact and Form Molecules
• Properties of Water
– High heat capacity – a lot of
energy is required to change
the temperature of water
because hydrogen bonds
absorb energy
• Organisms can maintain
stable body temperature
despite large fluctuations in
environmental temperature
• Bodies of water moderate
temperature on land
• Stabilizes ocean
temperature
2.2 Atoms Interact and Form Molecules
– High heat of vaporization
• Lots of energy is required to break H bonds
(evaporation)  cooling effect on the environment
– Ex: sweat
– Cohesion – H bonds hold water molecules together
• Creates surface tension allowing organisms to
float or walk on water
– Adhesion – water forms H bonds with other polar
molecules
• Permits narrow columns of water to move from roots
to leaves of plants (capillary action)
– Ice is less dense than water (ice floats)
• Ice insulates bodies of water making them more
suitable for life
Cohesion creates surface tension
2.2 Atoms Interact and Form Molecules
– Water is a versatile solvent due to its polarity
• Hydrophilic molecules (ions & polar) dissolve in
aqueous solutions because they become separated
and surrounded by water molecules
– Many biological fluids (e.g., blood & sap) are
water-based and readily dissolve ions and polar
molecules
• Nonpolar molecules (no charge) are called
hydrophobic (“water-hating”) & do not dissolve
Hydration shells
surround the
cation and anion
of a salt, causing
it to dissolve in
water
Ion in solution
Salt crystal
2.2 Atoms Interact and Form Molecules
2.2 Atoms Interact and Form Molecules
• Functional groups—small groups of atoms with
specific chemical properties
– confer these properties to larger molecules (e.g.,
polarity)
Functional Groups
Functional Groups
(11/2) Partner BR
3. Define condensation.
4. What does the word root lysis or lyso- mean?
2.2 Atoms Interact and Form Molecules
• Macromolecules – most biological molecules are
polymers, made by the covalent bonding of many
smaller molecules called monomers
2.2 Atoms Interact and Form Molecules
– Polymers are formed
and broken apart via
2 processes:
• Condensation—
removal of water
links monomers
together
• Hydrolysis—
addition of water
breaks a polymer
into monomers
(lysis means to
break apart!)
Condensation, or dehydration synthesis, reactions build
larger molecules through the removal of an H from one
molecule and an –OH from another
Hydrolysis breaks a larger molecule into smaller molecules
through the splitting of a water molecule (an H is added to
one molecule, and an –OH is added to the other where the
bond was formed)
(11/2) EXIT slip
Explain how water’s polarity gives it the following unique
properties:
a. Cohesion
b. Adhesion
c. Versatility as a solvent
d. High heat capacity
(11/4) Partner BR
1. During the winter, air temperatures in the northern United
States can remain below zero degrees Celsius (freezing) for
months; however, the fish and other animals living in the
lakes survive. Which 2 properties of water can explain this?
2. Though external temperatures vary considerably, the
water-based fluids in our bodies remain around 37˚ C.
Which property of water explains this?
3. Explain the difference between hydrolysis and
condensation reactions.
Review Exit slip
2.3 Carbohydrates Consist of Sugar Molecules
• Functions of carbohydrates:
– Stored energy
– Provide structure
– Recognition or signaling molecules
• Monosaccharides are simple sugars (monomers)
– Pentoses: ribose and deoxyribose
– Hexoses : glucose, fructose, galactose (all are
C6H12O6)
Draw a glucose diagram in your notes and label the carbons
1-6. Draw only the hexagonal ring and carbon atoms (don’t
worry about the peripheral hydrogen and oxygen atoms)
2.3 Carbohydrates Consist of Sugar Molecules
– Monosaccharides can be covalently bonded by
glycosidic linkages/bonds to form polymers
• Disaccharides like sucrose & lactose consist of 2
linked monosaccharides
What kind of reaction creates a glycosidic linkage?
2.3 Carbohydrates Consist of Sugar Molecules
• Oligosaccharides contain several monosaccharides
– often bonded to proteins and lipids on cell surfaces,
where they serve as recognition signals
• Polysaccharides are large polymers of
monosaccharides
– Starches—branched polymer of glucose used for
energy storage in plants
– Glycogen—highly branched; main energy storage
molecule in mammals
– Cellulose—the most abundant organic compound
on Earth; unbranched; good structural material in
plants
Hydrogen bonding to other cellulose
molecules can occur at the hydroxyl groups
(in blue)
4. List some examples of
lipids.
5. What are some functions
and characteristics of
lipids?
2.4 Lipids Are Hydrophobic Molecules
• Lipids are NONPOLAR hydrocarbons (composed of C
and H) that are insoluble in water (hydrophobic)
• When close together, weak van der Waals interactions
hold them together
• Functions in organisms:
– Store energy
– Form cellular membranes
– Thermal insulation
– Water-proofing
2.4 Lipids Are Hydrophobic Molecules
• Triglycerides include fats and oils
– Very hydrophobic
– Consist of:
• Three fatty acids—nonpolar hydrocarbon chain
attached to a polar carboxyl group (—COOH)
• One glycerol—an alcohol with 3 hydroxyl
groups (—OH)
– Synthesis from fatty acids and glycerol involves 3
condensation reactions
A triglyceride is formed from 3 condensation reactions
linking 3 fatty acids to 1 molecule of glycerol
Exit
What relationship do you see between the
structure of a polysaccharide and its function?
“Remember, remember the 5th of November…”
(11/5) Partner Bellringer (get out your notes!)
1. What are 3 polymers made of the monomer glucose?
2. What type of bond is formed when glucose and fructose
combine to form sucrose?
Exit Review
Don’t forget to watch
V for Vendetta tonight!!!!
3. Which functional groups can you identify in glycerol and
the fatty acids?
Functional Groups
Functional Groups
2.4 Lipids Are Hydrophobic Molecules
• Fatty acid chains vary in
length & structure
– saturated fatty
acids – only single
bonds between
carbon atoms
(saturated with
hydrogens)
Saturated fatty acids: all bonds
between carbon atoms are single
2.4 Lipids Are Hydrophobic Molecules
– unsaturated fatty
acids - hydrocarbon
chains contain one or
more double bonds
that cause kinks in
the chain that prevent
molecules from
packing together
tightly…what effect
does this have on the
melting point?
Kinks prevent
close packing
Unsaturated fatty acids: at least one
double bond between carbon atoms
Trans Fats
• Hydrogenated vegetable oils are naturally occurring
unsaturated fats synthetically converted to saturated fats
by adding hydrogens to make them solid at room temp.
(ex. Vegetable shortening (e.g., Crisco), margarine,
peanut butter, frosting)
– Create trans fats…trans position double bonds
rather than naturally occurring cis double bond –
linked to cardiovascular problems like high
cholesterol!
Which diagram shows a saturated fatty acid? Which
shows an unsaturated fatty acid? How can you tell?
Saturated fatty
acids are
straight
hydrocarbon
chains
Unsaturated
fatty acids
contain
“kinks” from
double
bonds in
chain (C=C)
2.4 Lipids Are Hydrophobic Molecules
– Fatty acids have a hydrophilic end and a hydrophobic
tail (they are amphipathic)
– Phospholipid—two fatty acids and a hyudrophilic
phosphate compound bound to glycerol
• phosphate group has a negative charge, making it
hydrophilic
2.4 Lipids Are Hydrophobic Molecules
• Cell membranes consist of a phospholipid
bilayer
– In an aqueous environment the nonpolar,
hydrophobic “tails” pack together, and the
hydrophilic phosphate “heads” face outward
• Other examples of lipids include waxes (e.g., leaf cuticle
for water proofing) and steroids (e.g., cholesterol &
some hormones)
Waxes
• Waterproofing:
– Lipids that serve as coatings for plant parts
and as animal coverings.
Steroids
• Structure: Four carbon rings with no fatty acid tails
• Functions:
– Cholesterol: precursor to vitamin D3 and sex hormones;
component of animal cell membranes that stabilizes their
structure
Exit
If fatty acids are carefully put onto the surface of
water, they form a single molecular layer. If the
mixture is then shaken vigorously, the fatty acids
will form hollow, round structures called
micelles. Explain these observations.
(11/6) Bellringer
1. What takes place during a chemical reaction?
2. Explain the difference endergonic and exergonic
reactions.
Exit Review
2.5 Biochemical Changes Involve Energy
• Chemical reactions occur when atoms have enough
energy to combine, or change, bonding partners
Reactants
Products
sucrose + H2O
glucose + fructose
(C12H22O11)
(C6H12O6) (C6H12O6)
2.5 Biochemical Changes Involve Energy
• Metabolism—the sum total of all chemical reactions
occurring in a biological system at a given time
– Anabolic reactions link simple molecules to build
more complex ones
• Endergonic—energy is stored in the chemical
bonds that form; require energy inputs
– Catabolic reactions break down complex molecules
into simpler ones
• Exergonic—energy stored in the chemical bonds
is released when bonds are broken
Is this reaction endergonic or exergonic?
• More energy in the products than reactants, so
Endergonic
Exergonic reaction: Energy is released; products
have LESS energy than reactants
2.5 Biochemical Changes Involve Energy
• Laws of thermodynamics
– First law: Energy is neither created nor destroyed
– Second law: Disorder (entropy) tends to increase
• When energy is converted from one form to another,
some of that energy becomes unavailable for doing work
(energy is “lost”)
∆G = ∆H - T∆S
G = free energy
H = enthalpy (heat content, or E gained or lost in Rxn)
S = entropy
T = temperature
2.5 Biochemical Changes Involve Energy
• If there are fewer products than reactants, disorder
decreases; this requires energy to achieve (endergonic)
• As a result of energy transformations, disorder tends to
increase
So how do we explain highly ordered organisms like us?
– Energy is always lost to random thermal motion
(entropy)
– Metabolism creates more disorder (more energy is
lost to entropy) than the amount of order that is
stored
• Ex: anabolic reactions needed to construct 1 kg of
biomass (flesh) require the catabolism of about 10
kg of food
The “Organic Soup” Hypothesis: The Rise of Life
1. Name the types of reaction shown below and
whether each is exergonic or endergonic.
2. Why are the following properties of water
important to life on Earth?
a. Water has a high specific heat
b. Water has a high heat of vaporization
c. Water’s greatest density is at 4°C
d. Water molecules form hydrogen bonds with
other polar molecules (cohesion/adhesion)
3. What type of bond/linkage is established in
the diagram below?
4. What type of molecules are shown below?
5. Which functional group is at the top of each molecule?
6. Which fatty acid would be more likely to pack together with
others in a triglyceride? Would it be liquid or solid?
7. Which of the
reactions to the right
is anabolic and
which is catabolic?
8.Which one forms
chemical bonds, and
which one breaks
them?
9. What does ∆G represent
in the diagram?
10. Which letter represents
the activation energy in
the enzyme-catalyzed
reaction?
11. Which letter represents
the uncatalyzed
reaction?
12. Is this an exergonic or
an endergonic reaction?
d.
a.
b.
Reactants
c.
∆G
Products
13. What do these
graphs reveal
about factors
affecting enzyme
activity?
Metabolic pathways
14. What is isoleucine doing in this figure?
15. If isoleucine were to allosterically inhibit enzyme B, the
amount of ______________ would increase.
16. What effect does isoleucine have on threonine production?
A.
B.