Exam unit 1 review

• Objective: Review the Principles of Life Science and the Chemistry of Life
1. Do Now 08/30/18
2. Mini Lectures on Chapters 1-5, 8
3. Supplements, just like N.O. Explode
a) Join Khan Academy
b) Reflect, when prompted
i. Intro to Biology: The Scientific Method Video (11 minutes)
ii. Chemistry of Life: Chemical bonds and reactions: Intermolecular Forces Video (8 minutes)
iii. Water, Acids, and Bases: Water as a Solvent Video: Hydrogen Bonding in Water: Water as a
Solvent Video (9 minutes)
iv. Properties of Carbon: Hydrocarbon structures and functional groups: Functional groups
Video (10 mimnutes)
4. Homework: See Schoology: Online Homework: Homework due
08/31/18

Overview: Inquiring About Life
• An organism’s adaptations to its environment are the
result of evolution
• For example, the ghost plant is adapted to conserving
water; this helps it to survive in the crevices of rock
walls
• Evolution is the process of change that has
transformed life on Earth
© 2011 Pearson Education, Inc.

Emergent Properties
• Emergent properties result from the arrangement and
interaction of parts within a system
• Emergent properties characterize nonbiological entities
as well
• For example, a functioning bicycle emerges only when
all of the necessary parts connect in the correct way

The Power and Limitations of
Reductionism
• Reductionism is the reduction of complex systems to
simpler components that are more manageable to
study
• For example, studying the molecular structure of
DNA helps us to understand the chemical basis of
inheritance

• An understanding of biology balances
reductionism with the study of emergent
properties
• For example, new understanding comes from
studying the interactions of DNA with other
molecules

Systems Biology
• A system is a combination of components that function
together
• Systems biology constructs models for the dynamic
behavior of whole biological systems
• The systems approach poses questions such as
• How does a drug for blood pressure affect other organs?
• How does increasing CO2 alter the biosphere?

Theme: Organisms Interact with Other
Organisms and the Physical Environment

Animals eat
leaves and fruit
from the tree.
Leaves take in
carbon dioxide
from the air
and release
oxygen.
Sunlight
CO2
O2
Cycling
of
chemical
nutrients
Leaves fall to
the ground and
are decomposed
by organisms
that return
minerals to the
soil.
Water and
minerals in
the soil are
taken up by
the tree
through
its roots.
Leaves absorb
light energy from
the sun.
Figure 1.5

• Humans have modified our environment
• For example, half the human-generated CO2 stays in
the atmosphere and contributes to global warming
• Global warming is a major aspect of global climate
change
• It is important to understand the effects of global
climate change on the Earth and its populations

Figure 1.6
Heat
Producers absorb light
energy and transform it into
chemical energy.
Chemical
energy
Chemical energy in
food is transferred
from plants to
consumers.
(b) Using energy to do work(a) Energy flow from sunlight to
producers to consumers
Sunlight
An animal’s muscle
cells convert
chemical energy
from food to kinetic
energy, the energy
of motion.
When energy is used
to do work, some
energy is converted to
thermal energy, which
is lost as heat.
A plant’s cells use
chemical energy to do
work such as growing
new leaves.

Theme: The Cell Is an Organism’s Basic
Unit of Structure and Function
• The cell is the lowest level of organization that can
perform all activities required for life
• All cells
• Are enclosed by a membrane
• Use DNA as their genetic information

Eukaryotic cell
Prokaryotic cell
Cytoplasm
DNA
(no nucleus)
Membrane
Nucleus
(membrane-
enclosed)
Membrane
Membrane-
enclosed organelles
DNA (throughout
nucleus) 1 m
Figure 1.8

Theme: The Continuity of Life Is Based on
Heritable Information in the Form of DNA
• Chromosomes contain most of a cell’s genetic material
in the form of DNA (deoxyribonucleic acid)
• DNA is the substance of genes
• Genes are the units of inheritance that transmit
information from parents to offspring
• The ability of cells to divide is the basis of all
reproduction, growth, and repair of multicellular
organisms

DNA Structure and Function
• Each chromosome has one long DNA molecule with
hundreds or thousands of genes
• Genes encode information for building proteins
• DNA is inherited by offspring from their parents
• DNA controls the development and maintenance of
organisms

Figure 1.10
Sperm cell
Nuclei
containing
DNA
Egg cell
Fertilized egg
with DNA from
both parents
Embryo’s cells with
copies of inherited DNA
Offspring with traits
inherited from
both parents

Figure 1.13
Negative
feedback
A
B
C
D
C
Enzyme 1
Enzyme 2
Enzyme 3
D
W
Enzyme 4
X
DD
Excess D
blocks a step.
(a) Negative feedback
Positive
feedback
Excess Z
stimulates a
step.
Y
Z

Z
Z
Z
(b) Positive feedback
Enzyme 5
Enzyme 6

Evolution, the Overarching Theme of
Biology
• Evolution makes sense of everything we know
about biology
• Organisms are modified descendants of common
ancestors

Inductive Reasoning
• Inductive reasoning draws conclusions through the
logical process of induction
• Repeating specific observations can lead to important
generalizations
• For example, “the sun always rises in the east”

Forming and Testing Hypotheses
• Observations and inductive reasoning can lead us to
ask questions and propose hypothetical explanations
called hypotheses

The Role of Hypotheses in Inquiry
• A hypothesis is a tentative answer to a well-framed
question
• A scientific hypothesis leads to predictions that can be
tested by observation or experimentation

Deductive Reasoning and Hypothesis
Testing
• Deductive reasoning uses general premises to make
specific predictions
• For example, if organisms are made of cells (premise
1), and humans are organisms (premise 2), then
humans are composed of cells (deductive prediction)

• Hypothesis-based science often makes use of two
or more alternative hypotheses
• Failure to falsify a hypothesis does not prove that
hypothesis
• For example, you replace your flashlight bulb, and
it now works; this supports the hypothesis that
your bulb was burnt out, but does not prove it
(perhaps the first bulb was inserted incorrectly)

Questions That Can and Cannot Be
Addressed by Science
• A hypothesis must be testable and falsifiable
• For example, a hypothesis that ghosts fooled with the
flashlight cannot be tested
• Supernatural and religious explanations are outside
the bounds of science

The Flexibility of the Scientific Method
• The scientific method is an idealized process of inquiry
• Hypothesis-based science is based on the “textbook”
scientific method but rarely follows all the ordered steps

The Value of Diverse Viewpoints in
Science
• Many important inventions have occurred where
different cultures and ideas mix
• For example, the printing press relied on
innovations from China (paper and ink) and
Europe (mass production in mills)
• Science benefits from diverse views from different
racial and ethnic groups, and from both women
and men

The Chemical Context of Life
Chapter 2

Elements and Compounds
• Matter is made up of elements
• An element is a substance that cannot be broken
down to other substances by chemical reactions
• A compound is a substance consisting of two or
more elements in a fixed ratio
• A compound has characteristics different from
those of its elements

The Elements of Life
• About 20–25% of the 92 elements are essential to
life
• Carbon, hydrogen, oxygen, and nitrogen make up
96% of living matter
• Most of the remaining 4% consists of calcium,
phosphorus, potassium, and sulfur
• Trace elements are those required by an
organism in minute quantities

Concept 2.2: An element’s properties
depend on the structure of its atoms
• Each element consists of unique atoms
• An atom is the smallest unit of matter that still
retains the properties of an element

Subatomic Particles
• Atoms are composed of subatomic particles
• Relevant subatomic particles include
• Neutrons (no electrical charge)
• Protons (positive charge)
• Electrons (negative charge)

Figure 2.6
Human cells
are incubated
with compounds used to make
DNA. One compound is labeled
with 3H.
Compounds including
radioactive tracer
(bright blue)
Cells from each
incubator are
placed in tubes;
their DNA is
isolated; and
unused labeled
compounds are
removed.
TECHNIQUE
Incubators
Human cells
DNA (old and new)
The test tubes are placed in a scintillation counter.
10° 15° 20° 25° 30° 35° 40° 45° 50°
10°C 15°C 20°C
25°C 30°C 35°C
40°C 45°C 50°C
RESULTS
Optimum
temperature
for DNA
synthesis
Countsperminute
(1,000)
Temperature (°C)
30
20
10
0
3010 20 40 50
1
2
3

• Valence electrons are those in the outermost
shell, or valence shell
• The chemical behavior of an atom is mostly
determined by the valence electrons
• Elements with a full valence shell are chemically
inert

Concept 2.3: The formation and function of
molecules depend on chemical bonding between
atoms
• Atoms with incomplete valence shells can share
or transfer valence electrons with certain other
atoms
• These interactions usually result in atoms staying
close together, held by attractions called chemical
bonds

Covalent Bonds
• A covalent bond is the sharing of a pair of valence
electrons by two atoms
• In a covalent bond, the shared electrons count as
part of each atom’s valence shell

• A molecule consists of two or more atoms held
together by covalent bonds
• A single covalent bond, or single bond, is the
sharing of one pair of valence electrons
• A double covalent bond, or double bond, is the
sharing of two pairs of valence electrons

• The notation used to represent atoms and
bonding is called a structural formula
• For example, H—H
• This can be abbreviated further with a molecular
formula
• For example, H2
Animation: Covalent Bonds

• In a nonpolar covalent bond, the atoms share the
electron equally
• In a polar covalent bond, one atom is more
electronegative, and the atoms do not share the
electron equally
• Unequal sharing of electrons causes a partial
positive or negative charge for each atom or
molecule

Ionic Bonds
• Atoms sometimes strip electrons from their
bonding partners
• An example is the transfer of an electron from
sodium to chlorine
• After the transfer of an electron, both atoms
have charges
• A charged atom (or molecule) is called an ion

Figure 2.14-1
Na
Sodium atom
Cl
Chlorine atom

Figure 2.14-2
+ –
Na
Sodium atom
Cl
Chlorine atom
Na+
Sodium ion
(a cation)
Cl–
Chloride ion
(an anion)
Sodium chloride (NaCl)

• A cation is a positively charged ion
• An anion is a negatively charged ion
• An ionic bond is an attraction between an anion
and a cation
Animation: Ionic Bonds

Weak Chemical Bonds
• Most of the strongest bonds in organisms are
covalent bonds that form a cell’s molecules
• Weak chemical bonds, such as ionic bonds and
hydrogen bonds, are also important
• Weak chemical bonds reinforce shapes of large
molecules and help molecules adhere to each
other

Hydrogen Bonds
• A hydrogen bond forms when a hydrogen atom
covalently bonded to one electronegative atom is
also attracted to another electronegative atom
• In living cells, the electronegative partners are
usually oxygen or nitrogen atoms

Figure 2.16
Water (H2O)
Ammonia (NH3)
Hydrogen bond
–
–
+
+
+
+
+

Van der Waals Interactions
• If electrons are distributed asymmetrically in
molecules or atoms, they can result in “hot spots”
of positive or negative charge
• Van der Waals interactions are attractions
between molecules that are close together as a
result of these charges

Concept 2.4: Chemical reactions make and
break chemical bonds
• Chemical reactions are the making and breaking
of chemical bonds
• The starting molecules of a chemical reaction are
called reactants
• The final molecules of a chemical reaction are
called products

Figure 2.UN02
Reactants Reaction Products
2 H2 2 H2OO2+

• Photosynthesis is an important chemical reaction
• Sunlight powers the conversion of carbon dioxide
and water to glucose and oxygen
6 CO2 + 6 H20 → C6H12O6 + 6 O2

Overview: The Molecule That Supports
All of Life
• Water is the biological medium on Earth
• All living organisms require water more than any
other substance
• Most cells are surrounded by water, and cells
themselves are about 70–95% water
• The abundance of water is the main reason the Earth
is habitable

Concept 3.2: Four emergent properties of
water contribute to Earth’s suitability for life
• Four of water’s properties that facilitate an
environment for life are
• Cohesive behavior
• Ability to moderate temperature
• Expansion upon freezing
• Versatility as a solvent

Cohesion of Water Molecules
• Collectively, hydrogen bonds hold water molecules
together, a phenomenon called cohesion
• Cohesion helps the transport of water against gravity
in plants
• Adhesion is an attraction between different
substances, for example, between water and plant
cell walls
Animation: Water Transport

Figure 3.3
Adhesion
Two types of
water-conducting
cells
Cohesion
300 m
Direction
of water
movement

• Surface tension is a measure of how hard it is to
break the surface of a liquid
• Surface tension is related to cohesion

Water’s High Specific Heat
• The specific heat of a substance is the amount of heat
that must be absorbed or lost for 1 g of that substance
to change its temperature by 1ºC
• The specific heat of water is 1 cal/g/ºC
• Water resists changing its temperature because of its
high specific heat

• Water’s high specific heat can be traced to hydrogen
bonding
• Heat is absorbed when hydrogen bonds break
• Heat is released when hydrogen bonds form
• The high specific heat of water minimizes temperature
fluctuations to within limits that permit life

Evaporative Cooling
• Evaporation is transformation of a substance from
liquid to gas
• Heat of vaporization is the heat a liquid must absorb
for 1 g to be converted to gas
• As a liquid evaporates, its remaining surface cools, a
process called evaporative cooling
• Evaporative cooling of water helps stabilize
temperatures in organisms and bodies of water

Hydrophilic and Hydrophobic Substances
• A hydrophilic substance is one that has an affinity for
water
• A hydrophobic substance is one that does not have
an affinity for water
• Oil molecules are hydrophobic because they have
relatively nonpolar bonds
• A colloid is a stable suspension of fine particles in a
liquid

Solute Concentration in Aqueous
Solutions
• Most biochemical reactions occur in water
• Chemical reactions depend on collisions of molecules
and therefore on the concentration of solutes in an
aqueous solution

Concept 3.3: Acidic and basic conditions
affect living organisms
• A hydrogen atom in a hydrogen bond between two
water molecules can shift from one to the other
• The hydrogen atom leaves its electron behind and is
transferred as a proton, or hydrogen ion (H+)
• The molecule with the extra proton is now a
hydronium ion (H3O+), though it is often represented as
H+
• The molecule that lost the proton is now a hydroxide
ion (OH–)

Buffers
• The internal pH of most living cells must remain
close to pH 7
• Buffers are substances that minimize changes in
concentrations of H+ and OH– in a solution
• Most buffers consist of an acid-base pair that
reversibly combines with H+

AP Biology
09/04/18
Objective: Continue Unit 1 Review

Carbon and the Molecular
Diversity of Life
Chapter 4

Overview: Carbon: The Backbone of Life
• Living organisms consist mostly of carbon-based
compounds
• Carbon is unparalleled in its ability to form large,
complex, and diverse molecules
• Proteins, DNA, carbohydrates, and other molecules that
distinguish living matter are all composed of carbon
compounds

• Vitalism, the idea that organic compounds arise
only in organisms, was disproved when chemists
synthesized these compounds
• Mechanism is the view that all natural phenomena
are governed by physical and chemical laws

Organic Molecules and the Origin of Life on Earth
• Stanley Miller’s classic experiment demonstrated
the abiotic synthesis of organic compounds
• Experiments support the idea that abiotic
synthesis of organic compounds, perhaps near
volcanoes, could have been a stage in the origin
of life

Figure 4.2
EXPERIMENT
“Atmosphere”
Electrode
Condenser
CH4
Water vapor
Cooled “rain”
containing
organic
molecules
Cold
water
Sample for chemical analysis
H2O
“sea”

Concept 4.2: Carbon atoms can form diverse
molecules by bonding to four other atoms
• Electron configuration is the key to an atom’s
characteristics
• Electron configuration determines the kinds and
number of bonds an atom will form with other
atoms

Figure 4.5
(a) Length
Ethane 1-Butene
(c) Double bond position
2-ButenePropane
(b) Branching (d) Presence of rings
Butane 2-Methylpropane
(isobutane)
Cyclohexane Benzene

Hydrocarbons
• Hydrocarbons are organic molecules consisting of
only carbon and hydrogen
• Many organic molecules, such as fats, have
hydrocarbon components
• Hydrocarbons can undergo reactions that release a
large amount of energy

Figure 4.7
(a) Structural isomers
(b) Cis-trans isomers
(c) Enantiomers
cis isomer: The two Xs
are on the same side.
trans isomer: The two Xs
are on opposite sides.
CO2HCO2H
CH3
H NH2
L isomer
NH2
CH3
H
D isomer

Concept 4.3: A few chemical groups are key to the
functioning of biological molecules
• Distinctive properties of organic molecules
depend on the carbon skeleton and on the
molecular components attached to it
• A number of characteristic groups can replace the
hydrogens attached to skeletons of organic
molecules

The Chemical Groups Most Important in the
Processes of Life
• Functional groups are the components of organic
molecules that are most commonly involved in
chemical reactions
• The number and arrangement of functional groups
give each molecule its unique properties

ATP: An Important Source of Energy for Cellular
Processes
• One phosphate molecule, adenosine triphosphate
(ATP), is the primary energy-transferring molecule in
the cell
• ATP consists of an organic molecule called adenosine
attached to a string of three phosphate groups

The Structure and Function of
Large Biological Molecules
Chapter 5

Overview: The Molecules of Life
• All living things are made up of four classes of
large biological molecules: carbohydrates, lipids,
proteins, and nucleic acids
• Macromolecules are large molecules composed
of thousands of covalently connected atoms
• Molecular structure and function are inseparable

Concept 5.1: Macromolecules are
polymers, built from monomers
• A polymer is a long molecule consisting of many
similar building blocks
• These small building-block molecules are called
monomers
• Three of the four classes of life’s organic molecules
are polymers
• Carbohydrates
• Proteins
• Nucleic acids

Figure 5.2
(a) Dehydration reaction: synthesizing a polymer
Short polymer Unlinked monomer
Dehydration removes
a water molecule,
forming a new bond.
Longer polymer
(b) Hydrolysis: breaking down a polymer
Hydrolysis adds
a water molecule,
breaking a bond.
1
1
1
2 3
2 3 4
2 3 4
1 2 3

Concept 5.2: Carbohydrates serve as fuel
and building material
• Carbohydrates include sugars and the polymers
of sugars
• The simplest carbohydrates are monosaccharides,
or single sugars
• Carbohydrate macromolecules are
polysaccharides, polymers composed of many
sugar building blocks

Figure 5.3
Aldoses (Aldehyde Sugars) Ketoses (Ketone Sugars)
Glyceraldehyde
Trioses: 3-carbon sugars (C3H6O3)
Dihydroxyacetone
Pentoses: 5-carbon sugars (C5H10O5)
Hexoses: 6-carbon sugars (C6H12O6)
Ribose Ribulose
Glucose Galactose Fructose

Figure 5.4
(a) Linear and ring forms
(b) Abbreviated ring structure
1
2
3
4
5
6
6
5
4
3
2
1 1
2
3
4
5
6
1
23
4
5
6

Figure 5.5
(a) Dehydration reaction in the synthesis of maltose
(b) Dehydration reaction in the synthesis of sucrose
Glucose Glucose
Glucose
Maltose
Fructose Sucrose
1–4
glycosidic
linkage
1–2
glycosidic
linkage
1 4
1 2

Polysaccharides
• Polysaccharides, the polymers of sugars, have
storage and structural roles
• The structure and function of a polysaccharide are
determined by its sugar monomers and the
positions of glycosidic linkages

Storage Polysaccharides
• Starch, a storage polysaccharide of plants, consists
entirely of glucose monomers
• Plants store surplus starch as granules within
chloroplasts and other plastids
• The simplest form of starch is amylose

Figure 5.6
(a) Starch:
a plant polysaccharide
(b) Glycogen:
an animal polysaccharide
Chloroplast Starch granules
Mitochondria Glycogen granules
Amylopectin
Amylose
Glycogen
1 m
0.5 m

Structural Polysaccharides
• The polysaccharide cellulose is a major component
of the tough wall of plant cells
• Like starch, cellulose is a polymer of glucose, but the
glycosidic linkages differ
• The difference is based on two ring forms for
glucose: alpha () and beta ()
Animation: Polysaccharides

Figure 5.7
(a)  and  glucose
ring structures
(b) Starch: 1–4 linkage of  glucose monomers (c) Cellulose: 1–4 linkage of  glucose monomers
 Glucose  Glucose
4 1 4 1
41
41

• Polymers with  glucose are helical
• Polymers with  glucose are straight
• In straight structures, H atoms on one strand can bond
with OH groups on other strands
• Parallel cellulose molecules held together this way are
grouped into microfibrils, which form strong building
materials for plants

Concept 5.3: Lipids are a diverse group
of hydrophobic molecules
• Lipids are the one class of large biological
molecules that do not form polymers
• The unifying feature of lipids is having little or no
affinity for water
• Lipids are hydrophobic because they consist mostly
of hydrocarbons, which form nonpolar covalent
bonds
• The most biologically important lipids are fats,
phospholipids, and steroids

Fats
• Fats are constructed from two types of smaller
molecules: glycerol and fatty acids
• Glycerol is a three-carbon alcohol with a hydroxyl
group attached to each carbon
• A fatty acid consists of a carboxyl group attached to a
long carbon skeleton

Figure 5.10
(a) One of three dehydration reactions in the synthesis of a fat
(b) Fat molecule (triacylglycerol)
Fatty acid
(in this case, palmitic acid)
Glycerol
Ester linkage

• Fatty acids vary in length (number of carbons) and in
the number and locations of double bonds
• Saturated fatty acids have the maximum number of
hydrogen atoms possible and no double bonds
• Unsaturated fatty acids have one or more double
bonds
Animation: Fats

Figure 5.11
(a) Saturated fat
(b) Unsaturated fat
Structural
formula of a
saturated fat
molecule
Space-filling
model of stearic
acid, a saturated
fatty acid
Structural
formula of an
unsaturated fat
molecule
Space-filling model
of oleic acid, an
unsaturated fatty
acid
Cis double bond
causes bending.

Phospholipids
• In a phospholipid, two fatty acids and a
phosphate group are attached to glycerol
• The two fatty acid tails are hydrophobic, but the
phosphate group and its attachments form a
hydrophilic head

Figure 5.12
Choline
Phosphate
Glycerol
Fatty acids
Hydrophilic
head
Hydrophobic
tails
(c) Phospholipid symbol(b) Space-filling model(a) Structural formula
HydrophilicheadHydrophobictails

• When phospholipids are added to water, they self-
assemble into a bilayer, with the hydrophobic tails
pointing toward the interior
• The structure of phospholipids results in a bilayer
arrangement found in cell membranes
• Phospholipids are the major component of all cell
membranes

Figure 5.13
Hydrophilic
head
Hydrophobic
tail
WATER
WATER

Steroids
• Steroids are lipids characterized by a carbon skeleton
consisting of four fused rings
• Cholesterol, an important steroid, is a component in
animal cell membranes
• Although cholesterol is essential in animals, high
levels in the blood may contribute to cardiovascular
disease

Concept 5.4: Proteins include a diversity of
structures, resulting in a wide range of
functions
• Proteins account for more than 50% of the dry mass of
most cells
• Protein functions include structural support, storage,
transport, cellular communications, movement, and
defense against foreign substances

Figure 5.15-a
Enzymatic proteins Defensive proteins
Storage proteins Transport proteins
Enzyme Virus
Antibodies
Bacterium
Ovalbumin Amino acids
for embryo
Transport
protein
Cell membrane
Function: Selective acceleration of chemical reactions
Example: Digestive enzymes catalyze the hydrolysis
of bonds in food molecules.
Function: Protection against disease
Example: Antibodies inactivate and help destroy
viruses and bacteria.
Function: Storage of amino acids Function: Transport of substances
Examples: Casein, the protein of milk, is the major
source of amino acids for baby mammals. Plants have
storage proteins in their seeds. Ovalbumin is the
protein of egg white, used as an amino acid source
for the developing embryo.
Examples: Hemoglobin, the iron-containing protein of
vertebrate blood, transports oxygen from the lungs to
other parts of the body. Other proteins transport
molecules across cell membranes.

Figure 5.15-b
Hormonal proteins
Function: Coordination of an organism’s activities
Example: Insulin, a hormone secreted by the
pancreas, causes other tissues to take up glucose,
thus regulating blood sugar concentration
High
blood sugar
Normal
blood sugar
Insulin
secreted
Signaling
molecules
Receptor
protein
Muscle tissue
Actin Myosin
100 m 60 m
Collagen
Connective
tissue
Receptor proteins
Function: Response of cell to chemical stimuli
Example: Receptors built into the membrane of a
nerve cell detect signaling molecules released by
other nerve cells.
Contractile and motor proteins
Function: Movement
Examples: Motor proteins are responsible for the
undulations of cilia and flagella. Actin and myosin
proteins are responsible for the contraction of
muscles.
Structural proteins
Function: Support
Examples: Keratin is the protein of hair, horns,
feathers, and other skin appendages. Insects and
spiders use silk fibers to make their cocoons and webs,
respectively. Collagen and elastin proteins provide a
fibrous framework in animal connective tissues.

Figure 5.UN01
Side chain (R group)
Amino
group
Carboxyl
group
 carbon

Figure 5.16
Nonpolar side chains; hydrophobic
Side chain
(R group)
Glycine
(Gly or G)
Alanine
(Ala or A)
Valine
(Val or V)
Leucine
(Leu or L)
Isoleucine
(Ile or I)
Methionine
(Met or M)
Phenylalanine
(Phe or F)
Tryptophan
(Trp or W)
Proline
(Pro or P)
Polar side chains; hydrophilic
Serine
(Ser or S)
Threonine
(Thr or T)
Cysteine
(Cys or C)
Tyrosine
(Tyr or Y)
Asparagine
(Asn or N)
Glutamine
(Gln or Q)
Electrically charged side chains; hydrophilic
Acidic (negatively charged)
Basic (positively charged)
Aspartic acid
(Asp or D)
Glutamic acid
(Glu or E)
Lysine
(Lys or K)
Arginine
(Arg or R)
Histidine
(His or H)

Amino Acid Polymers
• Amino acids are linked by peptide bonds
• A polypeptide is a polymer of amino acids
• Polypeptides range in length from a few to more
than a thousand monomers
• Each polypeptide has a unique linear sequence of
amino acids, with a carboxyl end (C-terminus) and
an amino end (N-terminus)

Figure 5.17
Peptide bond
New peptide
bond forming
Side
chains
Back-
bone
Amino end
(N-terminus)
Peptide
bond
Carboxyl end
(C-terminus)

Protein Structure and Function
• A functional protein consists of one or more
polypeptides precisely twisted, folded, and coiled
into a unique shape

• The sequence of amino acids determines a protein’s
three-dimensional structure
• A protein’s structure determines its function

Figure 5.20a
Primary structure
Amino
acids
Amino end
Carboxyl end
Primary structure of transthyretin

Figure 5.20b
Secondary
structure
Tertiary
structure
Quaternary
structure
Hydrogen bond
 helix
 pleated sheet
 strand
Hydrogen
bond
Transthyretin
polypeptide
Transthyretin
protein

Secondary structure
Hydrogen bond
 helix
 pleated sheet
 strand, shown as a flat
arrow pointing toward
the carboxyl end
Hydrogen bond
Figure 5.20c

Sickle-Cell Disease: A Change in Primary
Structure
• A slight change in primary structure can affect a
protein’s structure and ability to function
• Sickle-cell disease, an inherited blood disorder,
results from a single amino acid substitution in the
protein hemoglobin

Figure 5.21
Primary
Structure
Secondary
and Tertiary
Structures
Quaternary
Structure
Function
Red Blood
Cell Shape
 subunit
 subunit




Exposed
hydrophobic
region
Molecules do not
associate with one
another; each carries
oxygen.
Molecules crystallize
into a fiber; capacity
to carry oxygen is
reduced.
Sickle-cell
hemoglobin
Normal
hemoglobin
10 m
10 m
Sickle-cellhemoglobinNormalhemoglobin
1
2
3
4
5
6
7
1
2
3
4
5
6
7





What Determines Protein Structure?
• In addition to primary structure, physical and
chemical conditions can affect structure
• Alterations in pH, salt concentration, temperature,
or other environmental factors can cause a protein
to unravel
• This loss of a protein’s native structure is called
denaturation
• A denatured protein is biologically inactive

Figure 5.22
Normal protein Denatured protein
tu

Protein Folding in the Cell
• It is hard to predict a protein’s structure from its
primary structure
• Most proteins probably go through several stages
on their way to a stable structure
• Chaperonins are protein molecules that assist the
proper folding of other proteins
• Diseases such as Alzheimer’s, Parkinson’s, and
mad cow disease are associated with misfolded
proteins

Figure 5.23
The cap attaches, causing
the cylinder to change
shape in such a way that
it creates a hydrophilic
environment for the
folding of the polypeptide.
Cap
Polypeptide
Correctly
folded
protein
Chaperonin
(fully assembled)
Steps of Chaperonin
Action:
An unfolded poly-
peptide enters the
cylinder from
one end.
Hollow
cylinder
The cap comes
off, and the
properly folded
protein is
released.
1
2 3

• Scientists use X-ray crystallography to determine a
protein’s structure
• Another method is nuclear magnetic resonance
(NMR) spectroscopy, which does not require
protein crystallization
• Bioinformatics uses computer programs to predict
protein structure from amino acid sequences

Figure 5.24
Diffracted
X-rays
X-ray
source X-ray
beam
Crystal Digital detector X-ray diffraction
pattern
RNA DNA
RNA
polymerase II
EXPERIMENT
RESULTS

Concept 5.5: Nucleic acids store, transmit,
and help express hereditary information
• The amino acid sequence of a polypeptide is
programmed by a unit of inheritance called a gene
• Genes are made of DNA, a nucleic acid made of
monomers called nucleotides

The Roles of Nucleic Acids
• There are two types of nucleic acids
• Deoxyribonucleic acid (DNA)
• Ribonucleic acid (RNA)
• DNA provides directions for its own replication
• DNA directs synthesis of messenger RNA (mRNA)
and, through mRNA, controls protein synthesis
• Protein synthesis occurs on ribosomes

Figure 5.25-1
Synthesis of
mRNA
mRNA
DNA
NUCLEUS
CYTOPLASM
1

Figure 5.25-2
Synthesis of
mRNA
mRNA
DNA
NUCLEUS
CYTOPLASM
mRNA
Movement of
mRNA into
cytoplasm
1
2

Figure 5.25-3
Synthesis of
mRNA
mRNA
DNA
NUCLEUS
CYTOPLASM
mRNA
Ribosome
Amino
acidsPolypeptide
Movement of
mRNA into
cytoplasm
Synthesis
of protein
1
2
3

The Components of Nucleic Acids
• Nucleic acids are polymers called polynucleotides
• Each polynucleotide is made of monomers called
nucleotides
• Each nucleotide consists of a nitrogenous base, a
pentose sugar, and one or more phosphate groups
• The portion of a nucleotide without the phosphate
group is called a nucleoside

Figure 5.26
Sugar-phosphate backbone
5 end
5C
3C
5C
3C
3 end
(a) Polynucleotide, or nucleic acid
(b) Nucleotide
Phosphate
group Sugar
(pentose)
Nucleoside
Nitrogenous
base
5C
3C
1C
Nitrogenous bases
Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA)
Adenine (A) Guanine (G)
Sugars
Deoxyribose (in DNA) Ribose (in RNA)
(c) Nucleoside components
Pyrimidines
Purines

Figure 5.26ab
Sugar-phosphate backbone
5 end
5C
3C
5C
3C
3 end
(a) Polynucleotide, or nucleic acid
(b) Nucleotide
Phosphate
group Sugar
(pentose)
Nucleoside
Nitrogenous
base
5C
3C
1C

Figure 5.26c
Nitrogenous bases
Cytosine
(C)
Thymine
(T, in DNA)
Uracil
(U, in RNA)
Adenine (A) Guanine (G)
Sugars
Deoxyribose
(in DNA)
Ribose
(in RNA)
(c) Nucleoside components
Pyrimidines
Purines

• Nucleoside = nitrogenous base + sugar
• There are two families of nitrogenous bases
• Pyrimidines (cytosine, thymine, and uracil) have a
single six-membered ring
• Purines (adenine and guanine) have a six-
membered ring fused to a five-membered ring
• In DNA, the sugar is deoxyribose; in RNA, the sugar
is ribose
• Nucleotide = nucleoside + phosphate group

Nucleotide Polymers
• Nucleotide polymers are linked together to build a
polynucleotide
• Adjacent nucleotides are joined by covalent bonds
that form between the —OH group on the 3 carbon
of one nucleotide and the phosphate on the 5
carbon on the next
• These links create a backbone of sugar-phosphate
units with nitrogenous bases as appendages
• The sequence of bases along a DNA or mRNA
polymer is unique for each gene

The Structures of DNA and RNA Molecules
• RNA molecules usually exist as single polypeptide
chains
• DNA molecules have two polynucleotides spiraling
around an imaginary axis, forming a double helix
• In the DNA double helix, the two backbones run in
opposite 5→ 3 directions from each other, an
arrangement referred to as antiparallel
• One DNA molecule includes many genes

• The nitrogenous bases in DNA pair up and form
hydrogen bonds: adenine (A) always with thymine (T),
and guanine (G) always with cytosine (C)
• Called complementary base pairing
• Complementary pairing can also occur between two
RNA molecules or between parts of the same molecule
• In RNA, thymine is replaced by uracil (U) so A and U
pair

Figure 5.27
Sugar-phosphate
backbones
Hydrogen bonds
Base pair joined
by hydrogen bonding
Base pair joined
by hydrogen
bonding
(b) Transfer RNA(a) DNA
5 3
53

DNA and Proteins as Tape Measures of
Evolution
• The linear sequences of nucleotides in DNA molecules
are passed from parents to offspring
• Two closely related species are more similar in DNA
than are more distantly related species
• Molecular biology can be used to assess evolutionary
kinship

AP Biology
09/06/18
Objective: Review Concepts in Biological Chemistry;
1. Discussion of Learning in AP Biology`
2. Continue Review for Unit 1
3. Discussion of new learning structure for next unit

Concept 8.1: An organism’s metabolism
transforms matter and energy, subject to
the laws of thermodynamics
• Metabolism is the totality of an organism’s chemical
reactions
• Metabolism is an emergent property of life that arises
from interactions between molecules within the cell

Figure 8.UN01
Enzyme 1 Enzyme 2 Enzyme 3
Reaction 1 Reaction 2 Reaction 3
ProductStarting
molecule
A B C D

• Catabolic pathways release energy by breaking
down complex molecules into simpler compounds
• Cellular respiration, the breakdown of glucose in
the presence of oxygen, is an example of a pathway
of catabolism

• Anabolic pathways consume energy to build complex
molecules from simpler ones
• The synthesis of protein from amino acids is an example
of anabolism
• Bioenergetics is the study of how organisms manage
their energy resources

Forms of Energy
• Energy is the capacity to cause change
• Energy exists in various forms, some of which can
perform work

• Kinetic energy is energy associated with motion
• Heat (thermal energy) is kinetic energy associated with
random movement of atoms or molecules
• Potential energy is energy that matter possesses
because of its location or structure
• Chemical energy is potential energy available for
release in a chemical reaction
• Energy can be converted from one form to another
Animation: Energy Concepts

The Laws of Energy Transformation
• Thermodynamics is the study of energy transformations
• A isolated system, such as that approximated by liquid
in a thermos, is isolated from its surroundings
• In an open system, energy and matter can be
transferred between the system and its surroundings
• Organisms are open systems

Figure 8.3a
(a) First law of thermodynamics
Chemical
energy

Figure 8.3b
(b) Second law of thermodynamics
Heat

• Living cells unavoidably convert organized forms of
energy to heat
• Spontaneous processes occur without energy
input; they can happen quickly or slowly
• For a process to occur without energy input, it must
increase the entropy of the universe

• The evolution of more complex organisms does not
violate the second law of thermodynamics
• Entropy (disorder) may decrease in an organism, but
the universe’s total entropy increases

Concept 8.2: The free-energy change of a
reaction tells us whether or not the
reaction occurs spontaneously
• Biologists want to know which reactions occur
spontaneously and which require input of energy
• To do so, they need to determine energy changes
that occur in chemical reactions

Figure 8.6a
(a) Exergonic reaction: energy released, spontaneous
Reactants
Energy
Products
Progress of the reaction
Amount of
energy
released
(G  0)
Freeenergy

Figure 8.6b
(b) Endergonic reaction: energy required, nonspontaneous
Reactants
Energy
Products
Amount of
energy
required
(G  0)
Freeenergy

Equilibrium and Metabolism
• Reactions in a closed system eventually reach
equilibrium and then do no work
• Cells are not in equilibrium; they are open systems
experiencing a constant flow of materials
• A defining feature of life is that metabolism is never at
equilibrium
• A catabolic pathway in a cell releases free energy in a
series of reactions
• Closed and open hydroelectric systems can serve as
analogies

Figure 8.7
(a) An isolated hydroelectric system
(b) An open hydro-
electric system
(c) A multistep open hydroelectric system
G  0
G  0
G  0
G  0
G  0
G  0

Concept 8.3: ATP powers cellular work by
coupling exergonic reactions to
endergonic reactions
• A cell does three main kinds of work
• Chemical
• Transport
• Mechanical
• To do work, cells manage energy resources by energy
coupling, the use of an exergonic process to drive an
endergonic one
• Most energy coupling in cells is mediated by ATP

The Structure and Hydrolysis of ATP
• ATP (adenosine triphosphate) is the cell’s energy
shuttle
• ATP is composed of ribose (a sugar), adenine (a
nitrogenous base), and three phosphate groups

Figure 8.8
(a) The structure of ATP
Phosphate groups
Adenine
Ribose
Adenosine triphosphate (ATP)
Energy
Inorganic
phosphate
Adenosine diphosphate (ADP)
(b) The hydrolysis of ATP

Figure 8.9
Glutamic
acid
Ammonia Glutamine
(b)Conversion
reaction
coupled
with ATP
hydrolysis
Glutamic acid
conversion
to glutamine
(a)
(c) Free-energy
change for
coupled
reaction
Glutamic
acid
GlutaminePhosphorylated
intermediate
Glu
NH3 NH2
Glu
GGlu = +3.4 kcal/mol
ATP ADP ADP
NH3
Glu Glu
P
P i
P iADP
Glu
NH2
Glu Glu
NH3 NH2
ATP
GATP = 7.3 kcal/mol
+ GATP = 7.3 kcal/mol
Net G = 3.9 kcal/mol
1 2

• ATP drives endergonic reactions by phosphorylation,
transferring a phosphate group to some other
molecule, such as a reactant
• The recipient molecule is now called a
phosphorylated intermediate

Figure 8.10
Transport protein Solute
ATP
P P i
P iADP
P iADPATP
ATP
Solute transported
Vesicle Cytoskeletal track
Motor protein Protein and
vesicle moved
(b) Mechanical work: ATP binds noncovalently to motor
proteins and then is hydrolyzed.
(a) Transport work: ATP phosphorylates transport proteins.

The Regeneration of ATP
• ATP is a renewable resource that is regenerated by
addition of a phosphate group to adenosine
diphosphate (ADP)
•The energy to phosphorylate ADP comes from
catabolic reactions in the cell
•The ATP cycle is a revolving door through which
energy passes during its transfer from catabolic to
anabolic pathways

Figure 8.11
Energy from
catabolism (exergonic,
energy-releasing
processes)
Energy for cellular
work (endergonic,
energy-consuming
processes)
ATP
ADP P i
H2O

Concept 8.4: Enzymes speed up
metabolic reactions by lowering energy
barriers
• A catalyst is a chemical agent that speeds up a
reaction without being consumed by the reaction
• An enzyme is a catalytic protein or nucleic acid
• Hydrolysis of sucrose by the enzyme sucrase is an
example of an enzyme-catalyzed reaction

Figure 8.UN02
Sucrase
Sucrose
(C12H22O11)
Glucose
(C6H12O6)
Fructose
(C6H12O6)

The Activation Energy Barrier
• Every chemical reaction between molecules involves
bond breaking and bond forming
• The initial energy needed to start a chemical
reaction is called the free energy of activation, or
activation energy (EA)
• Activation energy is often supplied in the form of
thermal energy that the reactant molecules absorb
from their surroundings

Figure 8.12
Transition state
Reactants
Products
Freeenergy
EA
G  O
A B
C D
A B
C D
A B
C D

Figure 8.13
Course of
reaction
without
enzyme
EA
without
enzyme EA with
enzyme
is lower
Course of
reaction
with enzyme
Reactants
Products
G is unaffected
by enzyme
Freeenergy

Figure 8.15-3
Substrates
Substrates enter active site.
Enzyme-substrate
complex
Enzyme
Products
Substrates are held
in active site by weak
interactions.
Active site can
lower EA and speed
up a reaction.
Active
site is
available
for two new
substrate
molecules.
Products are
released.
Substrates are
converted to
products.
1
2
3
45
6

Effects of Local Conditions on Enzyme
Activity
• An enzyme’s activity can be affected by
• General environmental factors, such as temperature
and pH
• Chemicals that specifically influence the enzyme

Effects of Temperature and pH
• Each enzyme has an optimal temperature in which it
can function
• Each enzyme has an optimal pH in which it can
function
• Optimal conditions favor the most active shape for
the enzyme molecule

Figure 8.16
Optimal temperature for
typical human enzyme (37°C)
enzyme of thermophilic
(heat-tolerant)
bacteria (77°C)
Temperature (°C)
(a) Optimal temperature for two enzymes
RateofreactionRateofreaction
120100806040200
0 1 2 3 4 5 6 7 8 9 10
pH
(b) Optimal pH for two enzymes
Optimal pH for pepsin
(stomach
enzyme)
Optimal pH for trypsin
(intestinal
enzyme)

Figure 8.16a
typical human enzyme (37°C)
enzyme of thermophilic
(heat-tolerant)
bacteria (77°C)
Temperature (°C)
(a) Optimal temperature for two enzymes
Rateofreaction
120100806040200

Figure 8.16b
Rateofreaction
0 1 2 3 4 5 6 7 8 9 10
pH
(b) Optimal pH for two enzymes
Optimal pH for pepsin
(stomach
enzyme)
Optimal pH for trypsin
(intestinal
enzyme)

Cofactors
• Cofactors are nonprotein enzyme helpers
• Cofactors may be inorganic (such as a metal in ionic
form) or organic
• An organic cofactor is called a coenzyme
• Coenzymes include vitamins

Figure 8.17
(a) Normal binding (b) Competitive inhibition (c) Noncompetitive
inhibition
Substrate
Active
site
Enzyme
Competitive
inhibitor
Noncompetitive
inhibitor

Concept 8.5: Regulation of enzyme
activity helps control metabolism
• Chemical chaos would result if a cell’s metabolic
pathways were not tightly regulated
• A cell does this by switching on or off the genes
that encode specific enzymes or by regulating the
activity of enzymes

Figure 8.19
Regulatory
site (one
of four)
(a) Allosteric activators and inhibitors
Allosteric enzyme
with four subunits
Active site
(one of four)
Active form
Activator
Stabilized active form
Oscillation
Non-
functional
active site
Inactive form
Inhibitor
Stabilized inactive
form
Inactive form
Substrate
Stabilized active
form
(b) Cooperativity: another type of allosteric activation

Identification of Allosteric Regulators
• Allosteric regulators are attractive drug candidates
for enzyme regulation because of their specificity
• Inhibition of proteolytic enzymes called caspases
may help management of inappropriate
inflammatory responses

Figure 8.21
Active site
available
Isoleucine
used up by
cell
Feedback
inhibition
Active site of
enzyme 1 is
no longer able
to catalyze the
conversion
of threonine to
intermediate A;
pathway is
switched off. Isoleucine
binds to
allosteric
site.
Initial
substrate
(threonine)
Threonine
in active site
Enzyme 1
(threonine
deaminase)
Intermediate A
Intermediate B
Intermediate C
Intermediate D
Enzyme 2
Enzyme 3
Enzyme 4
Enzyme 5
End product
(isoleucine)

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