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AP REVIEW 1
Hydrogen
1H
Atomic mass
First
shell
2
He
4.00
Atomic number Helium
2He
Element symbol
Electron-shell
diagram
Lithium
3Li
Beryllium
4Be
Boron
3B
Carbon
6C
Nitrogen
7N
Oxygen Fluorine
8O
9F
Neon
10Ne
Second
shell
Sodium Magnesium Aluminum Silicon Phosphorus Sulfur
13Al
16S
11Na
12Mg
14Si
15P
Third
shell
Figure 2.8
Chlorine
17Cl
Argon
18Ar
Because oxygen (O) is more electronegative than hydrogen (H),
shared electrons are pulled more toward oxygen.
d–
This results in a
partial negative
charge on the
oxygen and a
partial positive
charge on
the hydrogens.
O
d+
H
H
H2O
d+
Carbon
Nitrogen
Hydrogen
Sulfur
Oxygen
Natural
endorphin
Morphine
(a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds to
receptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match.
Natural
endorphin
Brain cell
Morphine
Endorphin
receptors
(b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell
recognize and can bind to both endorphin and morphine.
Properties of water
What is electronegativity and how does it affect
interactions between water molecules?
Cohesion
Adhesion
Surface Tension
Describe how properties of
water contribute to the
upward movement of water
in a tree.
Turnover in lakes?
• Lakes
– Are sensitive to seasonal temperature change
– Experience seasonal turnover
Lake depth (m)
In winter, the coldest water in the lake (0°C) lies just
below the surface ice; water is progressively warmer at
deeper levels of the lake, typically 4–5°C at the bottom.
O2 (mg/L)
0
4
Spring
Winter
8
12
8
16
2
4
4
4
4C
24
O2 concentration
0
Lake depth (m)
1
2 In spring, as the sun melts the ice, the surface water warms to 4°C
and sinks below the cooler layers immediately below, eliminating the
thermal stratification. Spring winds mix the water to great depth,
bringing oxygen (O2) to the bottom waters (see graphs) and
nutrients to the surface.
O2 (mg/L)
0
4 8
12
8
16
4
4
4
4
4
4C
24
High
Medium
O2 (mg/L)
0
4
8
12
8
16
24
Figure 50.13
4
Autumn
4
4
4
4C
4
In autumn, as surface water cools rapidly, it sinks below the
underlying layers, remixing the water until the surface begins
to freeze and the winter temperature profile is reestablished.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
4
Thermocline
3
22
20
18
8
6
5
4C
Summer
Lake depth (m)
Lake depth (m)
Low
O2 (mg/L)
0
4
8
12
8
16
24
In summer, the lake regains a distinctive thermal profile, with
warm surface water separated from cold bottom water by a narrow
vertical zone of rapid temperature change, called a thermocline.
The four emergent properties of water that are
important for life are:
a) Cohesion, expansion upon freezing, high heat of
evaporation, and capillarity
b) Cohesion, moderation of temperature, expansion upon
freezing, and solvent properties
c) Moderation of temperature, solvent properties, high
surface tension, and capillarity
d) Heat of vaporization, high specific heat, high surface
tension, and capillarity
e) Polarity, hydrogen bonding, high specific heat, and high
surface tension
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Ascent of xylem sap
Xylem
sap
Outside air Y
= –100.0 MPa
Leaf Y (air spaces)
= –7.0 MPa
Transpiration
Leaf Y (cell walls)
= –1.0 MPa
Trunk xylem Y
= – 0.8 MPa
Atmosphere
Xylem
cells
Water potential gradient
Y
Mesophyll
cells
Stoma
Water
molecule
Cohesion
and adhesion
in the xylem
Adhesion
Cell
wall
Cohesion,
by
hydrogen
bonding
Water
molecule
Root xylem Y
= – 0.6 MPa
Root
hair
Soil Y
= – 0.3 MPa
Soil
particle
Figure 36.13
Water uptake
from soil
Water
pH Scale
0
Increasingly Acidic
[H+] > [OH–]
1
2
Digestive (stomach)
juice, lemon juice
3
Vinegar, beer, wine,
cola
4
Tomato juice
5
Black coffee
Rainwater
Urine
6
Neutral
[H+] = [OH–]
Battery acid
7
Pure water
Human blood
8
Increasingly Basic
[H+] < [OH–]
Seawater
9
10
11
Milk of magnesia
Household ammonia
12
Household bleach
13
Oven cleaner
Figure 3.8
14
Name and
Comments
Molecular Structural
Formula
Formula
H
(a) Methane
CH4
H C
H
H
(b) Ethane
H H
C2H
H C C H
6
(c) Ethene
Figure 4.3 A-C (ethylene)
H H
H
C2H4
H
C C
H
H
Ball-andStick Model
SpaceFilling
Model
H
(a) Structural isomers
H
H
H
H
H
H
C
C
C
C
C
H
H
H
H
H
X
H
(c) Enantiomers
C
C
C
H
H
H
X
C
C
C
X
H
H
CO2H
CO2H
C
C
H
H
NH2 NH2
CH3
Figure 4.7 A-C
H
C
H
H
H
C
H
X
C
(b) Geometric isomers
H
H
H
H
CH3
H
FUNCTIONAL
GROUP
HYDROXYL
CARBONYL
CARBOXYL
O
OH
(may be written HO
C
C
OH
)
STRUCTURE In a hydroxyl group (—OH),
a hydrogen atom is bonded
to an oxygen atom, which in
turn is bonded to the carbon
skeleton of the organic
molecule. (Do not confuse
this functional group with the
hydroxide ion, OH–.)
Figure 4.10
O
The carbonyl group
( CO) consists of a
carbon atom joined to
an oxygen atom by a
double bond.

When an oxygen atom is doublebonded to a carbon atom that is
also bonded to a hydroxyl group,
the entire assembly of atoms is
called a carboxyl group (—
COOH).
AMINO
SULFHYDRYL
H
N
H
Figure 4.10
O
SH
(may be written HS
The amino group (—NH2)
consists of a nitrogen atom
bonded to two hydrogen
atoms and to the carbon
skeleton.
PHOSPHATE
)
O P OH
OH
The sulfhydryl group
consists of a sulfur atom
bonded to an atom of
hydrogen; resembles a
hydroxyl group in shape.
In a phosphate group, a
phosphorus atom is bonded to four
oxygen atoms; one oxygen is
bonded to the carbon skeleton; two
oxygens carry negative charges;
abbreviated P . The phosphate
group (—OPO32–) is an ionized
form of a phosphoric acid group (—
OPO3H2; note the two hydrogens).
The Synthesis and Breakdown
of Polymers
HO
1
3
2
H
Unlinked monomer
Short polymer
Dehydration removes a water
molecule, forming a new bond
HO
Figure 5.2A
1
2
H
HO
3
H2O
4
H
Longer polymer
(a) Dehydration reaction in the synthesis of a polymer
• Polymers can disassemble by
– Hydrolysis
HO
1
2
3
4
Hydrolysis adds a water
molecule, breaking a bond
HO
1
2
3
H
Figure 5.2B (b) Hydrolysis of a polymer
H
H2O
HO
H
Macromolecules
•
•
•
•
Carbohydrates
Proteins
Lipids
Nucleic acids
Starch
– Is the major storage form of glucose in plants
Chloroplast
Starch
1 m
Amylose
Amylopectin
Figure 5.6 (a) Starch: a plant polysaccharide
• Glycogen
– Consists of glucose monomers
– Is the major storage form of glucose in
animals
Mitochondria
Giycogen
granules
0.5 m
Glycogen
Figure 5.6 (b) Glycogen: an animal polysaccharide
Cellulose
– Is a major component of the tough walls that
enclose plant cells
Cell walls
Cellulose microfibrils
in a plant cell wall
Microfibril
About 80 cellulose
molecules associate
to form a microfibril, the
main architectural unit
of the plant cell wall.
0.5 m
Plant cells
Parallel cellulose molecules are
held together by hydrogen
bonds between hydroxyl
groups attached to carbon
atoms 3 and 6.
Figure 5.8
OH CH2OH
OH
CH2OH
O O
O O
OH
OH
OH
OH
O
O O
O O
O CH OH
OH
CH2OH
2
H
CH2OH
OH CH2OH
OH
O O
O O
OH
OH
OH
OH
O
O O
O O
O CH OH
OH CH2OH
2
H
CH2OH
OH
OH CH2OH
O O
O O
OH
OH
OH O
O OH
O O
O
O CH OH
OH CH2OH
2
H
 Glucose
monomer
Cellulose
molecules
A cellulose molecule
is an unbranched 
glucose polymer.
Fats
• Fats
– Are constructed from two types of smaller
molecules, a single glycerol and usually three
fatty acids
H
H
C
O
C
OH
HO
H
C
OH
H
C
OH
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
Fatty acid
(palmitic acid)
H
Glycerol
(a) Dehydration reaction in the synthesis of a fat
Ester linkage
O
H
H
C
O
C
H
C
H
O
H
C
O
C
O
H
C
H
Figure 5.11
O
C
H
C
H
H
C
H
C
H
H
H
C
H
C
H
H
H
C
H
H
C
H
H
C
H
H
C
H
C
H
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
(b) Fat molecule (triacylglycerol)
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
H
C
C
H
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
H
C
H
H
H
C
H
H
H
C
H
H
• Phospholipid structure
– Consists of a hydrophilic “head” and
hydrophobic “tails”
CH2
+
N(CH )
3 3
Choline
CH2
O
O
P
O–
Phosphate
O
CH2
CH
O
O
C
O C
CH2
Glycerol
O
Fatty acids
Hydrophilic
head
Hydrophobic
tails
Figure 5.13
(a) Structural formula
(b) Space-filling model
(c) Phospholipid
symbol
• One steroid, cholesterol
– Is found in cell membranes
– Is a precursor for some hormones
H3C
CH3
CH3
Figure 5.15
HO
CH3
CH3
Table 5.1
• 20 different amino acids make up proteins
CH3
CH3
H
H3N+
C
CH3
O
H3N+
C
H
Glycine (Gly)
O–
C
H3N+
C
H
Alanine (Ala)
O–
CH
CH3
CH3
O
C
CH2
CH2
O
H3N+
C
H
Valine (Val)
CH3
CH3
O–
C
O
H3N+
C
H
Leucine (Leu)
H3C
O–
CH
C
O
C
O–
H
Isoleucine (Ile)
Nonpolar
CH3
CH2
S
NH
CH2
CH2
H3N+
C
H
H3N+
C
O–
Methionine (Met)
Figure 5.17
CH2
O
C
H
CH2
O
H3N+
C
C
O–
Phenylalanine (Phe)
H
O
H2C
CH2
H2N
C
O
C
O–
H
C
O–
Tryptophan (Trp)
Proline (Pro)
Amino Acid Polymers
• Amino acids
– Are linked by peptide bonds
OH
Peptide
bond
OH
CH2
CH2
H
N
H
SH
CH2
H
C C
H
N C C OH H N C
H O
H O
H
(a)
C OH
O DESMOSOMES
H2O
OH
DESMOSOMES
DESMOSOMES
SH
OH
Peptide
CH2 bond CH2
CH2
H
H N C C
H O
Figure 5.18
(b)
Amino end
(N-terminus)
H
H
N C C
H O
N C C OH
H O
Carboxyl end
(C-terminus)
Side
chains
Backbone
+H
3N
Amino end
Amino acid
subunits
helix
Denaturation
Normal protein
Figure 5.22
Denatured protein
Renaturation
The Structure of Nucleic Acids
5’ end
5’C
O
3’C
O
O
5’C
O
3’C
OH
3’ end
Figure 5.26
(a) Polynucleotide,
or nucleic acid
Pili: attachment structures on
the surface of some prokaryotes
Nucleoid: region where the
cell’s DNA is located (not
enclosed by a membrane)
Ribosomes: organelles that
synthesize proteins
Bacterial
chromosome
(a) A typical
rod-shaped bacterium
Figure 6.6 A, B
Plasma membrane: membrane
enclosing the cytoplasm
Cell wall: rigid structure outside
the plasma membrane
Capsule: jelly-like outer coating
of many prokaryotes
0.5 µm
Flagella: locomotion
organelles of
some bacteria
(b) A thin section through the
bacterium Bacillus coagulans
(TEM)
ENDOPLASMIC RETICULUM (ER)
Rough ER
Smooth ER
Nuclear envelope
Nucleolus
NUCLEUS
Chromatin
Flagelium
Plasma membrane
Centrosome
CYTOSKELETON
Microfilaments
Intermediate filaments
Ribosomes
Microtubules
Microvilli
Golgi apparatus
Peroxisome
Mitochondrion
Figure 6.9
Lysosome
In animal cells but not plant cells:
Lysosomes
Centrioles
Flagella (in some plant sperm)
Nuclear envelope
Nucleolus
Chromatin
NUCLEUS
Centrosome
Rough
endoplasmic
reticulum Smooth
endoplasmic
reticulum
Ribosomes (small brwon dots)
Central vacuole
Tonoplast
Golgi apparatus
Microfilaments
Intermediate
filaments
CYTOSKELETON
Microtubules
Mitochondrion
Peroxisome
Plasma membrane
Chloroplast
Cell wall
Plasmodesmata
Wall of adjacent cell
Figure 6.9
In plant cells but not animal cells:
Chloroplasts
Central vacuole and tonoplast
Cell wall
Plasmodesmata
• The cytoskeleton
– Is a network of fibers extending throughout
the cytoplasm
Microtubule
Figure 6.20
0.25 µm
Microfilaments
Table 6.1
P
P
P
Adenosine triphosphate (ATP)
H2O
P
Figure 8.9
i
+
Inorganic phosphate
P
P
Adenosine diphosphate (ADP)
Energy
Free energy
Products
Amount of
energy
released
(∆G>0)
Energy
Reactants
Progress of the reaction
Figure 8.6 (b) Endergonic reaction: energy required
Free energy
Reactants
Amount of
energy
released
(∆G <0)
Energy
Products
Progress of the reaction
Figure 8.6
(a) Exergonic reaction: energy released
TIGHT JUNCTIONS
Tight junction
Tight junctions prevent
fluid from moving
across a layer of cells
At tight junctions, the membranes of
neighboring cells are very tightly pressed
against each other, bound together by
specific proteins (purple). Forming continuous seals around the cells, tight junctions
prevent leakage of extracellular fluid across
A layer of epithelial cells.
0.5 µm
DESMOSOMES
Desmosomes (also called anchoring
junctions) function like rivets, fastening cells
Together into strong sheets. Intermediate
Filaments made of sturdy keratin proteins
Anchor desmosomes in the cytoplasm.
Tight junctions
Intermediate
filaments
Desmosome
Gap
junctions
Space
between
cells
Figure 6.31
1 µm
GAP JUNCTIONS
Gap junctions (also called communicating
junctions) provide cytoplasmic channels from
one cell to an adjacent cell. Gap junctions
consist of special membrane proteins that
surround a pore through which ions, sugars,
amino acids, and other small molecules may
pass. Gap junctions are necessary for communication between cells in many types of tissues,
including heart muscle and animal embryos.
Extracellular
matrix
Gap junction
Plasma membranes
of adjacent cells
0.1 µm
Glycoprotein
Carbohydrate
Glycolipid
EXTRACELLULAR
SIDE OF
MEMBRANE
Microfilaments
of cytoskeleton
Figure 7.7
Cholesterol
Peripheral
protein
Integral
protein
CYTOPLASMIC SIDE
OF MEMBRANE
(a) Diffusion of one solute. The membrane
has pores large enough for molecules
of dye to pass through. Random
movement of dye molecules will cause
some to pass through the pores; this
will happen more often on the side
with more molecules. The dye diffuses
from where it is more concentrated
to where it is less concentrated
(called diffusing down a concentration
gradient). This leads to a dynamic
equilibrium: The solute molecules
continue to cross the membrane,
but at equal rates in both directions.
Figure 7.11 A
Molecules of dye
Membrane (cross section)
Net diffusion
Net diffusion
Equilibrium
(b) Plant cell. Plant cells
are turgid (firm) and
generally healthiest in
a hypotonic environment, where the
uptake of water is
eventually balanced
by the elastic wall
pushing back on the
cell.
Turgid (normal)
Hypotonic solution
(a) Animal cell. An
animal cell fares best
in an isotonic environment unless it has
special adaptations to
offset the osmotic
uptake or loss of
water.
H2O
Lysed
Figure 7.13
H2O
H2O
H2O
Flaccid
H2O
Plasmolyzed
Isotonic solution
Hypertonic solution
H2O
H2O
Normal
H2O
Shriveled
Passive transport. Substances diffuse spontaneously
down their concentration gradients, crossing a
membrane with no expenditure of energy by the cell.
The rate of diffusion can be greatly increased by transport
proteins in the membrane.
Active transport. Some transport proteins act as
pumps, moving substances across a membrane
against their concentration gradients. Energy for this
work is usually supplied by ATP.
ATP
Diffusion. Hydrophobic
Facilitated diffusion. Many hydrophilic
molecules and (at a slow
substances diffuse through membranes
rate) very small uncharged
with the assistance of transport proteins,
polar molecules can diffuse through
either channel or carrier proteins.
the lipid bilayer.
EXTRACELLULAR
1 µm
CYTOPLASM
FLUID
In phagocytosis, a cell
Pseudopodium
PHAGOCYTOSIS
engulfs a particle by
Wrapping pseudopodia
Pseudopodium
around it and packaging
of amoeba
it within a membraneenclosed sac large
“Food” or
enough to be classified
other particle
Bacterium
as a vacuole. The
particle is digested after
Food
the vacuole fuses with a
Food vacuole
vacuole
lysosome containing
hydrolytic enzymes.
An amoeba engulfing a bacterium via
phagocytosis (TEM).
In pinocytosis, the cell
“gulps” droplets of
extracellular fluid into tiny
vesicles. It is not the fluid
itself that is needed by the
cell, but the molecules
dissolved in the droplet.
Because any and all
included solutes are taken
into the cell, pinocytosis
is nonspecific in the
substances it transports.
Figure 7.20
PINOCYTOSIS
0.5 µm
Plasma
membrane
Pinocytosis vesicles
forming (arrows) in
a cell lining a small
blood vessel (TEM).
Vesicle
Receptor-mediated endocytosis enables the
cell to acquire bulk quantities of specific
substances, even though those substances
may not be very concentrated in the
extracellular fluid. Embedded in the
membrane are proteins with
specific receptor sites exposed to
the extracellular fluid. The receptor
proteins are usually already clustered
in regions of the membrane called coated
pits, which are lined on their cytoplasmic
side by a fuzzy layer of coat proteins.
Extracellular substances (ligands) bind
to these receptors. When binding occurs,
the coated pit forms a vesicle containing the
ligand molecules. Notice that there are
relatively more bound molecules (purple)
inside the vesicle, other molecules
(green) are also present. After this ingested
material is liberated from the vesicle, the
receptors are recycled to the plasma
membrane by the same vesicle.
RECEPTOR-MEDIATED ENDOCYTOSIS
Coat protein
Receptor
Coated
vesicle
Ligand
Coated
pit
A coated pit
and a coated
vesicle formed
during
receptormediated
endocytosis
(TEMs).
Coat
protein
Plasma
membrane
0.25 µm
• Enzymes
– Are a type of protein that acts as a catalyst,
speeding up chemical reactions
1 Active site is available for
a molecule of substrate, the
reactant on which the enzyme acts.
Substrate
(sucrose)
2 Substrate binds to
enzyme.
Glucose
OH
Enzyme
(sucrase)
H2O
Fructose
H O
4 Products are released.
Figure 5.16
3 Substrate is converted
to products.
1 Substrates enter active site; enzyme
changes shape so its active site
embraces the substrates (induced fit).
Substrates
Enzyme-substrate
complex
6 Active site
Is available for
two new substrate
Mole.
Enzyme
5 Products are
Released.
Figure 8.17
Products
2 Substrates held in
active site by weak
interactions, such as
hydrogen bonds and
ionic bonds.
3 Active site (and R groups of
its amino acids) can lower EA
and speed up a reaction by
• acting as a template for
substrate orientation,
• stressing the substrates
and stabilizing the
transition state,
• providing a favorable
microenvironment,
• participating directly in the
catalytic reaction.
4 Substrates are
Converted into
Products.
Course of
reaction
without
enzyme
EA
without
enzyme
EA with
enzyme
is lower
Free energy
Reactants
∆G is unaffected
by enzyme
Course of
reaction
with enzyme
Products
Progress of the reaction
Figure 8.15
Effects of Temperature and pH
• Each enzyme
– Has an optimal temperature in which it can
function
Optimal temperature for
typical human enzyme
Optimal temperature for
enzyme of thermophilic
Rate of reaction
(heat-tolerant)
bacteria
0
20
40
Temperature (Cº)
(a) Optimal temperature for two enzymes
Figure 8.18
80
100
A substrate can
bind normally to the
active site of an
enzyme.
Substrate
Active site
Enzyme
(a) Normal binding
A competitive
inhibitor mimics the
substrate, competing
for the active site.
Figure 8.19
(b) Competitive inhibition
Competitive
inhibitor
• Feedback inhibition
Active site
available
Initial substrate
(threonine)
Threonine
in active site
Enzyme 1
(threonine
deaminase)
Isoleucine
used up by
cell
Intermediate A
Feedback
inhibition
Active site of
enzyme 1 no
longer binds
threonine;
pathway is
switched off
Enzyme 2
Intermediate B
Enzyme 3
Intermediate C
Isoleucine
binds to
allosteric
site
Enzyme 4
Intermediate D
Enzyme 5
Figure 8.21
End product
(isoleucine)
Light reaction
Calvin cycle
H2O
CO2
Light
NADP+
ADP
+P1
RuBP
3-Phosphoglycerate
Photosystem II
Electron transport chain
Photosystem I
ATP
NADPH
G3P
Starch
(storage)
Amino acids
Fatty acids
Chloroplast
O2
Figure 10.21
Light reactions:
• Are carried out by molecules in the
thylakoid membranes
• Convert light energy to the chemical
energy of ATP and NADPH
• Split H2O and release O2 to the
atmosphere
Sucrose (export)
Calvin cycle reactions:
• Take place in the stroma
• Use ATP and NADPH to convert
CO2 to the sugar G3P
• Return ADP, inorganic phosphate, and
NADP+ to the light reactions
Light
Reflected
Light
Chloroplast
Absorbed
light
Granum
Transmitted
light
Figure 10.7
H2O
CO2
LIGHT
NADP+
ADP
CALVIN
CYCLE
LIGHT
REACTOR
ATP
NADPH
STROMA
(Low H+ concentration)
O2
[CH2O] (sugar)
Photosystem II
Cytochrome
complex
Photosystem I
NADP+
reductase
Light
2 H+
Fd
3
NADP+ + 2H+
NADPH
+ H+
Pq
Pc
2
H2O
THYLAKOID SPACE
(High H+ concentration)
1⁄
2
1
O2
+2 H+
2 H+
To
Calvin
cycle
STROMA
(Low H+ concentration)
Thylakoid
membrane
ATP
synthase
ADP
ATP
P
Figure 10.17
H+
H2 O
CO2
Input
Light
(Entering one
3
CO2 at a time)
NADP+
ADP
CALVIN
CYCLE
LIGHT
REACTION
ATP
NADPH
Rubisco
O2
[CH2O] (sugar)
3 P
P
Phase 1: Carbon fixation
Short-lived
intermediate
3 P
P
6
P
Ribulose bisphosphate
(RuBP)
3-Phosphoglycerate
6
ATP
6 ADP
CALVIN
CYCLE
3 ADP
3
6 P
ATP
P
1,3-Bisphoglycerate
6 NADPH
6 NADPH+
6 P
Phase 3:
Regeneration
of P
5
the CO(G3P)
2 acceptor
(RuBP)
6
P
Glyceraldehyde-3-phosphate
(G3P)
P
1
Figure 10.18
G3P
(a sugar)
Output
Glucose and
other organic
compounds
Phase 2:
Reduction
Mesophyll
cell
Mesophyll cell
Photosynthetic
cells of C4 plant
leaf
CO
CO
2 2
PEP carboxylase
Bundlesheath
cell
PEP (3 C)
ADP
Oxaloacetate (4 C)
Vein
(vascular tissue)
Malate (4 C)
ATP
C4 leaf anatomy
BundleSheath
cell
Pyruate (3 C)
CO2
Stoma
CALVIN
CYCLE
Sugar
Vascular
tissue
Figure 10.19
Pineapple
Sugarcane
C4
Mesophyll Cell
Organic acid
Bundlesheath
cell
(a) Spatial separation of
steps. In C4 plants,
carbon fixation and the
Calvin cycle occur in
different
types of cells.
CALVIN
CYCLE
Sugar
CAM
CO2
1 CO2 incorporated
into four-carbon
organic acids
(carbon fixation)
2 Organic acids
release CO2 to
Calvin cycle
CO2
Organic acid
Night
Day
CALVIN
CYCLE
Sugar
(b) Temporal separation of
steps. In CAM plants,
carbon fixation and the
Calvin cycle occur in the
same cells
at different times.
Electrons carried
via NADH and
FADH2
Electrons
carried
via NADH
Glycolsis
Pyruvate
Glucose
Cytosol
ATP
Figure 9.6
Substrate-level
phosphorylation
Citric
acid
cycle
Oxidative
phosphorylation:
electron
transport and
chemiosmosis
Mitochondrion
ATP
Substrate-level
phosphorylation
ATP
Oxidative
phosphorylation
CYTOSOL
MITOCHONDRION
NAD+
NADH
+ H+
O–
S
CoA
C
O
2
C
C
O
O
1
3
CH3
Pyruvate
Transport protein
Figure 9.10
CH3
Acetyle CoA
CO2
Coenzyme A
Pyruvate
(from glycolysis,
2 molecules per glucose)
Glycolysis
Citric
acid
cycle
ATP
ATP
Oxidative
phosphorylation
ATP
CO2
CoA
NADH
+ 3 H+
Acetyle CoA
CoA
CoA
Citric
acid
cycle
2 CO2
3 NAD+
FADH2
FAD
3 NADH
+ 3 H+
ADP + P i
ATP
Figure 9.11
P1
2 ADP + 2
2 ATP
Glucose
Glucose
Glycolysis
O–
C
O
C
O
CH3
2 Pyruvate
CYTOSOL
Pyruvate
No O2 present
Fermentation
2 NADH
2 NAD+
H
O2 present
Cellular respiration
H
2 CO2
H
C
C
OH
CH3
O
CH3
2 Ethanol
2 Acetaldehyde
(a) Alcohol fermentation
MITOCHONDRION
Ethanol
or
lactate
2 ADP + 2
P1
2 ATP
Acetyl CoA
Glucose
Citric
acid
cycle
2 NAD+
O
H
O–
Glycolysis
C
O
C
OH
CH3
2 Lactate
(b) Lactic acid fermentation
2 NADH
C
O
C
O
CH3
Glucose
AMP
Glycolysis
Fructose-6-phosphate
Stimulates
+
–
Phosphofructokinase
–
Fructose-1,6-bisphosphate
Inhibits
Inhibits
Pyruvate
Citrate
ATP
Acetyl CoA
Citric
acid
cycle
Figure 9.20
Oxidative
phosphorylation
EXTRACELLULAR
FLUID
1 Reception
CYTOPLASM
Plasma membrane
2 Transduction
3 Response
Receptor
Activation
of cellular
response
Relay molecules in a signal transduction pathway
Signal
molecule
Figure 11.5
Signal-binding site
Segment that
interacts with
G proteins
G-protein-linked
Receptor
Plasma Membrane
Activated
Receptor
Inctivate
enzyme
Signal molecule
GDP
CYTOPLASM
G-protein
(inactive)
Enzyme
GDP
GTP
Activated
enzyme
GTP
GDP
Pi
Cellular response
• Multicellular organisms depend on cell division
for
– Development from a fertilized cell
– Growth
– Repair
200 µm
20 µm
(b) Growth and development.
(c) Tissue renewal. These dividing
This micrograph shows a
bone marrow cells (arrow) will
sand dollar embryo shortly
give rise to new blood cells (LM).
after the fertilized egg divided,
Figure 12.2 B, C forming two cells (LM).
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
0.5 µm
A eukaryotic cell has multiple
chromosomes, one of which is
represented here. Before
duplication, each chromosome
has a single DNA molecule.
Chromosome
duplication
(including DNA
synthesis)
Once duplicated, a chromosome
consists of two sister chromatids
connected at the centromere. Each
chromatid contains a copy of the
DNA molecule.
Centromere
Separation
of sister
chromatids
Sister
chromatids
Mechanical processes separate
the sister chromatids into two
chromosomes and distribute
them to two daughter cells.
Figure 12.4
Centromeres
Sister chromatids
Phases of the Cell Cycle
• The cell cycle consists of
– The mitotic phase
– Interphase
INTERPHASE
C
M yto
ito ki
si ne
s si
s
G1
MI
(M TOT
) P IC
HA
SE
Figure 12.5
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
S
(DNA synthesis)
G2
G2 OF
PROPHASE
INTERPHASE
Centrosomes
Aster
Early
mitotic
Chromatin
(with centriole pairs)
Centromere
spindle
(duplicated)
Figure 12.6
Nucleolus Nuclear Plasma
envelope
membrane
METAPHASE
Metaphase
plate
Figure 12.6 Spindle
PROMETAPHASE
Fragments
Kinetochore
of nuclear
envelope Nonkinetochore
microtubules
Chromosome, consisting
of two sister chromatids
Kinetochore
microtubule
ANAPHASETELOPHASE AND CYTOKINESIS
Daughter
Centrosome at
chromosomes
one spindle pole
Cleavage
furrow
Nuclear
envelope
forming
Nucleolus
forming
G0
G1 checkpoint
G1
Figure 12.15 A, B
(a) If a cell receives a go-ahead signal at
the G1 checkpoint, the cell continues
on in the cell cycle.
G1
(b) If a cell does not receive a go-ahead
signal at the G1checkpoint, the cell
exits the cell cycle and goes into G0, a
nondividing state.
Pair of homologous
chromosomes
karyotype
Centromere
Sister
chromatids
Figure 13.3
5 µm
• Interphase and meiosis I
• Telophase I, cytokinesis, and meiosis II
MEIOSIS I: Separates homologous chromosomes
INTERPHASE
PROPHASE I
METAPHASE I
ANAPHASE I
MEIOSIS II: Separates sister chromatids
TELOPHASE I AND
CYTOKINESIS
Sister
chromatids
Chiasmata
Spindle
METAPHASE II
Homologous
Microtubule
chromosomes
attached to
separate
kinetochore
Pairs of homologous
Chromosomes duplicate
Tertads line up
chromosomes split up
Homologous chromosomes
(red and blue) pair and exchange
Figure 13.8
Figure 13.8
segments; 2n = 6 in this example
Chromatin
TELOPHASE II AND
CYTOKINESIS
Metaphase
plate
Cleavage
furrow
Nuclear
envelope
ANAPHASE II
Sister chromatids
remain attached
Centromere
(with kinetochore)
Centrosomes
(with centriole pairs)
PROPHASE II
Sister chromatids
separate
Haploid daughter cells
forming
Tetrad
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Two haploid cells
form; chromosomes
are still double
During another round of cell division, the sister chromatids finally separate;
four haploid daughter cells result, containing single chromosomes
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Prophase I
of meiosis
Nonsister
chromatids
Tetrad
Chiasma,
site of
crossing
over
Metaphase I
Metaphase II
Daughter
cells
Figure 13.11
Recombinant
chromosomes
• Mendel’s law of segregation, probability and
the Punnett square
Each true-breeding plant of the
parental generation has identical
alleles, PP or pp.
Gametes (circles) each contain only
one allele for the flower-color gene.
In this case, every gamete produced
by one parent has the same allele.
P Generation
Gametes:
p
P
Union of the parental gametes
produces F1 hybrids having a Pp
combination. Because the purpleflower allele is dominant, all
these hybrids have purple flowers.
F1 Generation
When the hybrid plants produce
gametes, the two alleles segregate,
half the gametes receiving the P
allele and the other half the p allele.
Gametes:
This box, a Punnett square, shows
all possible combinations of alleles
in offspring that result from an
F1  F1 (Pp  Pp) cross. Each square
represents an equally probable product
of fertilization. For example, the bottom
left box shows the genetic combination
resulting from a p egg fertilized by
a P sperm.

Appearance:
Purple flowers White flowers
Genetic makeup:
PP
pp
Appearance:
Genetic makeup:
Purple flowers
Pp
1/
1/
2 P
F1 sperm
P
p
PP
Pp
F2 Generation
P
F1 eggs
p
pp
Pp
Figure 14.5
Random combination of the gametes
results in the 3:1 ratio that Mendel
observed in the F2 generation.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
2 p
3
:1
• A dihybrid cross
– Illustrates the inheritance of two characters
• Produces four phenotypes in the F2 generation
EXPERIMENT Two true-breeding pea plants—
one with yellow-round seeds and the other with
green-wrinkled seeds—were crossed, producing
dihybrid F1 plants. Self-pollination of the F1 dihybrids,
which are heterozygous for both characters,
produced the F2 generation. The two hypotheses
predict different phenotypic ratios. Note that yellow
color (Y) and round shape (R) are dominant.
P Generation
YYRR
yyrr
Gametes
F1 Generation
YR

Hypothesis of
dependent
assortment
yr
YyRr
Hypothesis of
independent
assortment
Sperm
RESULTS
1? YR
2
CONCLUSION The results support the hypothesis of
independent assortment. The alleles for seed color and seed
shape sort into gametes independently of each other.
Sperm
yr
1?
2
Eggs
1
F2 Generation ?2 YR YYRR YyRr
(predicted
offspring)
1 ? yr
2
YyRr yyrr
3?
4
1?
4
YR
1?
4
Yr
1?
4
yR
1?
4
yr
Eggs
1 ? YR
4
1?
4
Yr
1?
4
yR
1?
4
yr
YYRR YYRr YyRR YyRr
YYrr
YYrr
YyRr
Yyrr
YyRR YyRr yyRR yyRr
1?
4
Phenotypic ratio 3:1
9?
16
YyRr
3?
16
Yyrr
yyRr
3?
16
yyrr
1?
16
Phenotypic ratio 9:3:3:1
Figure 14.8
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
315
108
101
32
Phenotypic ratio approximately 9:3:3:1
• In incomplete dominance
– The phenotype of F1 hybrids is somewhere between
the phenotypes of the two parental varieties
P Generation
Red
CRCR
White
CWCW

Gametes CR
CW
Pink
CRCW
F1 Generation
Gametes
Eggs
F2 Generation
Figure 14.10
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
1?
2
CR
1?
2
Cw
1?
2
1?
2
CR
CR
1?
2
CR
1? CR
2
CR CR CR CW
CR CW CW CW
Sperm
• The ABO blood group in humans
– Is determined by multiple alleles
Table 14.2
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Inheritance patterns of particular traits
– Can be traced and described using pedigrees
Ww
ww
Ww ww ww Ww
WW
or
Ww
ww
Ww
Ww
ww
First generation
(grandparents)
Second generation
(parents plus aunts
and uncles)
FF or Ff
Ff
Ff
Third
generation
(two sisters)
ww
Widow’s peak
Ff
No Widow’s peak
(a) Dominant trait (widow’s peak)
Figure 14.14 A, B
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Attached earlobe
ff
ff
Ff
Ff
Ff
ff
ff
FF
or
Ff
Free earlobe
(b) Recessive trait (attached earlobe)
• Fetal testing
(b) Chorionic villus sampling (CVS)
(a) Amniocentesis
Amniotic
fluid
withdrawn
A sample of chorionic villus
tissue can be taken as early
as the 8th to 10th week of
pregnancy.
A sample of
amniotic fluid can
be taken starting at
the 14th to 16th
week of pregnancy.
Fetus
Fetus
Suction tube
Inserted through
cervix
Centrifugation
Placenta
Placenta
Uterus
Chorionic viIIi
Cervix
Fluid
Fetal
cells
Fetal
cells
Biochemical tests can be
Performed immediately on
the amniotic fluid or later
on the cultured cells.
Fetal cells must be cultured
for several weeks to obtain
sufficient numbers for
karyotyping.
Biochemical
tests
Several
weeks
Several
hours
Karyotyping
Figure 14.17 A, B
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Karyotyping and biochemical
tests can be performed on
the fetal cells immediately,
providing results within a day
or so.
CONCLUSION Since all F offspring had red eyes, the mutant
1
white-eye trait (w) must be recessive to the wild-type red-eye trait (w+).
Since the recessive trait—white eyes—was expressed only in males in
the F2 generation, Morgan hypothesized that the eye-color gene is
located on the X chromosome and that there is no corresponding locus
on the Y chromosome, as diagrammed here.
P
Generation
W+
X
X
X
X
Y
W
W+
W
Ova
(eggs)
F1
Generation
Sperm
W+
W+
W+
W
W+
Ova
(eggs)
F2
Generation
Sperm
W+
W
W+
W+
W+
W
W
W+
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Morgan crossed flies
– That differed in traits of two different
characters
P Generation
(homozygous)
EXPERIMENT
Morgan first mated true-breeding
Wild type
wild-type flies with black, vestigial-winged flies to produce
(gray
body,
heterozygous F1 dihybrids, all of which are wild-type in
normal
wings)
appearance. He then mated wild-type F1 dihybrid females with
+
+
b b vg+ vg+
black, vestigial-winged males, producing 2,300 F2 offspring,
which he “scored” (classified according to
F1 dihybrid
phenotype).
(wild type)
(gray body,
normal wings)
Double mutant
(black body,
vestigial wings)
Double mutant
(black body,
vestigial wings)
x
b b vg vg
Double mutant
(black body,
vestigial wings)
b b vg vg
Double mutant
TESTCROSS
(black body, x
vestigial wings)
CONCLUSION
If these two genes were on
different chromosomes, the alleles from the F1 dihybrid
would sort into gametes independently, and we would
expect to see equal numbers of the four types of offspring.
If these two genes were on the same chromosome,
we would expect each allele combination, B+ vg+ and b vg,
to stay together as gametes formed. In this case, only
offspring with parental phenotypes would be produced.
Since most offspring had a parental phenotype, Morgan
concluded that the genes for body color and wing size
are located on the same chromosome. However, the
production of a small number of offspring with
nonparental phenotypes indicated that some mechanism
occasionally breaks the linkage between genes on the
same chromosome.
Figure 15.5
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
b+ b vg+ vg
RESULTS
b vg
b+vg+
b vg
965
944
Wild type
Black(gray-normal) vestigial
b+ vg
b vg+
206
Grayvestigial
185
Blacknormal
Sperm
b+ b vg+ vg b b vg vg b+ b vg vgb b vg+ vg
Parental-type
offspring
Recombinant (nonparental-type)
offspring
• Linked genes
– Exhibit recombination frequencies less than 50%
Testcross
parents
b+ vg+
Gray body,
normal wings
b vg
(F1 dihybrid)
Replication of
chromosomes
b+ vg
Meiosis I: Crossing
over between b and vg
loci produces new allele
combinations.
b vg

b+ vg+
vg
b
b vg
vg
b
b vg
b vg
Meiosis II: Segregation
of chromatids produces
recombinant gametes
with the new allele
combinations.
Gametes
Black body,
vestigial wings
b vg (double mutant)
Replication of
chromosomes
b vg
Meiosis I and II:
Even if crossing over
occurs, no new allele
combinations are
produced.
Recombinant
chromosome
Ova
Sperm
b+vg+
b vg
b+
vg
b vg+
b vg
b+ vg+
Testcross
offspring
Sperm
b vg
Figure 15.6
b+ vg
b vg
965
944
BlackWild type
(gray-normal) vestigial
b+ vg+
b vg+
b
vg
b
vg
206
Grayvestigial
b+ vg+
b
vg
b vg+ Ova
185
BlackRecombination
normal
b vg+ frequency
b
vg
Parental-type offspring Recombinant offspring
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
391 recombinants
=2,300 total offspring 
100 = 17%
• Many fruit fly genes
– Were mapped initially using recombination
frequencies
I
Y
II
X
IV
III
Mutant phenotypes
Short
aristae
Black
body
0
Figure 15.8
Long aristae
(appendages
on head)
Cinnabar Vestigial Brown
eyes
wings
eyes
48.5 57.5 67.0
Gray
body
Red
eyes
Normal
wings
Wild-type phenotypes
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
104.5
Red
eyes
• Alterations of chromosome structure
(a) A deletion removes a chromosomal
segment.
(b) A duplication repeats a segment.
(c) An inversion reverses a segment within
a chromosome.
(d) A translocation moves a segment from
one chromosome to another,
nonhomologous one. In a reciprocal
translocation, the most common type,
nonhomologous chromosomes exchange
fragments. Nonreciprocal translocations
also occur, in which a chromosome
transfers a fragment without receiving a
fragment in return.
A B C D E
F G H
A B C D E
F G H
A B C D E
F G H
A B C D E
F G H
Deletion
Duplication
Inversion
A B C E
F G H
A B C B C D E
A D C B E
F G H
M N O C D E
Reciprocal
translocation
M N O P Q
Figure 15.14a–d
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
R
A B P
Q
F G H
R
F G H