General Biology

‫‪General Biology 102 Handouts‬‬
‫‪Dr . Sulaiman Alnaimat‬‬

‫‪2017‬بن طالل‬
‫جامعة الحسين‬
‫قسم العلوم الحياتية‬
‫علوم حياتية عامة‬

‫د‪.‬سليمان النعيمــات‬
‫األستاذ أحمد المعاقبة‬
‫األستاذ علي العسوفي‬
‫‪2017‬‬ ‫‪1‬‬
General biology 101 Syllabus
Topic Text
Brief Introduction Chapter 1+2+3
Carbon and the Molecular Diversity of Life Chapter 4
The Structure and Function of Large Biological Molecules Chapter 5
A Tour of the Cell Chapter 6
Membrane Structure and Function Chapter 7
An Introduction to Metabolism Chapter 8
Cellular Respiration and Fermentation Chapter 9
Photosynthesis Chapter 10
Cell Communication Chapter 11
The Cell Cycle Chapter 12
Meiosis and Sexual Life Cycles Chapter 13
The Molecular Basis of Inheritance Chapter 16
From Gene to Protein Chapter 17
Mendel and the Gene Idea Chapter 14
Textbook: Biology 9th edition. (2011); Campbell, NA, Reece , JB.
Distribution of grades
First Exam 25 Points
Second Exam 25 Points 2
Final exam 50 points
LECTURE PRESENTATIONS
For CAMPBELL BIOLOGY, NINTH EDITION
Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson
Chapter 1+2+3
Brief Introduction
Lectures by
Erin Barley
Kathleen Fitzpatrick
3
© 2011 Pearson Education, Inc.

• Biology is the scientific study of life
• Biologists ask questions such as
– How does a single cell develop into an organism?
– How does the human mind work?
– How do living things interact in communities?
• Life defies a simple, one-sentence definition
• Life is recognized by what living things do
4
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
5
Table 2.1
6
• Covalent bonds can form between atoms of
the same element or atoms of different
elements
• A compound is a combination of two or more
different elements
• Bonding capacity is called the atom’s
valence
7
• Atoms in a molecule attract electrons to
varying degrees
• Electronegativity is an atom’s attraction for
the electrons in a covalent bond
• The more electronegative an atom, the more
strongly it pulls shared electrons toward itself
8
• 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
9
Figure 2.13
–
H H
+ +
H2O
10
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
11
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
12
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
13
Figure 2.16
– +
Water (H2O)
+
Hydrogen bond
–
Ammonia (NH3)
+ +
+ 14
Figure 3.2

Hydrogen
+ bond
Polar covalent
bonds

+
 +

+
15
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
16
Chapter 4
Carbon and the Molecular

Diversity of Life
Lectures by
Erin Barley
17

Concept 4.1: Organic chemistry is the study
of carbon compounds
• Organic chemistry is the study of compounds
that contain carbon
• Organic compounds range from simple
molecules to colossal ones
• Most organic compounds contain hydrogen
atoms in addition to carbon atoms
18
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
19
The Formation of Bonds with Carbon
• With four valence electrons, carbon can form
four covalent bonds with a variety of atoms
• This ability makes large, complex molecules
possible
• In molecules with multiple carbons, each carbon
bonded to four other atoms has a tetrahedral
shape
• However, when two carbon atoms are joined by
a double bond, the atoms joined to the carbons
are in the same plane as the carbons
20
Figure 4.3
Name and Molecular Structural Ball-and- Space-Filling

Comment Formula Formula Stick Model Model
(a) Methane
CH4
(b) Ethane
C2H6
(c) Ethene
(ethylene)
C2H4
21
Figure 4.4
Hydrogen Oxygen Nitrogen Carbon

(valence  1) (valence  2) (valence  3) (valence  4)
22
Figure 4.5
(a) Length (c) Double bond position
Ethane Propane 1-Butene 2-Butene
(b) Branching (d) Presence of rings
Butane 2-Methylpropane Cyclohexane Benzene

(isobutane)
23
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
24
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
25
Figure 4.UN02
Estradiol
Testosterone
26
• The seven functional groups that are most
important in the chemistry of life:
– Hydroxyl group
– Carbonyl group
– Carboxyl group
– Amino group
– Sulfhydryl group
– Phosphate group
– Methyl group
27
Figure 4.9a
Hydroxyl
STRUCTURE Alcohols NAME OF

(Their specific COMPOUND
names usually
(may be written end in -ol.)
HO—)
EXAMPLE • Is polar as a result FUNCTIONAL

of the electrons PROPERTIES
spending more
time near the
electronegative
oxygen atom.
Ethanol • Can form hydrogen
bonds with water
molecules, helping
dissolve organic
compounds such
as sugars.
28
Figure 4.9b
Carbonyl
STRUCTURE Ketones if the carbonyl NAME OF

group is within a COMPOUND
carbon skeleton
Aldehydes if the carbonyl
group is at the end of the
carbon skeleton
EXAMPLE • A ketone and an FUNCTIONAL

aldehyde may be PROPERTIES
structural isomers
with different properties,
as is the case for
acetone and propanal.
• Ketone and aldehyde
Acetone groups are also found
in sugars, giving rise
to two major groups
of sugars: ketoses
(containing ketone
groups) and aldoses
(containing aldehyde
Propanal groups). 29
Figure 4.9c
Carboxyl
STRUCTURE Carboxylic acids, or organic NAME OF

acids COMPOUND
EXAMPLE • Acts as an acid; can FUNCTIONAL

donate an H+ because the PROPERTIES
covalent bond between
oxygen and hydrogen is so
polar:
Acetic acid
Nonionized Ionized
• Found in cells in the ionized

form with a charge of 1– and
called a carboxylate ion. 30
Figure 4.9d
Amino
STRUCTURE Amines NAME OF

COMPOUND
EXAMPLE • Acts as a base; can FUNCTIONAL

pick up an H+ from the PROPERTIES
surrounding solution
(water, in living
organisms):
Glycine
Nonionized Ionized
• Found in cells in the

ionized form with a
charge of 1. 31
Figure 4.9e
Sulfhydryl
STRUCTURE Thiols NAME OF

COMPOUND
(may be
written HS—)
EXAMPLE • Two sulfhydryl groups can FUNCTIONAL

react, forming a covalent PROPERTIES
bond. This “cross-linking”
helps stabilize protein
structure.
• Cross-linking of cysteines
in hair proteins maintains
the curliness or straightness
Cysteine
of hair. Straight hair can be
“permanently” curled by
shaping it around curlers
and then breaking and
re-forming the cross-linking
bonds. 32
Figure 4.9f
Phosphate
STRUCTURE Organic phosphates NAME OF

COMPOUND
EXAMPLE • Contributes negative FUNCTIONAL

charge to the molecule PROPERTIES
of which it is a part
(2– when at the end of
a molecule, as at left;
1– when located
internally in a chain of
phosphates).
Glycerol phosphate • Molecules containing
phosphate groups have
the potential to react
with water, releasing
energy.
33
Figure 4.9g
Methyl
STRUCTURE Methylated compounds NAME OF

COMPOUND
EXAMPLE • Addition of a methyl group FUNCTIONAL

to DNA, or to molecules PROPERTIES
bound to DNA, affects the
expression of genes.
• Arrangement of methyl
groups in male and female
sex hormones affects their
shape and function.
5-Methyl cytidine
34
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
35
Figure 4. UN05
Adenosine
Reacts
with H2O
Adenosine Adenosine Energy
ATP Inorganic ADP
phosphate
36
• The element present in all organic molecules is
A) hydrogen. B) oxygen. C) carbon. D) nitrogen.
37
Chapter 5
The Structure and Function of

Large Biological Molecules
Lectures by
Erin Barley
38

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
39
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
40
The Synthesis and Breakdown of Polymers
• A dehydration reaction occurs when two
monomers bond together through the loss of a
water molecule
• Polymers are disassembled to monomers by
hydrolysis, a reaction that is essentially the
reverse of the dehydration reaction
41
Figure 5.2
(a) Dehydration reaction: synthesizing a polymer
1 2 3
Short polymer Unlinked monomer
Dehydration removes
a water molecule,
forming a new bond.
1 2 3 4
Longer polymer
(b) Hydrolysis: breaking down a polymer
1 2 3 4
Hydrolysis adds
a water molecule,
breaking a bond.
1 2 3 42
The Diversity of Polymers
• Each cell has thousands of different
HO
macromolecules
• Macromolecules vary among cells of an
organism, vary more within a species, and
vary even more between species
• An immense variety of polymers can be built
from a small set of monomers
43
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
44
Sugars
• Monosaccharides have molecular formulas
that are usually multiples of CH2O
• Glucose (C6H12O6) is the most common
monosaccharide
• Monosaccharides are classified by
– The location of the carbonyl group (as aldose
or ketose)
– The number of carbons in the carbon skeleton
45
Figure 5.3a
Aldose (Aldehyde Sugar) Ketose (Ketone Sugar)

Trioses: 3-carbon sugars (C3H6O3)
Glyceraldehyde Dihydroxyacetone
46
Figure 5.3b

Pentoses: 5-carbon sugars (C5H10O5)
Ribose Ribulose
47
Figure 5.3c
Hexoses: 6-carbon sugars (C6H12O6)
Glucose Galactose Fructose

48
• Though often drawn as linear skeletons, in
aqueous solutions many sugars form rings
• Monosaccharides serve as a major fuel for
cells and as raw material for building
molecules
49
Figure 5.4
1 6 6
2
5 5
3
4 1 4 1
4
2 2
5 3 3
(a) Linear and ring forms
6
5
4 1
3 2
50
(b) Abbreviated ring structure
• A disaccharide is formed when a dehydration
reaction joins two monosaccharides
• This covalent bond is called a glycosidic
linkage
51
Figure 5.5
1–4
glycosidic
1 linkage 4
Glucose Glucose Maltose

(a) Dehydration reaction in the synthesis of maltose
1–2
glycosidic
1 linkage 2
Glucose Fructose Sucrose

(b) Dehydration reaction in the synthesis of sucrose
52
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
53
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
54
Figure 5.6
Chloroplast Starch granules
Amylopectin
Amylose
(a) Starch:
a plant polysaccharide1 m
Mitochondria Glycogen granules
Glycogen
(b) Glycogen:
0.5 m
an animal polysaccharide 55
• Glycogen is a storage polysaccharide in
animals
• Humans and other vertebrates store
glycogen mainly in liver and muscle cells
56
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 ()
57
Figure 5.7
(a)  and  glucose

ring structures
4 1 4 1
 Glucose  Glucose
1 4
1 4
(b) Starch: 1–4 linkage of  glucose monomers (c) Cellulose: 1–4 linkage of  glucose monomers
58
Figure 5.7a
4 1 4 1
 Glucose  Glucose
(a)  and  glucose ring structures
59
Figure 5.7b
1 4
(b) Starch: 1–4 linkage of  glucose monomers
1 4
(c) Cellulose: 1–4 linkage of  glucose monomers 60

• 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
61
Figure 5.8
Cell wall Cellulose

microfibrils in a
plant cell wall
Microfibril
10 m
0.5 m
Cellulose
molecules
 Glucose
monomer 62
• Enzymes that digest starch by hydrolyzing 
linkages can’t hydrolyze  linkages in cellulose
• Cellulose in human food passes through the
digestive tract as insoluble fiber
• Some microbes use enzymes to digest
cellulose
• Many herbivores, from cows to termites, have
symbiotic relationships with these microbes
63
• Chitin, another structural polysaccharide, is
found in the exoskeleton of arthropods
• Chitin also provides structural support for the
cell walls of many fungi
64
Figure 5.9
The structure
of the chitin
monomer
Chitin forms the exoskeleton

of arthropods.
Chitin is used to make a strong and flexibl

65
surgical thread that decomposes after the
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
66
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
67
Figure 5.10
Fatty acid
(in this case, palmitic acid)
Glycerol
(a) One of three dehydration reactions in the synthesis of a fat
Ester linkage
(b) Fat molecule (triacylglycerol) 68

• Fats separate from water because water
molecules form hydrogen bonds with each
other and exclude the fats
• In a fat, three fatty acids are joined to
glycerol by an ester linkage, creating a
triacylglycerol, or triglyceride
69
Figure 5.10b
Ester linkage
(b) Fat molecule (triacylglycerol)

70
• 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
71
Figure 5.11a
(a) Saturated fat
Structural
formula of a
saturated fat
molecule
Space-filling
model of stearic
acid, a saturated
fatty acid 72
Figure 5.11b
(b) Unsaturated fat
Structural
formula of an
unsaturated fat
molecule
Space-filling model
of oleic acid, an
unsaturated fatty
acid
Cis double bond
causes bending. 73
• Fats made from saturated fatty acids are
called saturated fats, and are solid at room
temperature
• Most animal fats are saturated
• Fats made from unsaturated fatty acids are
called unsaturated fats or oils, and are liquid
at room temperature
• Plant fats and fish fats are usually unsaturated
74
• The major function of fats is energy storage
• Humans and other mammals store their fat in
adipose cells
• Adipose tissue also cushions vital organs and
insulates the body
75
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
76
Figure 5.12a
Choline
Hydrophilic head
Phosphate
Glycerol
Hydrophobic tails
Fatty acids
(a) Structural formula 77

(b) Space-filling model
• 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
78
Figure 5.13
Hydrophilic WATER
head
Hydrophobic
tail WATER
79
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
80
Figure 5.14
81
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
82
• Enzymes are a type of protein that acts as a
catalyst to speed up chemical reactions
• Enzymes can perform their functions
repeatedly, functioning as workhorses that
carry out the processes of life
83
Polypeptides
• Polypeptides are unbranched polymers built
from the same set of 20 amino acids
• A protein is a biologically functional molecule
that consists of one or more polypeptides
84
Amino Acid Monomers
• Amino acids are organic molecules with
carboxyl and amino groups
• Amino acids differ in their properties due to
differing side chains, called R groups
85
Figure 5.UN01
Side chain (R group)
 carbon
Amino Carboxyl
group group
86
Figure 5.16a
Nonpolar side chains; hydrophobic

Side chain
Glycine Alanine Valine Leucine Isoleucine

(Gly or G) (Ala or A) (Val or V) (Leu or L) (Ile or I)
Methionine Phenylalanine Tryptophan Proline

(Met or M) (Phe or F) (Trp or W) (Pro or P)
87
Figure 5.16b
Polar side chains; hydrophilic
Serine Threonine Cysteine

(Ser or S) (Thr or T) (Cys or C)
Tyrosine Asparagine Glutamine

(Tyr or Y) (Asn or N) (Gln or Q) 88
Figure 5.16c
Electrically charged side chains; hydrophilic

Basic (positively charged)
Acidic (negatively charged)
Aspartic acid Glutamic acid Lysine Arginine Histidine

(Asp or D) (Glu or E) (Lys or K) (Arg or R) (His or H)
89
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)
90
Figure 5.17
Peptide bond
New peptide
bond forming
Side
chains
Back-
bone
Amino end Peptide

Carboxyl end 91
(N-terminus) bond(C-terminus)
Protein Structure and Function
• A functional protein consists of one or more
polypeptides precisely twisted, folded, and
coiled into a unique shape
92
Four Levels of Protein Structure
• The primary structure of a protein is its unique
sequence of amino acids
• Secondary structure, found in most proteins,
consists of coils and folds in the polypeptide
chain
• Tertiary structure is determined by interactions
among various side chains (R groups)
• Quaternary structure results when a protein
consists of multiple polypeptide chains
93
Figure 5.20a
Primary structure
Amino
acids
Amino end
Primary structure of transthyretin
Carboxyl end 94
• Primary structure, the sequence of amino
acids in a protein, is like the order of letters
in a long word
• Primary structure is determined by inherited
genetic information
95
Figure 5.20b
Secondary Tertiary Quaternary

structure structure structure
 helix
Hydrogen bond
 pleated sheet
 strand
Transthyretin
Hydrogen Transthyretin protein
bond polypeptide
96
• The coils and folds of secondary structure
result from hydrogen bonds between repeating
constituents of the polypeptide backbone
• Typical secondary structures are a coil called
an  helix and a folded structure called a 
pleated sheet
97
Figure 5.20c
Secondary structure
 helix
Hydrogen bond
 pleated sheet
 strand, shown as a flat

arrow pointing toward
the carboxyl end
Hydrogen bond
98
• Tertiary structure is determined by
interactions between R groups, rather than
interactions between backbone constituents
• These interactions between R groups include
hydrogen bonds, ionic bonds, hydrophobic
interactions, and van der Waals interactions
• Strong covalent bonds called disulfide
bridges may reinforce the protein’s structure
99
Figure 5.20f
Hydrogen
bond
Hydrophobic
interactions and
van der Waals
interactions
Disulfide
bridge
Ionic bond
Polypeptide
backbone
100
Figure 5.20i
Heme
Iron
 subunit
 subunit
 subunit
 subunit
Hemoglobin 101
• Quaternary structure results when two or
more polypeptide chains form one
macromolecule
• Collagen is a fibrous protein consisting of three
polypeptides coiled like a rope
• Hemoglobin is a globular protein consisting of
four polypeptides: two alpha and two beta
chains
102
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
103
Figure 5.22
tu
Normal protein Denatured protein
104
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
105
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
106
Figure 5.25-3
DNA
1 Synthesis of
mRNA
mRNA
NUCLEUS
CYTOPLASM
mRNA
2 Movement of
mRNA into Ribosome
cytoplasm
3 Synthesis
of protein
Amino
Polypeptide acids 107
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
108
Figure 5.26
Sugar-phosphate backbone
5 end Nitrogenous bases
Pyrimidines
5C
3C
Nucleoside
Nitrogenous
base Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA)
5C Purines
1C
Phosphate 3C
group Sugar
5C
(pentose)
Adenine (A) Guanine (G)
3C (b) Nucleotide
Sugars
3 end
(a) Polynucleotide, or nucleic acid
Deoxyribose (in DNA) Ribose (in RNA)
(c) Nucleoside components

109
Figure 5.26ab
Sugar-phosphate backbone
5 end
5C
3C
Nucleoside
Nitrogenous
base
5C
1C
Phosphate 3C
5C group Sugar
(pentose)
3C (b) Nucleotide
3 end
110
(a) Polynucleotide, or nucleic acid
Figure 5.26c
Nitrogenous bases
Pyrimidines
Cytosine Thymine Uracil

(C) (T, in DNA) (U, in RNA)
Sugars
Purines
Deoxyribose Ribose
Adenine (A) Guanine (G) (in DNA) (in RNA)
(c) Nucleoside components

111
• 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
112
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
113
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
114
• 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
115
• Which two functional groups are always found
in amino acids?
A) carboxyl and amino B) hydroxyl and carboxyl
C) ketone and methyl D) carbonyl and amino
• Which bonds are created during the formation

of the primary structure of a protein?
A) peptide bonds B) peptide bonds, hydrogen bonds
C) disulfide bonds D) hydrogen bonds 116
Chapter 6
A Tour of the Cell
Lectures by
Erin Barley
117

Overview: The Fundamental Units of Life
• All organisms are made of cells
• The cell is the simplest collection of matter
that can be alive
• Cell structure is correlated to cellular function
• All cells are related by their descent from earlier
cells
118
Concept 6.1: Biologists use microscopes and
the tools of biochemistry to study cells
• Though usually too small to be seen by the
unaided eye, cells can be complex
119
Microscopy
• Scientists use microscopes to visualize cells too
small to see with the naked eye
• In a light microscope (LM), visible light is
passed through a specimen and then through
glass lenses
• Lenses refract (bend) the light, so that the image
is magnified
120
• Two basic types of electron microscopes
(EMs) are used to study subcellular structures
• Scanning electron microscopes (SEMs) focus
a beam of electrons onto the surface of a
specimen, providing images that look 3-D
• Transmission electron microscopes (TEMs)
focus a beam of electrons through a specimen
• TEMs are used mainly to study the internal
structure of cells
121
Concept 6.2: Eukaryotic cells have internal
membranes that compartmentalize their
functions
• The basic structural and functional unit of every
organism is one of two types of cells: prokaryotic
or eukaryotic
• Only organisms of the domains Bacteria and
Archaea consist of prokaryotic cells
• Protists, fungi, animals, and plants all consist of
eukaryotic cells
122
Comparing Prokaryotic and Eukaryotic
Cells
• Basic features of all cells
– Plasma membrane
– Semifluid substance called cytosol
– Chromosomes (carry genes)
– Ribosomes (make proteins)
123
• Prokaryotic cells are characterized by having
– No nucleus
– DNA in an unbound region called the nucleoid
– No membrane-bound organelles
– Cytoplasm bound by the plasma membrane
124
Figure 6.5
Fimbriae
Nucleoid
Ribosomes
Plasma
membrane
Bacterial
chromosome Cell wall
Capsule
0.5 m
(a) A typical Flagella (b) A thin section
rod-shaped through the
bacterium bacterium Bacillus
coagulans (TEM)
125
• Eukaryotic cells are characterized by having
– DNA in a nucleus that is bounded by a
membranous nuclear envelope
– Membrane-bound organelles
– Cytoplasm in the region between the plasma
membrane and nucleus
• Eukaryotic cells are generally much larger than
prokaryotic cells
126
• The plasma membrane is a selective barrier
that allows sufficient passage of oxygen,
nutrients, and waste to service the volume of
every cell
• The general structure of a biological membrane
is a double layer of phospholipids
127
Figure 6.6
(a) TEM of a plasma
Outside of cell membrane
Inside of cell
0.1 m
Carbohydrate side chains
Hydrophilic
region
Hydrophobic
region
Hydrophilic Phospholipid Proteins
region
(b) Structure of the plasma membrane 128
A Panoramic View of the Eukaryotic Cell
• A eukaryotic cell has internal membranes that
partition the cell into organelles
• Plant and animal cells have most of the same
organelles
129
Figure 6.8a
ENDOPLASMIC RETICULUM (ER)

Nuclear
Rough Smooth envelope
Flagellum ER ER NUCLEUS
Nucleolus
Chromatin
Centrosome
Plasma
membrane
CYTOSKELETON:
Microfilaments
Intermediate filaments
Microtubules
Ribosomes
Microvilli
Golgi apparatus
Peroxisome
Mitochondrion Lysosome
130
Figure 6.8c
Nuclear Rough
envelope endoplasmic
NUCLEUS reticulum Smooth
Nucleolus endoplasmic
reticulum
Chromatin
Ribosomes
Central vacuole
Golgi
apparatus Microfilaments
Intermediate CYTOSKELETON
filaments
Microtubules
Mitochondrion
Peroxisome
Plasma membrane Chloroplast
Cell wall Plasmodesmata

Wall of adjacent cell
131
Concept 6.3: The eukaryotic cell’s genetic
instructions are housed in the nucleus and
carried out by the ribosomes
• The nucleus contains most of the DNA in a
eukaryotic cell
• Ribosomes use the information from the DNA to
make proteins
132
The Nucleus: Information Central
• The nucleus contains most of the cell’s genes
and is usually the most conspicuous organelle
• The nuclear envelope encloses the nucleus,
separating it from the cytoplasm
• The nuclear membrane is a double membrane;
each membrane consists of a lipid bilayer
133
Figure 6.9a
Nucleus
Nucleolus
Chromatin
Nuclear envelope:
Inner membrane
Outer membrane
Nuclear pore
Rough ER
Pore
complex
Ribosome
Close-up
of nuclear Chromatin
envelope 134
Figure 6.9b
1 m
Nuclear envelope:
Inner membrane
Outer membrane
Nuclear pore
Surface of nuclear
envelope
135
• In the nucleus, DNA is organized into discrete
units called chromosomes
• Each chromosome is composed of a single DNA
molecule associated with proteins
• The DNA and proteins of chromosomes are
together called chromatin
• Chromatin condenses to form discrete
chromosomes as a cell prepares to divide
• The nucleolus is located within the nucleus and
is the site of ribosomal RNA (rRNA) synthesis
136
Ribosomes: Protein Factories
• Ribosomes are particles made of ribosomal
RNA and protein
• Ribosomes carry out protein synthesis in two
locations
– In the cytosol (free ribosomes)
– On the outside of the endoplasmic reticulum or
the nuclear envelope (bound ribosomes)
137
Figure 6.10
0.25 m
Free ribosomes in cytosol

Endoplasmic reticulum (ER)
Ribosomes bound to ER
Large
subunit
Small
subunit
TEM showing ER and
ribosomes Diagram of a ribosome
138
Concept 6.4: The endomembrane system
regulates protein traffic and performs
metabolic functions in the cell
• Components of the endomembrane system
– Nuclear envelope
– Endoplasmic reticulum
– Golgi apparatus
– Lysosomes
– Vacuoles
– Plasma membrane
• These components are either continuous or
connected via transfer by vesicles 139
The Endoplasmic Reticulum: Biosynthetic
Factory
• The endoplasmic reticulum (ER) accounts for
more than half of the total membrane in many
eukaryotic cells
• The ER membrane is continuous with the
nuclear envelope
• There are two distinct regions of ER
– Smooth ER, which lacks ribosomes
– Rough ER, surface is studded with ribosomes
140
Figure 6.11 Smooth ER
Nuclear
envelope
Rough ER
ER lumen
Cisternae Transitional ER
Ribosomes
Transport vesicle
200 nm
Smooth ER Rough ER
141
Functions of Smooth ER
• The smooth ER
– Synthesizes lipids
– Metabolizes carbohydrates
– Detoxifies drugs and poisons
– Stores calcium ions
142
Functions of Rough ER
• The rough ER
– Has bound ribosomes, which secrete
glycoproteins (proteins covalently bonded to
carbohydrates)
– Distributes transport vesicles, proteins
surrounded by membranes
– Is a membrane factory for the cell
143
The Golgi Apparatus: Shipping and
Receiving Center
• The Golgi apparatus consists of flattened
membranous sacs called cisternae
• Functions of the Golgi apparatus
– Modifies products of the ER
– Manufactures certain macromolecules
– Sorts and packages materials into transport
vesicles
144
Figure 6.12
cis face
(“receiving” side of 0.1 m
Golgi apparatus)
Cisternae
trans face
(“shipping” side of TEM of Golgi apparatus
Golgi apparatus)
145
Lysosomes: Digestive Compartments
• A lysosome is a membranous sac of
hydrolytic enzymes that can digest
macromolecules
• Lysosomal enzymes can hydrolyze proteins,
fats, polysaccharides, and nucleic acids
• Lysosomal enzymes work best in the acidic
environment inside the lysosome
146
• Some types of cell can engulf another cell by
phagocytosis; this forms a food vacuole
• A lysosome fuses with the food vacuole and
digests the molecules
• Lysosomes also use enzymes to recycle the
cell’s own organelles and macromolecules, a
process called autophagy
147
Figure 6.13a
1 m
Nucleus
Lysosome
Digestive
enzymes
Lysosome
Plasma membrane
Digestion
Food vacuole
(a) Phagocytosis 148

Vacuoles: Diverse Maintenance
Compartments
• A plant cell or fungal cell may have one or
several vacuoles, derived from endoplasmic
reticulum and Golgi apparatus
149
• Food vacuoles are formed by phagocytosis
• Contractile vacuoles, found in many freshwater
protists, pump excess water out of cells
• Central vacuoles, found in many mature plant
cells, hold organic compounds and water
150
Figure 6.14
Central vacuole
Cytosol
Central
Nucleus vacuole
Cell wall
Chloroplast
5 m
151
Concept 6.5: Mitochondria and chloroplasts
change energy from one form to another
• Mitochondria are the sites of cellular respiration,
a metabolic process that uses oxygen to
generate ATP
• Chloroplasts, found in plants and algae, are the
sites of photosynthesis
• Peroxisomes are oxidative organelles
152
Mitochondria: Chemical Energy Conversion
• Mitochondria are in nearly all eukaryotic cells
• They have a smooth outer membrane and an
inner membrane folded into cristae
• The inner membrane creates two compartments:
intermembrane space and mitochondrial matrix
• Some metabolic steps of cellular respiration are
catalyzed in the mitochondrial matrix
• Cristae present a large surface area for enzymes
that synthesize ATP
153
Figure 6.17a
Intermembrane space
Outer
membrane
DNA
Inner
Free membrane
ribosomes
in the Cristae
mitochondrial
Matrix
matrix 0.1 m
(a) Diagram and TEM of mitochondrion
154
Chloroplasts: Capture of Light Energy
• Chloroplasts contain the green pigment
chlorophyll, as well as enzymes and other
molecules that function in photosynthesis
• Chloroplasts are found in leaves and other
green organs of plants and in algae
155
• Chloroplast structure includes
– Thylakoids, membranous sacs, stacked to
form a granum
– Stroma, the internal fluid
• The chloroplast is one of a group of plant
organelles, called plastids
156
Figure 6.18a
Ribosomes
Stroma
Inner and outer

membranes
Granum
DNA
Thylakoid Intermembrane space 1 m
(a) Diagram and TEM of chloroplast
157
Peroxisomes: Oxidation
• Peroxisomes are specialized metabolic
compartments bounded by a single membrane
• Peroxisomes produce hydrogen peroxide and
convert it to water
• Peroxisomes perform reactions with many
different functions
• How peroxisomes are related to other organelles
is still unknown
158
Figure 6.19
1 m
Chloroplast
Peroxisome
Mitochondrion
159
Concept 6.6: The cytoskeleton is a network
of fibers that organizes structures and
activities in the cell
• The cytoskeleton is a network of fibers
extending throughout the cytoplasm
• It organizes the cell’s structures and activities,
anchoring many organelles
• It is composed of three types of molecular
structures
– Microtubules
– Microfilaments
– Intermediate filaments 160
Roles of the Cytoskeleton:
Support and Motility
• The cytoskeleton helps to support the cell and
maintain its shape
• It interacts with motor proteins to produce
motility
• Inside the cell, vesicles can travel along
“monorails” provided by the cytoskeleton
• Recent evidence suggests that the cytoskeleton
may help regulate biochemical activities
161
Figure 6.21
Vesicle
ATP
Receptor for
motor protein
Motor protein Microtubule

(ATP powered) of cytoskeleton
(a)
Microtubule Vesicles 0.25 m
(b) 162
Components of the Cytoskeleton
• Three main types of fibers make up the
cytoskeleton
– Microtubules are the thickest of the three
components of the cytoskeleton
– Microfilaments, also called actin filaments, are
the thinnest components
– Intermediate filaments are fibers with
diameters in a middle range
163
Cilia and Flagella
• Microtubules control the beating of cilia and
flagella, locomotor appendages of some cells
• Cilia and flagella differ in their beating patterns
164
Figure 6.23
Direction of swimming
(a) Motion of flagella

5 m
Direction of organism’s movement
Power stroke Recovery stroke
(b) Motion of cilia

15 m165
Concept 6.7: Extracellular components and
connections between cells help coordinate
cellular activities
• Most cells synthesize and secrete materials that
are external to the plasma membrane
• These extracellular structures include
– Cell walls of plants
– The extracellular matrix (ECM) of animal cells
– Intercellular junctions
166
Cell Walls of Plants
• The cell wall is an extracellular structure that
distinguishes plant cells from animal cells
• Prokaryotes, fungi, and some protists also have
cell walls
• The cell wall protects the plant cell, maintains its
shape, and prevents excessive uptake of water
• Plant cell walls are made of cellulose fibers
embedded in other polysaccharides and protein
167
Figure 6.28
Secondary
cell wall
Primary
cell wall
Middle
lamella
1 m
Central vacuole
Cytosol
Plasma membrane
Plant cell walls
Plasmodesmata 168
The Extracellular Matrix (ECM) of Animal
Cells
• Animal cells lack cell walls but are covered by an
elaborate extracellular matrix (ECM)
• The ECM is made up of glycoproteins such as
collagen, proteoglycans, and fibronectin
• ECM proteins bind to receptor proteins in the
plasma membrane called integrins
169
Figure 6.30a
Collagen EXTRACELLULAR FLUID
Proteoglycan
complex
Fibronectin
Integrins
Plasma
membrane
CYTOPLASM
Micro-
filaments
170
• Functions of the ECM
– Support
– Adhesion
– Movement
– Regulation
171
• All of the following are part of a prokaryotic cell except
A) a cell wall. B) a plasma membrane. C) DNA.
D) an endoplasmic reticulum. E) ribosomes.
• Which of the following contains hydrolytic enzymes? A)

peroxisome B) vacuole C) mitochondrion D)
lysosome
172
Chapter 7
Membrane Structure and

Function
Lectures by
Erin Barley
173

Overview: Life at the Edge
• The plasma membrane is the boundary that
separates the living cell from its surroundings
• The plasma membrane exhibits selective
permeability, allowing some substances to
cross it more easily than others
174
Concept 7.1: Cellular membranes are fluid
mosaics of lipids and proteins
• Phospholipids are the most abundant lipid in the
plasma membrane
• Phospholipids are amphipathic molecules,
containing hydrophobic and hydrophilic regions
• The fluid mosaic model states that a
membrane is a fluid structure with a “mosaic” of
various proteins embedded in it
175
The Fluidity of Membranes
• Phospholipids in the plasma membrane can
move within the bilayer
• Most of the lipids, and some proteins, drift
laterally
• Rarely does a molecule flip-flop transversely
across the membrane
176
Figure 7.5
Fibers of extra-
cellular matrix (ECM)
Glyco- Carbohydrate
protein
Glycolipid
EXTRACELLULAR
SIDE OF
MEMBRANE
Cholesterol
Microfilaments Peripheral
of cytoskeleton proteins
Integral
protein
CYTOPLASMIC SIDE
OF MEMBRANE
177
Figure 7.6
Lateral movement occurs Flip-flopping across the membrane

107 times per second. is rare ( once per month).
178
Figure 7.8
Fluid Viscous
Unsaturated hydrocarbon Saturated hydrocarbon tails

tails
(a) Unsaturated versus saturated hydrocarbon tails
(b) Cholesterol within the animal

cell membrane
Cholesterol 179
Membrane Proteins and Their Functions
• A membrane is a collage of different proteins,
often grouped together, embedded in the fluid
matrix of the lipid bilayer
• Proteins determine most of the membrane’s
specific functions
180
• Peripheral proteins are bound to the surface
of the membrane
• Integral proteins penetrate the hydrophobic
core
• Integral proteins that span the membrane are
called transmembrane proteins
• The hydrophobic regions of an integral protein
consist of one or more stretches of nonpolar
amino acids, often coiled into alpha helices
181
Figure 7.9
EXTRACELLULAR
SIDE
N-terminus
 helix
C-terminus
CYTOPLASMIC
SIDE
182
• Six major functions of membrane proteins
– Transport
– Enzymatic activity
– Signal transduction
– Cell-cell recognition
– Intercellular joining
– Attachment to the cytoskeleton and
extracellular matrix (ECM)
183
Figure 7.10a
Signaling molecule
Receptor
Enzymes
ATP
Signal transduction
(a) Transport (b) Enzymatic activity (c) Signal transduction
184
Figure 7.10b
Glyco-
protein
(d) Cell-cell recognition (e) Intercellular joining (f) Attachment to

the cytoskeleton
and extracellular
matrix (ECM)
185
The Role of Membrane Carbohydrates in
Cell-Cell Recognition
• Cells recognize each other by binding to surface
molecules, often containing carbohydrates, on
the extracellular surface of the plasma
membrane
• Membrane carbohydrates may be covalently
bonded to lipids (forming glycolipids) or more
commonly to proteins (forming glycoproteins)
• Carbohydrates on the external side of the
plasma membrane vary among species,
individuals, and even cell types in an individual
186
Concept 7.2: Membrane structure results
in selective permeability
• A cell must exchange materials with its
surroundings, a process controlled by the
plasma membrane
• Plasma membranes are selectively permeable,
regulating the cell’s molecular traffic
187
The Permeability of the Lipid Bilayer
• Hydrophobic (nonpolar) molecules, such as
hydrocarbons, can dissolve in the lipid bilayer
and pass through the membrane rapidly
• Polar molecules, such as sugars, do not cross
the membrane easily
188
Transport Proteins
• Transport proteins allow passage of
hydrophilic substances across the membrane
• Some transport proteins, called channel
proteins, have a hydrophilic channel that
certain molecules or ions can use as a tunnel
• Channel proteins called aquaporins facilitate
the passage of water
189
• Other transport proteins, called carrier proteins,
bind to molecules and change shape to shuttle
them across the membrane
• A transport protein is specific for the substance
it moves
190
Concept 7.3: Passive transport is diffusion of
a substance across a membrane with no
energy investment
• Diffusion is the tendency for molecules to spread
out evenly into the available space
• Although each molecule moves randomly, diffusion
of a population of molecules may be directional
• At dynamic equilibrium, as many molecules cross
the membrane in one direction as in the other
191
Figure 7.13a
Molecules of dye
Membrane (cross section)
WATER
Net diffusion Net diffusion Equilibrium
(a) Diffusion of one solute
192
Figure 7.13b

(b) Diffusion of two solutes
193
• Substances diffuse down their concentration
gradient, the region along which the density of
a chemical substance increases or decreases
• No work must be done to move substances
down the concentration gradient
• The diffusion of a substance across a biological
membrane is passive transport because no
energy is expended by the cell to make it
happen
194
Effects of Osmosis on Water Balance
• Osmosis is the diffusion of water across a
selectively permeable membrane
• Water diffuses across a membrane from the
region of lower solute concentration to the
region of higher solute concentration until the
solute concentration is equal on both sides
195
Figure 7.14
Lower Higher Same concentration
concentration concentration of solute
of solute (sugar) of solute
Sugar
molecule
H2O
Selectively
permeable
membrane
Osmosis 196
Water Balance of Cells Without Walls
• Tonicity is the ability of a surrounding solution
to cause a cell to gain or lose water
• Isotonic solution: Solute concentration is the
same as that inside the cell; no net water
movement across the plasma membrane
• Hypertonic solution: Solute concentration is
greater than that inside the cell; cell loses
water
• Hypotonic solution: Solute concentration is
less than that inside the cell; cell gains water
197
Figure 7.15
Hypotonic Isotonic Hypertonic

solution solution solution
(a) Animal cell
H2O H2O H2O H2O
Lysed Normal Shriveled

H2O Cell wall H2O H2O H2O
(b) Plant cell
Turgid (normal) Flaccid Plasmolyzed
Osmosis 198
Facilitated Diffusion: Passive Transport
Aided by Proteins
• In facilitated diffusion, transport proteins speed
the passive movement of molecules across the
plasma membrane
• Channel proteins provide corridors that allow a
specific molecule or ion to cross the membrane
• Channel proteins include
– Aquaporins, for facilitated diffusion of water
– Ion channels that open or close in response
to a stimulus (gated channels)
199
Figure 7.17
EXTRACELLULAR
FLUID
(a) A channel
protein
Channel protein
Solute
CYTOPLASM
Carrier protein Solute
(b) A carrier protein 200

• Carrier proteins undergo a subtle change in
shape that translocates the solute-binding site
across the membrane
201
Concept 7.4: Active transport uses energy to
move solutes against their gradients
• Facilitated diffusion is still passive because the
solute moves down its concentration gradient,
and the transport requires no energy
• Some transport proteins, however, can move
solutes against their concentration gradients
202
The Need for Energy in Active Transport
• Active transport moves substances against
their concentration gradients
• Active transport requires energy, usually in the
form of ATP
• Active transport is performed by specific
proteins embedded in the membranes
203
• Active transport allows cells to maintain
concentration gradients that differ from their
surroundings
• The sodium-potassium pump is one type of
active transport system
204
Figure 7.18-6
EXTRACELLULAR [Na] high Na

FLUID [K] low Na
Na Na Na
Na Na
Na
[Na] low ATP

CYTOPLASM Na P
[K] high P
1 2 ADP 3
K
K
K
K
K
P
6 K 5 4 Pi
205
Figure 7.19
Passive transport Active transport
Diffusion Facilitated diffusion ATP
206
Concept 7.5: Bulk transport across the
plasma membrane occurs by exocytosis
and endocytosis
• Small molecules and water enter or leave the
cell through the lipid bilayer or via transport
proteins
• Large molecules, such as polysaccharides and
proteins, cross the membrane in bulk via
vesicles
• Bulk transport requires energy
207
Exocytosis
• In exocytosis, transport vesicles migrate to the
membrane, fuse with it, and release their
contents
• Many secretory cells use exocytosis to export
their products
208
Endocytosis
• In endocytosis, the cell takes in macromolecules
by forming vesicles from the plasma membrane
• Endocytosis is a reversal of exocytosis, involving
different proteins
• There are three types of endocytosis
– Phagocytosis (“cellular eating”)
– Pinocytosis (“cellular drinking”)
– Receptor-mediated endocytosis
209
• In phagocytosis a cell engulfs a particle in a
vacuole
• The vacuole fuses with a lysosome to digest
the particle
210
• In pinocytosis, molecules are taken up when
extracellular fluid is “gulped” into tiny vesicles
211
Figure 7.22a
Phagocytosis EXTRACELLULAR
FLUID Solutes
Pseudopodium Pseudopodium
of amoeba
Bacterium
1 m
Food vacuole
An amoeba engulfing a bacterium “Food”

via phagocytosis (TEM). or other
particle
Food
vacuole
CYTOPLASM 212
Figure 7.22b
Pinocytosis
0.5 m
Plasma
membrane
Pinocytosis vesicles forming

in a cell lining a small blood
vessel (TEM).
Vesicle
213
• All of the following are part of a prokaryotic cell except
A) a cell wall. B) a plasma membrane. C) DNA.
D) an endoplasmic reticulum. E) ribosomes.
• Which of the following contains hydrolytic enzymes?

A) peroxisome B) vacuole C) mitochondrion D) lysosome
214
Chapter 8
An Introduction to Metabolism
Lectures by
Erin Barley
215

Overview: The Energy of Life
• The living cell is a miniature chemical factory
where thousands of reactions occur
• The cell extracts energy and applies energy to
perform work
• Some organisms even convert energy to light,
as in bioluminescence
216
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
217
Organization of the Chemistry of Life into
Metabolic Pathways
• A metabolic pathway begins with a specific
molecule and ends with a product
• Each step is catalyzed by a specific enzyme
218
Figure 8.UN01
Enzyme 1 Enzyme 2 Enzyme 3

A B C D
Reaction 1 Reaction 2 Reaction 3
Starting Product
molecule
219
• 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
220
• 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
221
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
222
The First Law of Thermodynamics
• According to the first law of thermodynamics,
the energy of the universe is constant
– Energy can be transferred and transformed,
but it cannot be created or destroyed
• The first law is also called the principle of
conservation of energy
223
The Second Law of Thermodynamics
• During every energy transfer or transformation,
some energy is unusable, and is often lost as
heat
• According to the second law of
thermodynamics
– Every energy transfer or transformation
increases the entropy (disorder) of the
universe
224
• 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
225
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
226
Free-Energy Change, G
• A living system’s free energy is energy that
can do work when temperature and pressure
are uniform, as in a living cell
227
• The change in free energy (∆G) during a
process is related to the change in enthalpy, or
change in total energy (∆H), change in entropy
(∆S), and temperature in Kelvin (T)
∆G = ∆H – T∆S
• Only processes with a negative ∆G are
spontaneous
• Spontaneous processes can be harnessed to
perform work
228
Free Energy, Stability, and Equilibrium
• Free energy is a measure of a system’s
instability, its tendency to change to a more
stable state
• During a spontaneous change, free energy
decreases and the stability of a system
increases
• Equilibrium is a state of maximum stability
• A process is spontaneous and can perform
work only when it is moving toward equilibrium
229
Figure 8.5a
• More free energy (higher G)

• Less stable
• Greater work capacity
In a spontaneous change
• The free energy of the system
decreases (G  0)
• The system becomes more
stable
• The released free energy can
be harnessed to do work
• Less free energy (lower G)

• More stable
• Less work capacity
230
Free Energy and Metabolism
• The concept of free energy can be applied to
the chemistry of life’s processes
231
Exergonic and Endergonic Reactions in
Metabolism
• An exergonic reaction proceeds with a net
release of free energy and is spontaneous
• An endergonic reaction absorbs free energy
from its surroundings and is nonspontaneous
232
Figure 8.6a
(a) Exergonic reaction: energy released, spontaneous
Reactants
Amount of
energy
released
Free energy
(G  0)
Energy
Products
Progress of the reaction
233
Figure 8.6b
(b) Endergonic reaction: energy required, nonspontaneous
Products
Amount of
energy
required
Free energy
(G  0)
Energy
Reactants
234
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
235
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
236
Figure 8.8a
Adenine
Phosphate groups
Ribose
(a) The structure of ATP
237
Figure 8.8b
Adenosine triphosphate (ATP)
Energy
Inorganic Adenosine diphosphate (ADP)

phosphate
(b) The hydrolysis of ATP 238

• The bonds between the phosphate groups
of ATP’s tail can be broken by hydrolysis
• Energy is released from ATP when the
terminal phosphate bond is broken
• This release of energy comes from the
chemical change to a state of lower free
energy, not from the phosphate bonds
themselves
239
How the Hydrolysis of ATP Performs Work
• The three types of cellular work (mechanical,
transport, and chemical) are powered by the
hydrolysis of ATP
• In the cell, the energy from the exergonic
reaction of ATP hydrolysis can be used to
drive an endergonic reaction
• Overall, the coupled reactions are exergonic
240
Figure 8.9
(a) Glutamic acid

conversion NH3 NH2
Glu Glu
GGlu = +3.4 kcal/mol
to glutamine
Glutamic Ammonia Glutamine
acid
(b) Conversion NH3

reaction
coupled P
1 2 NH2
with ATP ADP ADP Pi
hydrolysis Glu ATP Glu Glu
Glutamic Phosphorylated Glutamine
acid intermediate
(c) Free-energy
change for NH3 NH2
Glu ATP Glu
ADP Pi
coupled
reaction
GATP = 7.3 kcal/mol
+ GATP = 7.3 kcal/mol
Net G = 3.9 kcal/mol
241
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
242
Figure 8.11
ATP H2O
Energy from Energy for cellular

catabolism (exergonic, work (endergonic,
energy-releasing ADP Pi energy-consuming
processes) processes)
243
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
• Hydrolysis of sucrose by the enzyme sucrase
is an example of an enzyme-catalyzed
reaction
244
Figure 8.UN02
Sucrase
Sucrose Glucose Fructose

(C12H22O11) (C6H12O6) (C6H12O6)
245
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
246
Figure 8.12
A B
C D
Transition state
A B
Free energy
EA
C D
Reactants
A B
G  O
C D
Products
Progress of the reaction 247

How Enzymes Lower the EA Barrier
• Enzymes catalyze reactions by lowering the EA
barrier
• Enzymes do not affect the change in free
energy (∆G); instead, they hasten reactions
that would occur eventually
248
Figure 8.13
Course of
reaction EA
without without
enzyme enzyme EA with
enzyme
is lower
Free energy
Reactants
Course of G is unaffected
reaction by enzyme
with enzyme
Products

249
Substrate Specificity of Enzymes
• The reactant that an enzyme acts on is called the
enzyme’s substrate
• The enzyme binds to its substrate, forming an
enzyme-substrate complex
• The active site is the region on the enzyme
where the substrate binds
• Induced fit of a substrate brings chemical
groups of the active site into positions that
enhance their ability to catalyze the reaction
250
Figure 8.14
Substrate
Active site
Enzyme Enzyme-substrate
complex
(a) (b)
251
• Which term most precisely describes the cellular
process of breaking down large molecules into smaller
ones?
A) catalysis B) anabolism C) metabolism D) catabolism
• Choose the pair of terms that correctly completes this

sentence: Catabolism is to anabolism as ________ is
to ________.
A) exergonic; spontaneous B) free energy; entropy
C) exergonic; endergonic D) work; energy
252
Chapter 9
Cellular Respiration and

Fermentation
Lectures by
Erin Barley
253

Overview: Life Is Work
• Living cells require energy from outside
sources
• Some animals, such as the chimpanzee, obtain
energy by eating plants, and some animals
feed on other organisms that eat plants
254
• Energy flows into an ecosystem as sunlight
and leaves as heat
• Photosynthesis generates O2 and organic
molecules, which are used in cellular
respiration
• Cells use chemical energy stored in organic
molecules to regenerate ATP, which powers
work
255
Figure 9.2
Light
energy
ECOSYSTEM
Photosynthesis
in chloroplasts
CO2  H2O Organic
 O2
molecules
Cellular respiration
in mitochondria
ATP powers
ATP
most cellular work
Heat
energy
256
Concept 9.1: Catabolic pathways yield
energy by oxidizing organic fuels
• Several processes are central to cellular
respiration and related pathways
257
Catabolic Pathways and Production of ATP
• The breakdown of organic molecules is
exergonic
• Fermentation is a partial degradation of
sugars that occurs without O2
• Aerobic respiration consumes organic
molecules and O2 and yields ATP
• Anaerobic respiration is similar to aerobic
respiration but consumes compounds other
than O2
258
• Cellular respiration includes both aerobic and
anaerobic respiration but is often used to refer to
aerobic respiration
• Although carbohydrates, fats, and proteins are all
consumed as fuel, it is helpful to trace cellular
respiration with the sugar glucose
C6H12O6 + 6 O2  6 CO2 + 6 H2O + Energy (ATP + heat)
259
Oxidation of Organic Fuel Molecules During
Cellular Respiration
• During cellular respiration, the fuel (such as
glucose) is oxidized, and O2 is reduced
260
Figure 9.UN03
becomes oxidized
becomes reduced
261
• NADH passes the electrons to the electron
transport chain
• Unlike an uncontrolled reaction, the electron
transport chain passes electrons in a series of
steps instead of one explosive reaction
• O2 pulls electrons down the chain in an energy-
yielding tumble
• The energy yielded is used to regenerate ATP
262
Figure 9.5
H2  1/2 O2 2H  1/
2 O2
(from food via NADH)
Controlled
release of
2H  2e
+ 
energy for
synthesis of
ATP
ATP
Free energy, G
Free energy, G
Explosive ATP
release of
heat and light ATP
energy
2 e
1/ O2
2
2 H+
H2O H2O
(a) Uncontrolled reaction (b) Cellular respiration
263
The Stages of Cellular Respiration:
A Preview
• Harvesting of energy from glucose has three
stages
– Glycolysis (breaks down glucose into two
molecules of pyruvate)
– The citric acid cycle (completes the
breakdown of glucose)
– Oxidative phosphorylation (accounts for
most of the ATP synthesis)
264
Figure 9.UN05
1. Glycolysis (color-coded teal throughout the chapter)

2. Pyruvate oxidation and the citric acid cycle
(color-coded salmon)
3. Oxidative phosphorylation: electron transport and
chemiosmosis (color-coded violet)
265
Figure 9.6-3
Electrons Electrons carried

carried via NADH and
via NADH FADH2
Pyruvate Oxidative
Glycolysis Citric phosphorylation:
oxidation
acid electron transport
Glucose Pyruvate Acetyl CoA cycle and
chemiosmosis
CYTOSOL MITOCHONDRION
ATP ATP ATP
Substrate-level Substrate-level Oxidative

phosphorylation phosphorylation phosphorylation
266
• The process that generates most of the ATP is
called oxidative phosphorylation because it is
powered by redox reactions
267
• Oxidative phosphorylation accounts for almost
90% of the ATP generated by cellular
respiration
• A smaller amount of ATP is formed in glycolysis
and the citric acid cycle by substrate-level
phosphorylation
• For each molecule of glucose degraded to CO2
and water by respiration, the cell makes up to
32 molecules of ATP
268
Concept 9.2: Glycolysis harvests chemical
energy by oxidizing glucose to pyruvate
• Glycolysis (“splitting of sugar”) breaks down
glucose into two molecules of pyruvate
• Glycolysis occurs in the cytoplasm and has two
major phases
– Energy investment phase
– Energy payoff phase
• Glycolysis occurs whether or not O2 is present
269
Concept 9.3: After pyruvate is oxidized, the
citric acid cycle completes the energy-
yielding oxidation of organic molecules
• In the presence of O2, pyruvate enters the
mitochondrion (in eukaryotic cells) where the
oxidation of glucose is completed
270
Oxidation of Pyruvate to Acetyl CoA
• Before the citric acid cycle can begin, pyruvate
must be converted to acetyl Coenzyme A
(acetyl CoA), which links glycolysis to the citric
acid cycle
• This step is carried out by a multienzyme
complex that catalyses three reactions
271
Figure 9.10
MITOCHONDRION
CYTOSOL CO2 Coenzyme A
1 3
NAD NADH + H Acetyl CoA

Pyruvate
Transport protein
272
The Citric Acid Cycle
• The citric acid cycle, also called the Krebs
cycle, completes the break down of pyruvate
to CO2
• The cycle oxidizes organic fuel derived from
pyruvate, generating 1 ATP, 3 NADH, and 1
FADH2 per turn
273
Concept 9.4: During oxidative
phosphorylation, chemiosmosis couples
electron transport to ATP synthesis
• Following glycolysis and the citric acid cycle,
NADH and FADH2 account for most of the
energy extracted from food
• These two electron carriers donate electrons to
the electron transport chain, which powers ATP
synthesis via oxidative phosphorylation
274
The Pathway of Electron Transport
• The electron transport chain is in the inner
membrane (cristae) of the mitochondrion
• Most of the chain’s components are proteins,
which exist in multiprotein complexes
• The carriers alternate reduced and oxidized
states as they accept and donate electrons
• Electrons drop in free energy as they go down
the chain and are finally passed to O2, forming
H2O
275
Chemiosmosis: The Energy-Coupling
Mechanism
• Electron transfer in the electron transport chain
causes proteins to pump H+ from the
mitochondrial matrix to the intermembrane space
• H+ then moves back across the membrane,
passing through the proton, ATP synthase
• ATP synthase uses the exergonic flow of H+ to
drive phosphorylation of ATP
• This is an example of chemiosmosis, the use of
energy in a H+ gradient to drive cellular work
276
Figure 9.14
INTERMEMBRANE SPACE
H
Stator
Rotor
Internal
rod
Catalytic
knob
ADP
+
Pi ATP
MITOCHONDRIAL MATRIX 277

Figure 9.15
H
H
H 
Protein
complex H
Cyt c
of electron
carriers
IV
Q
III
I
ATP
II synth-
2 H + 1/2O2 H2O ase
FADH2 FAD
NADH NAD
ADP  P i ATP
(carrying electrons
from food) H
1 Electron transport chain 2 Chemiosmosis

Oxidative phosphorylation
278
• The energy stored in a H+ gradient across a
membrane couples the redox reactions of the
electron transport chain to ATP synthesis
• The H+ gradient is referred to as a proton-
motive force, emphasizing its capacity to do
work
279
An Accounting of ATP Production by
Cellular Respiration
• During cellular respiration, most energy flows
in this sequence:
glucose  NADH  electron transport chain
 proton-motive force  ATP
• About 34% of the energy in a glucose molecule
is transferred to ATP during cellular respiration,
making about 32 ATP
• There are several reasons why the number of
ATP is not known exactly
280
Figure 9.16
Electron shuttles MITOCHONDRION

span membrane 2 NADH
or
2 FADH2
2 NADH 2 NADH 6 NADH 2 FADH2
Glycolysis Pyruvate oxidation Oxidative

Citric phosphorylation:
Glucose 2 Pyruvate 2 Acetyl CoA acid electron transport
cycle and
chemiosmosis
 2 ATP  2 ATP  about 26 or 28 ATP
About
Maximum per glucose: 30 or 32 ATP
CYTOSOL
281
Concept 9.5: Fermentation and anaerobic
respiration enable cells to produce ATP
without the use of oxygen
• Most cellular respiration requires O2 to produce
ATP
• Without O2, the electron transport chain will
cease to operate
• In that case, glycolysis couples with
fermentation or anaerobic respiration to
produce ATP
282
• Anaerobic respiration uses an electron
transport chain with a final electron acceptor
other than O2, for example sulfate
• Fermentation uses substrate-level
phosphorylation instead of an electron
transport chain to generate ATP
283
Types of Fermentation
• Fermentation consists of glycolysis plus
reactions that regenerate NAD+, which can be
reused by glycolysis
• Two common types are alcohol fermentation
and lactic acid fermentation
284
• In alcohol fermentation, pyruvate is converted
to ethanol in two steps, with the first releasing
CO2
• Alcohol fermentation by yeast is used in
brewing, winemaking, and baking
285
Figure 9.17
2 ADP  2 P 2 ATP 2 ADP  2 P 2 ATP

i i
Glucose Glycolysis Glucose Glycolysis
2 Pyruvate
2 NAD  2 NADH 2 CO2 2 NAD  2 NADH

 2 H  2 H
2 Pyruvate
2 Ethanol 2 Acetaldehyde 2 Lactate
(a) Alcohol fermentation (b) Lactic acid fermentation
286
Figure 9.17a
2 ADP  2 P i 2 ATP
Glucose Glycolysis
2 Pyruvate
2 NAD  2 NADH 2 CO2

 2 H
2 Ethanol 2 Acetaldehyde
(a) Alcohol fermentation 287

• In lactic acid fermentation, pyruvate is reduced
to NADH, forming lactate as an end product,
with no release of CO2
• Lactic acid fermentation by some fungi and
bacteria is used to make cheese and yogurt
• Human muscle cells use lactic acid
fermentation to generate ATP when O2 is
scarce
288
Figure 9.17b
2 ADP  2 P i 2 ATP
Glucose Glycolysis
2 NAD  2 NADH
 2 H
2 Pyruvate
2 Lactate
(b) Lactic acid fermentation 289

• In addition to ATP, what are the end products of
glycolysis?
A) NADH and pyruvate B) CO2 and NADH
C) CO2 and pyruvate D) CO2 and H2O
• In the absence of oxygen, yeast cells can obtain

energy by fermentation, resulting in the production of
A) ATP, CO2, and lactate. B) ATP, pyruvate, and oxygen.

C) ATP, CO2, and ethanol (ethyl alcohol). D) ATP, NADH, and pyruvate.
290
Chapter 10
Photosynthesis
Lectures by
Erin Barley
291

Overview: The Process That Feeds the
Biosphere
• Photosynthesis is the process that converts
solar energy into chemical energy
• Directly or indirectly, photosynthesis nourishes
almost the entire living world
292
• Autotrophs sustain themselves without eating
anything derived from other organisms
• Autotrophs are the producers of the biosphere,
producing organic molecules from CO2 and other
inorganic molecules
• Almost all plants are photoautotrophs, using the
energy of sunlight to make organic molecules
293
• Photosynthesis occurs in plants, algae, certain
other protists, and some prokaryotes
• These organisms feed not only themselves but
also most of the living world
294
Figure 10.2
(b) Multicellular
(a) Plants alga
(d) Cyanobacteria
40 m
(c) Unicellular
10 m
protists
(e) Purple sulfur 295

1 m
bacteria
Concept 10.1: Photosynthesis converts
light energy to the chemical energy of food
• Chloroplasts are structurally similar to and
likely evolved from photosynthetic bacteria
• The structural organization of these cells
allows for the chemical reactions of
photosynthesis
296
Chloroplasts: The Sites of Photosynthesis
in Plants
• Leaves are the major locations of
photosynthesis
• Their green color is from chlorophyll, the
green pigment within chloroplasts
• Chloroplasts are found mainly in cells of the
mesophyll, the interior tissue of the leaf
• Each mesophyll cell contains 30–40
chloroplasts
297
• CO2 enters and O2 exits the leaf through
microscopic pores called stomata
• The chlorophyll is in the membranes of
thylakoids (connected sacs in the chloroplast);
thylakoids may be stacked in columns called
grana
• Chloroplasts also contain stroma, a dense
interior fluid
298
Figure 10.4a
Leaf cross section
Chloroplasts Vein
Mesophyll
Stomata
CO2 O2
Chloroplast Mesophyll
cell
20 m 299
Figure 10.4b
Chloroplast
Outer
membrane
Thylakoid Intermembrane
Stroma Granum Thylakoid space
space Inner
membrane
1 m 300
Photosynthesis as a Redox Process
• Photosynthesis reverses the direction of electron
flow compared to respiration
• Photosynthesis is a redox process in which H2O
is oxidized and CO2 is reduced
• Photosynthesis is an endergonic process; the
energy boost is provided by light
301
Figure 10.UN01
becomes reduced
Energy  6 CO2  6 H2O C6 H12 O6  6 O2

becomes oxidized
302
The Two Stages of Photosynthesis:
A Preview
• Photosynthesis consists of the light
reactions (the photo part) and Calvin cycle
(the synthesis part)
• The light reactions (in the thylakoids)
– Split H2O
– Release O2
– Reduce NADP+ to NADPH
– Generate ATP from ADP by
photophosphorylation
303
• The Calvin cycle (in the stroma) forms sugar
from CO2, using ATP and NADPH
• The Calvin cycle begins with carbon fixation,
incorporating CO2 into organic molecules
304
Figure 10.6-4
H2O CO2
Light
NADP
ADP
+ Pi
Calvin
Light Cycle
Reactions
ATP
NADPH
Chloroplast
O2 [CH2O]
(sugar)
305
A Photosystem: A Reaction-Center Complex
Associated with Light-Harvesting
Complexes
• A photosystem consists of a reaction-center
complex (a type of protein complex) surrounded
by light-harvesting complexes
• The light-harvesting complexes (pigment
molecules bound to proteins) transfer the energy
of photons to the reaction center
306
Figure 10.13a
Photosystem STROMA
Photon
Light- Reaction- Primary
harvesting center electron
complexes complex acceptor
Thylakoid membrane
e
Transfer Special pair of Pigment

of energy chlorophyll a molecules
molecules
THYLAKOID SPACE
(INTERIOR OF THYLAKOID)
(a) How a photosystem harvests light 307
• A primary electron acceptor in the reaction
center accepts excited electrons and is reduced
as a result
• Solar-powered transfer of an electron from a
chlorophyll a molecule to the primary electron
acceptor is the first step of the light reactions
308
• There are two types of photosystems in the
thylakoid membrane
• Photosystem II (PS II) functions first (the
numbers reflect order of discovery) and is best at
absorbing a wavelength of 680 nm
• The reaction-center chlorophyll a of PS II is
called P680
309
• Photosystem I (PS I) is best at absorbing a
wavelength of 700 nm
• The reaction-center chlorophyll a of PS I is
called P700
310
Concept 10.3: The Calvin cycle uses the
chemical energy of ATP and NADPH to
reduce CO2 to sugar
• The Calvin cycle, like the citric acid cycle,
regenerates its starting material after molecules
enter and leave the cycle
• The cycle builds sugar from smaller molecules
by using ATP and the reducing power of
electrons carried by NADPH
311
• Carbon enters the cycle as CO2 and leaves as
a sugar named glyceraldehyde 3-phospate
(G3P)
• For net synthesis of 1 G3P, the cycle must take
place three times, fixing 3 molecules of CO2
• The Calvin cycle has three phases
– Carbon fixation (catalyzed by rubisco)
– Reduction
– Regeneration of the CO2 acceptor (RuBP)
312
Figure 10.22
H2O CO2
Light
NADP
ADP
+ Pi
Light RuBP
Reactions: 3-Phosphoglycerate
Photosystem II Calvin
Electron transport chain Cycle
Photosystem I
Electron transport chain
ATP
G3P
Starch
NADPH (storage)
Chloroplast
O2 Sucrose (export)
313
Figure 10.UN02
Primary
Primary acceptor
acceptor Fd
H2O NADP
Pq NADP + H
O2 reductase
Cytochrome NADPH
complex
Pc
Photosystem I
ATP
Photosystem II
314
• In addition to ATP, what are the end products of
glycolysis?
A) NADH and pyruvate B) CO2 and NADH
C) CO2 and pyruvate D) CO2 and H2O
• In the absence of oxygen, yeast cells can obtain

energy by fermentation, resulting in the production of
A) ATP, CO2, and lactate. B) ATP, pyruvate, and oxygen.

C) ATP, CO2, and ethanol (ethyl alcohol). D) ATP, NADH, and pyruvate.
315
Chapter 11
Cell Communication
Lectures by
Erin Barley
316

Overview: Cellular Messaging
• Cell-to-cell communication is essential for
both multicellular and unicellular organisms
• Biologists have discovered some universal
mechanisms of cellular regulation
• Cells most often communicate with each
other via chemical signals
• For example, the fight-or-flight response is
triggered by a signaling molecule called
epinephrine
317
Concept 11.1: External signals are
converted to responses within the cell
• Microbes provide a glimpse of the role of
cell signaling in the evolution of life
318
Local and Long-Distance Signaling
• Cells in a multicellular organism
communicate by chemical messengers
• Animal and plant cells have cell junctions
that directly connect the cytoplasm of
adjacent cells
• In local signaling, animal cells may
communicate by direct contact, or cell-cell
recognition
319
Figure 11.4
Plasma membranes
Gap junctions Plasmodesmata

between animal cells between plant cells
(a) Cell junctions
(b) Cell-cell recognition 320

• In many other cases, animal cells
communicate using local regulators,
messenger molecules that travel only short
distances
• In long-distance signaling, plants and
animals use chemicals called hormones
• The ability of a cell to respond to a signal
depends on whether or not it has a receptor
specific to that signal
321
Figure 11.5
Local signaling Long-distance signaling
Target cell Electrical signal Endocrine cell

along nerve cell Blood
triggers release of vessel
neurotransmitter.
Neurotransmitter
Secreting Secretory diffuses across
cell vesicle synapse.
Hormone travels
in bloodstream.
Target cell
Local regulator specifically
diffuses through Target cell binds
extracellular fluid. is stimulated. hormone.
(a) Paracrine signaling (b) Synaptic signaling
(c) Endocrine (hormonal) signaling
322
Figure 11.5a
Local signaling
Target cell Electrical signal

along nerve cell
triggers release of
neurotransmitter.
Neurotransmitter
Secreting Secretory diffuses across
cell vesicle synapse.
Local regulator
diffuses through Target cell
extracellular fluid. is stimulated.
(a) Paracrine signaling (b) Synaptic signaling
323
Figure 11.5b
Long-distance signaling
Endocrine cell
Blood
vessel
Hormone travels
in bloodstream.
Target cell
specifically
binds
hormone.
(c) Endocrine (hormonal) signaling 324

The Three Stages of Cell Signaling:
A Preview
• Earl W. Sutherland discovered how the
hormone epinephrine acts on cells
• Sutherland suggested that cells receiving
signals went through three processes
– Reception
– Transduction
– Response
325
Figure 11.6-3
EXTRACELLULAR CYTOPLASM
FLUID Plasma membrane
1 Reception 2 Transduction 3 Response
Receptor
Activation
of cellular
response
Relay molecules in a signal transduction
pathway
Signaling
molecule
326
Concept 11.2: Reception: A signaling
molecule binds to a receptor protein, causing
it to change shape
• The binding between a signal molecule
(ligand) and receptor is highly specific
• A shape change in a receptor is often the
initial transduction of the signal
• Most signal receptors are plasma
membrane proteins
327
Receptors in the Plasma Membrane
• Most water-soluble signal molecules bind to
specific sites on receptor proteins that span
the plasma membrane
• There are three main types of membrane
receptors
– G protein-coupled receptors
– Receptor tyrosine kinases
– Ion channel receptors
328
Intracellular Receptors
• Intracellular receptor proteins are found in
the cytosol or nucleus of target cells
• Small or hydrophobic chemical
messengers can readily cross the
membrane and activate receptors
• Examples of hydrophobic messengers are
the steroid and thyroid hormones of
animals
• An activated hormone-receptor complex
can act as a transcription factor, turning on
329
specific genes
Figure 11.9-5
Hormone EXTRACELLULAR
(testosterone) FLUID
Plasma
membrane
Receptor
protein
Hormone-
receptor
complex
DNA
mRNA
NUCLEUS
New protein
CYTOPLASM 330
Concept 11.3: Transduction: Cascades of
molecular interactions relay signals from
receptors to target molecules in the cell
• Signal transduction usually involves multiple
steps
• Multistep pathways can amplify a signal: A
few molecules can produce a large cellular
response
• Multistep pathways provide more
opportunities for coordination and regulation
of the cellular response 331
Signal Transduction Pathways
• The molecules that relay a signal from
receptor to response are mostly proteins
• Like falling dominoes, the receptor activates
another protein, which activates another,
and so on, until the protein producing the
response is activated
• At each step, the signal is transduced into a
different form, usually a shape change in a
protein
332
Protein Phosphorylation and
Dephosphorylation
• In many pathways, the signal is transmitted
by a cascade of protein phosphorylations
• Protein kinases transfer phosphates from
ATP to protein, a process called
phosphorylation
333
• Protein phosphatases remove the
phosphates from proteins, a process called
dephosphorylation
• This phosphorylation and dephosphorylation
system acts as a molecular switch, turning
activities on and off or up or down, as
required
334
Figure 11.10
Signaling molecule
Receptor
Activated relay
molecule
Inactive
protein kinase
1 Active
protein
kinase
1
Inactive
protein kinase ATP
2 ADP P
Active
protein
PP kinase
Pi 2
Inactive
protein kinase ATP
3 ADP P
Active
protein
PP kinase
Pi 3
Inactive
protein ATP
ADP P
Active Cellular
PP
protein response
Pi 335
Concept 11.4: Response: Cell signaling leads
to regulation of transcription or cytoplasmic
activities
• The cell’s response to an extracellular signal
is sometimes called the “output response”
336
Nuclear and Cytoplasmic Responses
• Ultimately, a signal transduction pathway
leads to regulation of one or more cellular
activities
• The response may occur in the cytoplasm or
in the nucleus
• Many signaling pathways regulate the
synthesis of enzymes or other proteins,
usually by turning genes on or off in the
nucleus
• The final activated molecule in the signaling
pathway may function as a transcription
factor 337
Figure 11.15
Growth factor Reception
Receptor
Phosphorylation
cascade
Transduction
CYTOPLASM
Inactive Active
transcription transcription
factor factor Response
P
DNA
Gene
NUCLEUS mRNA
338
• Other pathways regulate the activity of
enzymes rather than their synthesis
339
• Signaling pathways can also affect the
overall behavior of a cell, for example,
changes in cell shape
340
Concept 11.5: Apoptosis integrates multiple
cell-signaling pathways
• Apoptosis is programmed or controlled cell
suicide
• Components of the cell are chopped up and
packaged into vesicles that are digested by
scavenger cells
• Apoptosis prevents enzymes from leaking
out of a dying cell and damaging
neighboring cells
341
Figure 11.20
2 m
342
Apoptotic Pathways and the Signals That
Trigger Them
• Caspases are the main proteases (enzymes
that cut up proteins) that carry out apoptosis
• Apoptosis can be triggered by
– An extracellular death-signaling ligand
– DNA damage in the nucleus
– Protein misfolding in the endoplasmic
reticulum
343
Figure 11.UN01
1 Reception 2 Transduction 3 Response
Receptor
Activation
of cellular
response
Relay molecules
Signaling
molecule
344
• Apoptosis involves all but which of the following?
A) lysis of the cell B) activation of cellular enzymes
C) cell-signaling pathways D) fragmentation of the DNA
• Which of the following is characterized by a cell releasing a

signal molecule into the environment, followed by a
number of cells in the immediate vicinity responding?
A) endocrine signaling B) hormonal signaling
C) paracrine signaling D) synaptic signaling
345
Chapter 12
The Cell Cycle
Lectures by
Erin Barley
346

Overview: The Key Roles of Cell Division
• The ability of organisms to produce more of
their own kind best distinguishes living
things from nonliving matter
• The continuity of life is based on the
reproduction of cells, or cell division
347
• In unicellular organisms, division of one cell
reproduces the entire organism
• Multicellular organisms depend on cell
division for
– Development from a fertilized cell
– Growth
– Repair
• Cell division is an integral part of the cell
cycle, the life of a cell from formation to its
own division
348
Figure 12.2
100 m (a) Reproduction
200 m
(b) Growth and
development
20 m
(c) Tissue renewal 349
Concept 12.1: Most cell division results in
genetically identical daughter cells
• Most cell division results in daughter cells
with identical genetic information, DNA
• The exception is meiosis, a special type of
division that can produce sperm and egg
cells
350
Cellular Organization of the Genetic
Material
• All the DNA in a cell constitutes the cell’s
genome
• A genome can consist of a single DNA
molecule (common in prokaryotic cells) or a
number of DNA molecules (common in
eukaryotic cells)
• DNA molecules in a cell are packaged into
chromosomes
351
Figure 12.3
20 m
352
• Eukaryotic chromosomes consist of
chromatin, a complex of DNA and protein
that condenses during cell division
• Every eukaryotic species has a
characteristic number of chromosomes in
each cell nucleus
• Somatic cells (nonreproductive cells) have
two sets of chromosomes
• Gametes (reproductive cells: sperm and
eggs) have half as many chromosomes as
somatic cells
353
Distribution of Chromosomes During
Eukaryotic Cell Division
• In preparation for cell division, DNA is
replicated and the chromosomes condense
• Each duplicated chromosome has two
sister chromatids (joined copies of the
original chromosome), which separate
during cell division
• The centromere is the narrow “waist” of the
duplicated chromosome, where the two
chromatids are most closely attached
354
Figure 12.4
Sister
chromatids
Centromere 0.5 m
355
• During cell division, the two sister
chromatids of each duplicated chromosome
separate and move into two nuclei
• Once separate, the chromatids are called
chromosomes
356
Figure 12.5-3
Chromosomal
Chromosomes DNA molecules
1 Centromere
Chromosome
arm
Chromosome duplication
(including DNA replication)
and condensation
2
Sister
chromatids
Separation of sister
chromatids into
two chromosomes
3
357
• Eukaryotic cell division consists of
– Mitosis, the division of the genetic material in
the nucleus
– Cytokinesis, the division of the cytoplasm
• Gametes are produced by a variation of cell
division called meiosis
• Meiosis yields nonidentical daughter cells
that have only one set of chromosomes, half
as many as the parent cell
358
Phases of the Cell Cycle
• The cell cycle consists of
– Mitotic (M) phase (mitosis and cytokinesis)
– Interphase (cell growth and copying of
chromosomes in preparation for cell division)
359
• Interphase (about 90% of the cell cycle) can
be divided into subphases
– G1 phase (“first gap”)
– S phase (“synthesis”)
– G2 phase (“second gap”)
• The cell grows during all three phases, but
chromosomes are duplicated only during the
S phase
360
Figure 12.6
INTERPHASE
G1 S
(DNA synthesis)
G2
361
• Mitosis is conventionally divided into five
phases
– Prophase ‫الطور التمهيدي‬
– Prometaphase ‫طليعة الطور اإلستوائي‬
– Metaphase ‫الطور اإلستوائي‬
– Anaphase ‫الطور االنفصالي‬
– Telophase ‫الطور النهائي‬
• Cytokinesis overlaps the latter stages of
mitosis
362
• Prophase- mitotic spindle begins to form,
and chromosomes condense so that sister
chromatids are attached at the centromere.
• Prometaphase- the nuclear envelope
disassembles, and chromosomes attach to
spindle apparatus via kinetochores.
• Metaphase- chromosomes migrate to align
centrally on the metaphase plate.
363
• Anaphase-
– A- sister chromatids separate and move
towards the pole.
– B- two spindle poles move apart. Cytokinesis
begins.
• Telophase- nuclear envelope reforms,

chromosomes decondense, and cytokinesis
is completed
364
G2 of Interphase Prophase Prometaphase
Centrosomes Fragments
(with centriole Chromatin Early mitotic Aster of nuclear Nonkinetochore
pairs) (duplicated) spindle envelope microtubules
Centromere
Figure 12.7c
Plasma
Nucleolus membrane Kinetochore Kinetochore
Chromosome, consisting
Nuclear of two sister chromatids microtubule
envelope
10 m
365
G2 of Interphase Prophase Prometaphase
Metaphase Anaphase Telophase and Cytokinesis
Metaphase Cleavage Nucleolus

plate furrow forming
Figure 12.7d
Nuclear
Spindle Centrosome at Daughter envelope
one spindle pole chromosomes forming
10 m
Metaphase Anaphase Telophase and Cytokinesis
366
Figure 12.8
Centrosome
Aster
Metaphase
Sister plate
chromatids (imaginary) Microtubules
Chromosomes
Kineto-
chores Centrosome
1 m
Overlapping
nonkinetochore
microtubules Kinetochore
microtubules
0.5 m
367
Cytokinesis: A Closer Look
• In animal cells, cytokinesis occurs by a
process known as cleavage, forming a
cleavage furrow
• In plant cells, a cell plate forms during
cytokinesis
368
Figure 12.10a
(a) Cleavage of an animal cell (SEM)
100 m
Cleavage furrow
Contractile ring of Daughter cells

microfilaments 369
Figure 12.10b
(b) Cell plate formation in a plant cell (TEM)
Vesicles Wall of parent cell

1 m
forming
cell plate Cell plate New cell wall
Daughter cells 370

Figure 12.11
Chromatin
Nucleus condensing
10 m
Nucleolus Chromosomes Cell plate
1 Prophase 2 Prometaphase 3 Metaphase 4 Anaphase 5 Telophase
371
Binary Fission in Bacteria
• Prokaryotes (bacteria and archaea)
reproduce by a type of cell division called
binary fission
• In binary fission, the chromosome replicates
(beginning at the origin of replication), and
the two daughter chromosomes actively
move apart
• The plasma membrane pinches inward,
dividing the cell into two
372
Figure 12.12-4
Origin of Cell wall
replication Plasma membrane
E. coli cell
Bacterial chromosome
1 Chromosome Two copies
replication of origin
begins.
2 Replication Origin Origin

continues.
3 Replication
finishes.
4 Two daughter
cells result. 373
Concept 12.3: The eukaryotic cell cycle is
regulated by a molecular control system
• The frequency of cell division varies with the
type of cell
• These differences result from regulation at
the molecular level
• Cancer cells manage to escape the usual
controls on the cell cycle
374
The Cell Cycle Control System
• The sequential events of the cell cycle are
directed by a distinct cell cycle control
system, which is similar to a clock
• The cell cycle control system is regulated by
both internal and external controls
• The clock has specific checkpoints where
the cell cycle stops until a go-ahead signal is
received
375
Figure 12.15
G1 checkpoint
Control
system S
G1
M G2
M checkpoint
G2 checkpoint 376
• For many cells, the G1 checkpoint seems to
be the most important
• If a cell receives a go-ahead signal at the G1
checkpoint, it will usually complete the S,
G2, and M phases and divide
• If the cell does not receive the go-ahead
signal, it will exit the cycle, switching into a
nondividing state called the G0 phase
377
Figure 12.16
G0
G1 checkpoint
G1 G1
(a) Cell receives a go-ahead (b) Cell does not receive a

signal. go-ahead signal.
378
Loss of Cell Cycle Controls in Cancer Cells
• Cancer cells do not respond normally to the
body’s control mechanisms
• Cancer cells may not need growth factors to
grow and divide
– They may make their own growth factor
– They may convey a growth factor’s signal
without the presence of the growth factor
– They may have an abnormal cell cycle control
system
379
• A normal cell is converted to a cancerous
cell by a process called transformation
• Cancer cells that are not eliminated by the
immune system form tumors, masses of
abnormal cells within otherwise normal
tissue
• If abnormal cells remain only at the original
site, the lump is called a benign tumor
• Malignant tumors invade surrounding
tissues and can metastasize, exporting
cancer cells to other parts of the body,
where they may form additional tumors 380
Figure 12.UN01
P
G1 S
Cytokinesis
Mitosis G2
MITOTIC (M) PHASE
Prophase
Telophase and
Cytokinesis
Prometaphase
Anaphase
Metaphase 381
• If there are 20 chromatids in a cell, how many
centromeres are there?
A) 30 B) 10 C) 20 D) 40
• After which checkpoint is the cell first committed to

continue the cell cycle through M?
A) G1 B) G0 C) S D) G2
.
382
Chapter 13
Meiosis and Sexual

Life Cycles
Lectures by
Erin Barley
383

Overview: Variations on a Theme
• Living organisms are distinguished by their
ability to reproduce their own kind
• Genetics is the scientific study of heredity
and variation
• Heredity is the transmission of traits from
one generation to the next
• Variation is demonstrated by the
differences in appearance that offspring
show from parents and siblings
384
Concept 13.1: Offspring acquire genes from
parents by inheriting chromosomes
• In a literal sense, children do not inherit
particular physical traits from their parents
• It is genes that are actually inherited
385
Inheritance of Genes
• Genes are the units of heredity, and are
made up of segments of DNA
• Genes are passed to the next generation
via reproductive cells called gametes
(sperm and eggs)
• Each gene has a specific location called a
locus on a certain chromosome
• Most DNA is packaged into
chromosomes
386
Comparison of Asexual and Sexual
Reproduction
• In asexual reproduction, a single
individual passes genes to its offspring
without the fusion of gametes
• A clone is a group of genetically identical
individuals from the same parent
• In sexual reproduction, two parents give
rise to offspring that have unique
combinations of genes inherited from the
two parents 387
Concept 13.2: Fertilization and meiosis
alternate in sexual life cycles
• A life cycle is the generation-to-
generation sequence of stages in the
reproductive history of an organism
388
Sets of Chromosomes in Human Cells
• Human somatic cells (any cell other than
a gamete) have 23 pairs of chromosomes
• A karyotype is an ordered display of the
pairs of chromosomes from a cell
• The two chromosomes in each pair are
called homologous chromosomes, or
homologs
• Chromosomes in a homologous pair are
the same length and shape and carry
genes controlling the same inherited
characters 389
• The sex chromosomes, which determine
the sex of the individual, are called X and
Y
• Human females have a homologous pair
of X chromosomes (XX)
• Human males have one X and one Y
chromosome
• The remaining 22 pairs of chromosomes
are called autosomes
390
• Each pair of homologous chromosomes
includes one chromosome from each
parent
• The 46 chromosomes in a human somatic
cell are two sets of 23: one from the
mother and one from the father
• A diploid cell (2n) has two sets of
chromosomes
• For humans, the diploid number is 46 (2n
= 46) 391
• In a cell in which DNA synthesis has
occurred, each chromosome is replicated
• Each replicated chromosome consists of
two identical sister chromatids
392
Figure 13.4
Key
Maternal set of
2n  6 chromosomes (n  3)
Paternal set of
chromosomes (n  3)
Sister chromatids
of one duplicated
chromosome
Centromere
Two nonsister Pair of homologous

chromatids in chromosomes
a homologous pair (one from each set)
393
• A gamete (sperm or egg) contains a
single set of chromosomes, and is
haploid (n)
• For humans, the haploid number is 23 (n
= 23)
• Each set of 23 consists of 22 autosomes
and a single sex chromosome
• In an unfertilized egg (ovum), the sex
chromosome is X
• In a sperm cell, the sex chromosome may
be either X or Y 394
Behavior of Chromosome Sets in the
Human Life Cycle
• Fertilization is the union of gametes (the
sperm and the egg)
• The fertilized egg is called a zygote and
has one set of chromosomes from each
parent
• The zygote produces somatic cells by
mitosis and develops into an adult
395
• At sexual maturity, the ovaries and testes
produce haploid gametes
• Gametes are the only types of human
cells produced by meiosis, rather than
mitosis
• Meiosis results in one set of
chromosomes in each gamete
• Fertilization and meiosis alternate in
sexual life cycles to maintain
chromosome number
396
Figure 13.5
Key Haploid gametes (n  23)
Haploid (n) Egg (n)
Diploid (2n)
Sperm (n)
MEIOSIS FERTILIZATION
Ovary Testis
Diploid
zygote
(2n  46)
Mitosis and
development
Multicellular diploid
adults (2n  46) 397
Concept 13.3: Meiosis reduces the number of
chromosome sets from diploid to haploid
• Like mitosis, meiosis is preceded by the
replication of chromosomes
• Meiosis takes place in two sets of cell
divisions, called meiosis I and meiosis II
• The two cell divisions result in four
daughter cells, rather than the two
daughter cells in mitosis
• Each daughter cell has only half as many
chromosomes as the parent cell 398
The Stages of Meiosis
• After chromosomes duplicate, two
divisions follow
– Meiosis I (reductional division): homologs
pair up and separate, resulting in two
haploid daughter cells with replicated
chromosomes
– Meiosis II (equational division) sister
chromatids separate
• The result is four haploid daughter cells
with unreplicated chromosomes
399
Figure 13.7-3
Interphase
Pair of homologous
chromosomes in
diploid parent cell
Duplicated pair Chromosomes

of homologous duplicate
chromosomes
Sister
Diploid cell with
chromatids
duplicated
chromosomes
Meiosis I
1 Homologous
chromosomes separate
Haploid cells with
duplicated chromosomes
Meiosis II
2 Sister chromatids
separate
Haploid cells with unduplicated chromosomes 400

• Division in meiosis I occurs in four phases
– Prophase I
– Metaphase I
– Anaphase I
– Telophase I and cytokinesis
401
Figure 13.8a
Metaphase I Anaphase I Telophase I and

Prophase I
Cytokinesis
Centrosome
(with centriole pair) Sister chromatids
remain attached
Sister Chiasmata Centromere
chromatids (with kinetochore)
Spindle
Metaphase
plate
Cleavage
furrow
Homologous
Homologous Fragments chromosomes
chromosomes of nuclear separate
envelope
Microtubule Each pair of homologous Two haploid
attached to chromosomes separates. cells form; each
kinetochore chromosome
Duplicated homologous Chromosomes line up still consists
chromosomes (red and blue) by homologous pairs. of two sister
pair and exchange segments; chromatids.
2n  6 in this example.
402
• Division in meiosis II also occurs in four
phases
– Prophase II
– Metaphase II
– Anaphase II
– Telophase II and cytokinesis
• Meiosis II is very similar to mitosis
403
Figure 13.8b
Telophase II and
Prophase II Metaphase II Anaphase II
Cytokinesis
During another round of cell division, the sister chromatids finally separate;
four haploid daughter cells result, containing unduplicated chromosomes.
Sister chromatids Haploid daughter
separate cells forming
404
A Comparison of Mitosis and Meiosis
• Mitosis conserves the number of
chromosome sets, producing cells that
are genetically identical to the parent cell
• Meiosis reduces the number of
chromosomes sets from two (diploid) to
one (haploid), producing cells that differ
genetically from each other and from the
parent cell
405
Figure 13.9a
MITOSIS MEIOSIS
Parent cell MEIOSIS I
Chiasma
Prophase Prophase I
Chromosome Chromosome
Duplicated Homologous
duplication duplication
chromosome 2n  6 chromosome pair
Metaphase Metaphase I
Anaphase Anaphase I
Telophase Daughter Telophase I
cells of Haploid
meiosis I n3
2n 2n MEIOSIS II
Daughter cells n n n n
of mitosis
Daughter cells of meiosis II 406
Figure 13.9b
SUMMARY
Property Mitosis Meiosis
DNA Occurs during interphase before Occurs during interphase before meiosis I begins
replication mitosis begins
Number of One, including prophase, metaphase, Two, each including prophase, metaphase, anaphase,
divisions anaphase, and telophase and telophase
Synapsis of Does not occur Occurs during prophase I along with crossing over
homologous between nonsister chromatids; resulting chiasmata
chromosomes hold pairs together due to sister chromatid cohesion
Number of Two, each diploid (2n) and genetically Four, each haploid (n), containing half as many
daughter cells identical to the parent cell chromosomes as the parent cell; genetically different
and genetic from the parent cell and from each other
composition
Role in the Enables multicellular adult to arise from Produces gametes; reduces number of chromosomes
animal body zygote; produces cells for growth, repair, by half and introduces genetic variability among the
and, in some species, asexual reproduction gametes
407
• A given organism has 46 chromosomes in its karyotype. We
can therefore conclude which of the following?
A) It must be a primate. B) It must be human.
C) Its gametes must have 23 chromosomes. D) It must be an animal.
• A human cell containing 22 autosomes and a Y chromosome is

A) a zygote. B) a somatic cell of a male.
C) an egg. D) a sperm.
.
408
Chapter 16
The Molecular Basis of Inheritance
Lectures by
Erin Barley
409

Concept 16.1: DNA is the genetic material
• Early in the 20th century, the identification of the
molecules of inheritance loomed as a major
challenge to biologists
410
Figure 16.5
Sugar–phosphate Nitrogenous bases
backbone
5 end
Thymine (T)
Adenine (A)
Cytosine (C)
Phosphate
Guanine (G)
Sugar
(deoxyribose)
DNA Nitrogenous base
nucleotide 3 end
411
Figure 16.7
G
5 end
C
C G Hydrogen bond
3 end
G C
G C T A
3.4 nm
T A
G C G C
C G
A T
1 nm C G
T A
C G
G C
C G A T
A T 3 end
A T
0.34 nm
T A 5 end
(a) Key features of (b) Partial chemical structure (c) Space-filling

DNA structure model
412
Figure 16.7a
5 end
C G
C G Hydrogen bond
3 end
G C
G C T A
3.4 nm
T A
G C G C
C G
A T
1 nm C G
T A
C G
G C
C G A T
A T 3 end
A T
0.34 nm
T A 5 end
(a) Key features of (b) Partial chemical structure

DNA structure 413
• adenine (A) paired only with thymine (T), and
guanine (G) paired only with cytosine (C)
• in any organism the amount of A = T, and the
amount of G = C
414
Figure 16.8
Sugar
Sugar
Adenine (A) Thymine (T)
Sugar
Sugar
Guanine (G) Cytosine (C) 415

Concept 16.2: Many proteins work
together in DNA replication and repair
• The relationship between structure and function is
manifest in the double helix
• Watson and Crick noted that the specific base
pairing suggested a possible copying mechanism
for genetic material
416
The Basic Principle: Base Pairing to a
Template Strand
• Since the two strands of DNA are complementary,
each strand acts as a template for building a new
strand in replication
• In DNA replication, the parent molecule unwinds,
and two new daughter strands are built based on
base-pairing rules
417
Figure 16.9-3
A T A T A T A T
C G C G C G C G
T A T A T A T A
A T A T A T A T
G C G C G C G C
(a) Parent molecule (b) Separation of (c) “Daughter” DNA molecules,

strands each consisting of one
parental strand and one
new strand
418
DNA Replication: A Closer Look
• The copying of DNA is remarkable in its speed
and accuracy
• More than a dozen enzymes and other proteins
participate in DNA replication
419
Getting Started
• Replication begins at particular sites called
origins of replication, where the two DNA
strands are separated, opening up a replication
“bubble”
• A eukaryotic chromosome may have hundreds or
even thousands of origins of replication
• Replication proceeds in both directions from each
origin, until the entire molecule is copied
Animation: Origins of Replication

420
• At the end of each replication bubble is a
replication fork, a Y-shaped region where new
DNA strands are elongating
• Helicases are enzymes that untwist the double
helix at the replication forks
• Single-strand binding proteins bind to and
stabilize single-stranded DNA
• Topoisomerase corrects “overwinding” ahead of
replication forks by breaking, swiveling, and
rejoining DNA strands
421
Figure 16.13
Primase
3
Topoisomerase
5 RNA
3 primer
5
3
Helicase
5
Single-strand binding
proteins
422
• DNA polymerases cannot initiate synthesis of a
polynucleotide; they can only add nucleotides to
the 3 end
• The initial nucleotide strand is a short RNA
primer
423
• An enzyme called primase can start an RNA
chain from scratch and adds RNA nucleotides one
at a time using the parental DNA as a template
• The primer is short (5–10 nucleotides long), and
the 3 end serves as the starting point for the new
DNA strand
424
Synthesizing a New DNA Strand
• Enzymes called DNA polymerases catalyze the
elongation of new DNA at a replication fork
• Most DNA polymerases require a primer and a
DNA template strand
• The rate of elongation is about 500 nucleotides
per second in bacteria and 50 per second in
human cells
425
• Each nucleotide that is added to a growing DNA
strand is a nucleoside triphosphate
• dATP supplies adenine to DNA and is similar to
the ATP of energy metabolism
• The difference is in their sugars: dATP has
deoxyribose while ATP has ribose
• As each monomer of dATP joins the DNA strand,
it loses two phosphate groups as a molecule of
pyrophosphate
426
Figure 16.14
New strand Template strand

5 3 5 3
Sugar A T A T
Phosphate Base
C G C G
G C G C
DNA
OH
polymerase
3 A T A
P PiOH
C Pyrophosphate 3 C
Nucleoside 2Pi
triphosphate 5 5
427
Antiparallel Elongation
• The antiparallel structure of the double helix
affects replication
• DNA polymerases add nucleotides only to the free
3end of a growing strand; therefore, a new DNA
strand can elongate only in the 5to3direction
428
• Along one template strand of DNA, the DNA
polymerase synthesizes a leading strand
continuously, moving toward the replication fork
429
Figure 16.15
Overview
Leading
Origin of replication Lagging
strand
strand
Primer
Lagging Leading
strand strand Origin of
Overall directions replication
of replication
3
5
5 RNA primer
3
3 Sliding clamp
DNA pol III

Parental DNA 5
3
5
5
3
3
5 430
Figure 16.15a
Overview
Leading
strand Origin of replication Lagging
strand
Primer
Lagging Leading
strand strand
Overall directions
of replication
431
Figure 16.15b
Origin of
replication
3
5
5 RNA primer
3
3 Sliding clamp
DNA pol III

Parental DNA 5
3
5
5
3
3
5 432
• To elongate the other new strand, called the
lagging strand, DNA polymerase must work in the
direction away from the replication fork
• The lagging strand is synthesized as a series of
segments called Okazaki fragments, which are
joined together by DNA ligase
Animation: Lagging Strand

433
Figure 16.16b-6
3
5 3
Template
strand 5
3 RNA primer
for fragment 1
5
1 3
5
3 Okazaki
fragment 1
5
1
RNA primer 3
for fragment 2 5
5
3
2
Okazaki
fragment 2 1 3
5
5
3
2
1 3
5 5
3
2
1 3
5
434
Overall direction of replication
Figure 16.17a
Overview
Leading Origin of
replication Lagging
strand strand
Leading
Lagging strand
strand Overall directions
of replication
Leading strand
5 DNA pol III

3 Primer
Primase
3 5
3
Parental
DNA
435
Figure 16.17b
Overview
Leading Origin of
replication Lagging
strand strand
Leading
Lagging strand
strand Overall directions
Leading strand of replication
Primer
DNA pol III Lagging strand

5
DNA pol I DNA ligase
4 35
3 3 2 1 3
436
5
The DNA Replication Complex
• The proteins that participate in DNA replication
form a large complex, a “DNA replication machine”
• The DNA replication machine may be stationary
during the replication process
• Recent studies support a model in which DNA
polymerase molecules “reel in” parental DNA and
“extrude” newly made daughter DNA molecules
Animation: DNA Replication Review

437
Figure 16.18
DNA pol III

Parental DNA Leading strand
5
5 3 3
3
3 5 5
Connecting Helicase
protein
3 5 Lagging
DNA strand
Lagging strand template
pol III 5 3
438
Proofreading and Repairing DNA
• DNA polymerases proofread newly made DNA,
replacing any incorrect nucleotides
• In mismatch repair of DNA, repair enzymes
correct errors in base pairing
• DNA can be damaged by exposure to harmful
chemical or physical agents such as cigarette
smoke and X-rays; it can also undergo
spontaneous changes
• In nucleotide excision repair, a nuclease cuts
out and replaces damaged stretches of DNA
439
Figure 16.19
5 3
3 5
Nuclease
5 3
3 5
DNA
polymerase
5 3
3 5
DNA
ligase
5 3
3 5 440
• The shortening of telomeres might protect cells
from cancerous growth by limiting the number of
cell divisions
• There is evidence of telomerase activity in cancer
cells, which may allow cancer cells to persist
441
Figure 16.UN03
DNA pol III synthesizes

leading strand continuously 3
5
Parental
DNA DNA pol III starts DNA
synthesis at 3 end of primer, Origin of
5 continues in 5  3 direction replication
3
5 Lagging strand synthesized
in short Okazaki fragments,
Helicase later joined by DNA ligase
Primase synthesizes 3
a short RNA primer 5
DNA pol I replaces the RNA
primer with DNA nucleotides
442
• Cytosine makes up 42% of the nucleotides in a sample of DNA
from an organism. Approximately what percentage of the
nucleotides in this sample will be thymine?
A) 42% B) 16% C) 31% D) 8%
• What is meant by the description "antiparallel" regarding the

strands that make up DNA?
A) Base pairings create unequal spacing between the two DNA strands.
B) One strand is positively charged and the other is negatively charged.
C) The 5' to 3' direction of one strand runs counter to the 5' to 3' direction of the
other strand.
.
443
Chapter 17
From Gene to Protein
Lectures by
Erin Barley
444

Overview: The Flow of Genetic Information
• The information content of DNA is in the
form of specific sequences of nucleotides
• The DNA inherited by an organism leads to
specific traits by dictating the synthesis of
proteins
• Proteins are the links between genotype
and phenotype
• Gene expression, the process by which
DNA directs protein synthesis, includes two
stages: transcription and translation 445
Concept 17.1: Genes specify proteins via
transcription and translation
• How was the fundamental relationship
between genes and proteins discovered?
446
Basic Principles of Transcription and
Translation
• RNA is the bridge between genes and the
proteins for which they code
• Transcription is the synthesis of RNA using
information in DNA
• Transcription produces messenger RNA
(mRNA)
• Translation is the synthesis of a
polypeptide, using information in the mRNA
• Ribosomes are the sites of translation
447
• In prokaryotes, translation of mRNA can
begin before transcription has finished
• In a eukaryotic cell, the nuclear envelope
separates transcription from translation
• Eukaryotic RNA transcripts are modified
through RNA processing to yield the
finished mRNA
448
• A primary transcript is the initial RNA
transcript from any gene prior to
processing
• The central dogma is the concept that
cells are governed by a cellular chain of
command: DNA RNA protein
449
Figure 17.UN01
DNA RNA Protein
450
Figure 17.3
Nuclear
envelope
TRANSCRIPTION DNA
Pre-mRNA
RNA PROCESSING
mRNA
DNA
TRANSCRIPTION
mRNA
Ribosome TRANSLATION Ribosome
TRANSLATION
Polypeptide Polypeptide
(a) Bacterial cell (b) Eukaryotic cell
451
Figure 17.3a-2
DNA
TRANSCRIPTION
mRNA
Ribosome
TRANSLATION
Polypeptide
(a) Bacterial cell

452
Figure 17.3b-3
Nuclear
envelope
DNA
TRANSCRIPTION
Pre-mRNA
RNA PROCESSING
mRNA
TRANSLATION Ribosome
Polypeptide
(b) Eukaryotic cell 453

The Genetic Code
• How are the instructions for assembling
amino acids into proteins encoded into
DNA?
• There are 20 amino acids, but there are only
four nucleotide bases in DNA
• How many nucleotides correspond to an
amino acid?
454
Codons: Triplets of Nucleotides
• The flow of information from gene to protein
is based on a triplet code: a series of
nonoverlapping, three-nucleotide words
• The words of a gene are transcribed into
complementary nonoverlapping three-
nucleotide words of mRNA
• These words are then translated into a
chain of amino acids, forming a polypeptide
455
Figure 17.4
DNA
template 3 5 DNA
strand A C C A A A C C G A G T molecule
T G G T T T G G C T C A
3 Gene 1
5
TRANSCRIPTION
Gene 2
U G G U U U G G C U C A
mRNA 5 3
Codon
TRANSLATION
Protein Trp Phe Gly Ser

Gene 3
Amino acid
456
• During transcription, one of the two DNA
strands, called the template strand,
provides a template for ordering the
sequence of complementary nucleotides in
an RNA transcript
• The template strand is always the same
strand for a given gene
• During translation, the mRNA base triplets,
called codons, are read in the 5 to 3
direction 457
• Codons along an mRNA molecule are read
by translation machinery in the 5 to 3
direction
• Each codon specifies the amino acid (one
of 20) to be placed at the corresponding
position along a polypeptide
458
Figure 17.5
Second mRNA base
U C A G
UUU UCU UAU UGU U
Phe Tyr Cys
UUC UCC UAC UGC C
U Ser
UUA UCA UAA Stop UGA Stop A
Leu
Third mRNA base (3 end of codon)

First mRNA base (5 end of codon) UUG UCG UAG Stop UGG Trp G
CUU CCU CAU CGU U

His
CUC CCC CAC CGC C
C Leu Pro Arg
CUA CCA CAA CGA A
Gln
CUG CCG CAG CGG G
AUU ACU AAU AGU U

Asn Ser
AUC Ile ACC AAC AGC C
A Thr
AUA ACA AAA AGA A
Lys Arg
Met or
AUG start
ACG AAG AGG G
GUU GCU GAU GGU U

Asp
GUC GCC GAC GGC C
G Val Ala Gly
GUA GCA GAA GGA A
Glu
GUG GCG GAG GGG G 459
Concept 17.2: Transcription is the DNA-
directed synthesis of RNA: a closer look
• Transcription is the first stage of gene
expression
460
Molecular Components of Transcription
• RNA synthesis is catalyzed by RNA
polymerase, which pries the DNA strands
apart and hooks together the RNA
nucleotides
• The RNA is complementary to the DNA
template strand
• RNA synthesis follows the same base-
pairing rules as DNA, except that uracil
substitutes for thymine
461
Concept 17.3: Eukaryotic cells modify RNA
after transcription
• Enzymes in the eukaryotic nucleus modify
pre-mRNA (RNA processing) before the
genetic messages are dispatched to the
cytoplasm
• During RNA processing, both ends of the
primary transcript are usually altered
• Also, usually some interior parts of the
molecule are cut out, and the other parts
spliced together 462
Alteration of mRNA Ends
• Each end of a pre-mRNA molecule is
modified in a particular way
– The 5 end receives a modified nucleotide 5
cap
– The 3 end gets a poly-A tail
• These modifications share several
functions
– They seem to facilitate the export of mRNA
to the cytoplasm
– They protect mRNA from hydrolytic
enzymes
– They help ribosomes attach to the 5 end463
Figure 17.10
Protein-coding Polyadenylation
segment signal
5 3
G P P P AAUAAA AAA … AAA
Start Stop
5 Cap 5 UTR 3 UTR Poly-A tail
codon codon
464
Split Genes and RNA Splicing
• Most eukaryotic genes and their RNA
transcripts have long noncoding stretches of
nucleotides that lie between coding regions
• These noncoding regions are called
intervening sequences, or introns
• The other regions are called exons because
they are eventually expressed, usually
translated into amino acid sequences
• RNA splicing removes introns and joins
exons, creating an mRNA molecule with a
continuous coding sequence
465
Figure 17.11
5 Exon Intron Exon Intron Exon 3

Pre-mRNA 5 Cap Poly-A tail
Codon 130 31104 105
numbers
146
Introns cut out and
exons spliced together
mRNA 5 Cap Poly-A tail

1146
5 UTR 3 UTR
Coding
segment
466
Concept 17.4: Translation is the RNA-
directed synthesis of a polypeptide: a
closer look
• Genetic information flows from mRNA to
protein through the process of translation
467
Molecular Components of Translation
• A cell translates an mRNA message into
protein with the help of transfer RNA
(tRNA)
• tRNAs transfer amino acids to the growing
polypeptide in a ribosome
• Translation is a complex process in terms of
its biochemistry and mechanics
468
Figure 17.14
Amino
Polypeptide acids
tRNA with
amino acid
attached
Ribosome
tRNA
C
G
Anticodon
U G G U U U G G C
5 Codons 3
mRNA 469
The Structure and Function of Transfer RNA
• Molecules of tRNA are not identical
– Each carries a specific amino acid on one end
– Each has an anticodon on the other end; the
anticodon base-pairs with a complementary
codon on mRNA
470
• A tRNA molecule consists of a single RNA
strand that is only about 80 nucleotides
long
• Flattened into one plane to reveal its base
pairing, a tRNA molecule looks like a
cloverleaf
471
Figure 17.15
3
Amino acid
attachment
site 5
Amino acid
attachment
5 site
3
Hydrogen
bonds
Hydrogen
bonds
A A G
3 5
Anticodon Anticodon
Anticodon
(c) Symbol used
(a) Two-dimensional structure (b) Three-dimensional structure in this book
472
Ribosomes
• Ribosomes facilitate specific coupling of
tRNA anticodons with mRNA codons in
protein synthesis
• The two ribosomal subunits (large and small)
are made of proteins and ribosomal RNA
(rRNA)
• Bacterial and eukaryotic ribosomes are
somewhat similar but have significant
differences: some antibiotic drugs
specifically target bacterial ribosomes 473
Figure 17.17a
Growing
polypeptide Exit tunnel
tRNA
molecules
Large
subunit
E P
A
Small
subunit
5
mRNA 3
(a) Computer model of functioning ribosome
474
Figure 17.17b
P site (Peptidyl-tRNA
Exit tunnel
binding site)
A site (Aminoacyl-
tRNA binding site)
E site
(Exit site)
E P A Large
subunit
mRNA
binding site Small
subunit
(b) Schematic model showing binding sites
475
Figure 17.17c
Growing polypeptide
Amino end
Next amino
acid to be
added to
polypeptide
chain
E tRNA
mRNA 3
5 Codons
(c) Schematic model with mRNA and tRNA

476
• A ribosome has three binding sites for tRNA
– The P site holds the tRNA that carries the
growing polypeptide chain
– The A site holds the tRNA that carries the
next amino acid to be added to the chain
– The E site is the exit site, where discharged
tRNAs leave the ribosome
477
Building a Polypeptide
• The three stages of translation
– Initiation
– Elongation
– Termination
• All three stages require protein “factors” that
aid in the translation process
478
Figure 17.18
Large
ribosomal
subunit
3 U A C 5 P site
5 A U G 3
Pi
Initiator 
tRNA GTP GDP
E A
mRNA
5 5
3 3
Start codon
Small
mRNA binding site ribosomal Translation initiation complex
subunit
479
Figure 17.19-4
Amino end of
polypeptide
E
mRNA 3
Ribosome ready for P A
site site GTP
next aminoacyl tRNA 5
GDP  P i
E E
P A P A
GDP  P i
GTP
P A
480
Polyribosomes
• A number of ribosomes can translate a
single mRNA simultaneously, forming a
polyribosome (or polysome)
• Polyribosomes enable a cell to make many
copies of a polypeptide very quickly
481
Figure 17.21
Completed
Growing polypeptide
polypeptides
Incoming
ribosomal
subunits
Start of
mRNA End of
(5 end) mRNA
(a) (3 end)
Ribosomes
mRNA
(b)
0.1 m 482
Protein Folding and Post-Translational
Modifications
• During and after synthesis, a polypeptide
chain spontaneously coils and folds into its
three-dimensional shape
• Proteins may also require post-translational
modifications before doing their job
• Some polypeptides are activated by
enzymes that cleave them
• Other polypeptides come together to form
the subunits of a protein
483
Concept 17.5: Mutations of one or a few
nucleotides can affect protein structure and
function
• Mutations are changes in the genetic
material of a cell or virus
• Point mutations are chemical changes in
just one base pair of a gene
• The change of a single nucleotide in a
DNA template strand can lead to the
production of an abnormal protein
484
Figure 17.23
Wild-type hemoglobin Sickle-cell hemoglobin

Wild-type hemoglobin DNA Mutant hemoglobin DNA
3 C T T 5 3 C A T 5
5 G A A 3 5 G T A 3
mRNA mRNA
5 G A A 3 5 G U A 3
Normal hemoglobin Sickle-cell hemoglobin

Glu Val
485
Types of Small-Scale Mutations
• Point mutations within a gene can be
divided into two general categories
– Nucleotide-pair substitutions
– One or more nucleotide-pair insertions or
deletions
486
Mutagens
• Spontaneous mutations can occur during
DNA replication, recombination, or repair
• Mutagens are physical or chemical agents
that can cause mutations
487
• The nitrogenous base adenine is found in all members of which
group?
A) proteins, ATP, and DNA B) ATP, RNA, and DNA
C) α glucose, ATP, and DNA D) proteins, carbohydrates, and ATP
• 2) A particular triplet of bases in the coding sequence of DNA is

AAA. The anticodon on the tRNA that binds the mRNA codon is
A) AAA. B) TTT. C) UUA. D) UUU.
.
488
Chapter 14
Mendel and the Gene Idea
Lectures by
Erin Barley
489

Concept 14.1: Mendel used the scientific
approach to identify two laws of inheritance
• Mendel discovered the basic principles of
heredity by breeding garden peas in
carefully planned experiments
490
Mendel’s Experimental, Quantitative
Approach
• Advantages of pea plants for genetic study
– There are many varieties with distinct
heritable features, or characters (such as
flower color); character variants (such as
purple or white flowers) are called traits
– Mating can be controlled
– Each flower has sperm-producing organs
(stamens) and an egg-producing organ
(carpel)
– Cross-pollination (fertilization between
different plants) involves dusting one plant
with pollen from another 491
Figure 14.2
TECHNIQUE
1
2
Parental
generation
(P) Stamens
3 Carpel
RESULTS
5
First filial
generation
offspring
(F1)
492
Figure 14.2a
TECHNIQUE
1
2
Parental
generation
(P) Stamens
3 Carpel
493
Figure 14.2b
RESULTS
5
First filial
generation
offspring
(F1)
494
• Mendel chose to track only those
characters that occurred in two distinct
alternative forms
• He also used varieties that were true-
breeding (plants that produce offspring of
the same variety when they self-pollinate)
495
• In a typical experiment, Mendel mated two
contrasting, true-breeding varieties, a
process called hybridization
• The true-breeding parents are the P
generation
• The hybrid offspring of the P generation are
called the F1 generation
• When F1 individuals self-pollinate or cross-
pollinate with other F1 hybrids, the F2
generation is produced
496
The Law of Segregation
• When Mendel crossed contrasting, true-
breeding white- and purple-flowered pea
plants, all of the F1 hybrids were purple
• When Mendel crossed the F1 hybrids,
many of the F2 plants had purple flowers,
but some had white
• Mendel discovered a ratio of about three
to one, purple to white flowers, in the F2
generation
497
Figure 14.3-3
EXPERIMENT
P Generation
(true-breeding
parents) Purple White
flowers flowers
F1 Generation
(hybrids)
All plants had purple flowers
Self- or cross-pollination
F2 Generation
705 purple- 224 white

flowered flowered
plants plants 498
• Mendel reasoned that only the purple
flower factor was affecting flower color in
the F1 hybrids
• Mendel called the purple flower color a
dominant trait and the white flower color a
recessive trait
• The factor for white flowers was not diluted
or destroyed because it reappeared in the
F2 generation
499
• Mendel observed the same pattern of
inheritance in six other pea plant
characters, each represented by two traits
• What Mendel called a “heritable factor” is
what we now call a gene
500
Table 14.1
501
Mendel’s Model
• Mendel developed a hypothesis to explain
the 3:1 inheritance pattern he observed in
F2 offspring
• Four related concepts make up this model
• These concepts can be related to what we
now know about genes and chromosomes
502
• First: alternative versions of genes
account for variations in inherited
characters
• For example, the gene for flower color in
pea plants exists in two versions, one for
purple flowers and the other for white
flowers
• These alternative versions of a gene are
now called alleles
• Each gene resides at a specific locus on a
specific chromosome 503
Figure 14.4
Allele for purple flowers
Pair of
Locus for flower-color gene homologous
chromosomes
Allele for white flowers
504
• Second: for each character, an organism
inherits two alleles, one from each parent
• Mendel made this deduction without
knowing about the role of chromosomes
• The two alleles at a particular locus may
be identical, as in the true-breeding plants
of Mendel’s P generation
• Alternatively, the two alleles at a locus
may differ, as in the F1 hybrids
505
• Third: if the two alleles at a locus differ, then
one (the dominant allele) determines the
organism’s appearance, and the other (the
recessive allele) has no noticeable effect
on appearance
• In the flower-color example, the F1 plants
had purple flowers because the allele for
that trait is dominant
506
• Fourth (now known as the law of
segregation): the two alleles for a heritable
character separate (segregate) during
gamete formation and end up in different
gametes
• Thus, an egg or a sperm gets only one of
the two alleles that are present in the
organism
• This segregation of alleles corresponds to
the distribution of homologous
chromosomes to different gametes in 507
meiosis
• Mendel’s segregation model accounts for
the 3:1 ratio he observed in the F2
generation of his numerous crosses
• The possible combinations of sperm and
egg can be shown using a Punnett square,
a diagram for predicting the results of a
genetic cross between individuals of known
genetic makeup
• A capital letter represents a dominant allele,
and a lowercase letter represents a
recessive allele 508
Figure 14.5-3
P Generation
Appearance: Purple flowers White flowers

Genetic makeup: PP pp
Gametes: P p
F1 Generation
Appearance: Purple flowers

Genetic makeup: Pp
2 p
1/
2 P
1/
Gametes:
Sperm from F1 (Pp) plant

F2 Generation P p
P
Eggs from PP Pp
F1 (Pp) plant
p
Pp pp
3 :1
509
Useful Genetic Vocabulary
• An organism with two identical alleles for
a character is said to be homozygous for
the gene controlling that character
• An organism that has two different alleles
for a gene is said to be heterozygous for
the gene controlling that character
• Unlike homozygotes, heterozygotes are
not true-breeding
510
• Because of the different effects of dominant
and recessive alleles, an organism’s traits
do not always reveal its genetic composition
• Therefore, we distinguish between an
organism’s phenotype, or physical
appearance, and its genotype, or genetic
makeup
• In the example of flower color in pea plants,
PP and Pp plants have the same phenotype
(purple) but different genotypes 511
Figure 14.6
Phenotype Genotype
Purple PP 1
(homozygous)
3 Purple Pp
(heterozygous)
Purple Pp
(heterozygous)
White pp
1 1
(homozygous)
Ratio 3:1 Ratio 1:2:1 512

The Testcross
• How can we tell the genotype of an
individual with the dominant phenotype?
• Such an individual could be either
homozygous dominant or heterozygous
• The answer is to carry out a testcross:
breeding the mystery individual with a
homozygous recessive individual
• If any offspring display the recessive
phenotype, the mystery parent must be
heterozygous
513
Figure 14.7
TECHNIQUE
Dominant phenotype, Recessive phenotype,

unknown genotype: known genotype:
PP or Pp? pp
Predictions
If purple-flowered or If purple-flowered
parent is PP parent is Pp
Sperm Sperm
p p p p
P P
Pp Pp Pp Pp
Eggs Eggs
P p
Pp Pp pp pp
RESULTS
or
All offspring purple 1/ offspring purple and
2
1/ offspring white 514
2
The Law of Independent Assortment
• Mendel derived the law of segregation by
following a single character
• The F1 offspring produced in this cross
were monohybrids, individuals that are
heterozygous for one character
• A cross between such heterozygotes is
called a monohybrid cross
515
• Mendel identified his second law of
inheritance by following two characters at
the same time
• Crossing two true-breeding parents differing
in two characters produces dihybrids in the
F1 generation, heterozygous for both
characters
• A dihybrid cross, a cross between F1
dihybrids, can determine whether two
characters are transmitted to offspring as a
package or independently 516
Figure 14.8
EXPERIMENT
P Generation YYRR yyrr
Gametes YR yr
F1 Generation
YyRr
Predictions Hypothesis of Hypothesis of

dependent assortment independent assortment
Sperm
Predicted or
offspring of
1/
4 YR 1/
4 Yr 1/
4 yR 1/
4 yr
Sperm
F2 generation
1/
2 YR 1/
2 yr
1/
4 YR
YYRR YYRr YyRR YyRr
1/
2 YR
YYRR YyRr 1/
Yr
Eggs 4
YYRr YYrr YyRr Yyrr
1/ Eggs
2 yr
YyRr yyrr 1/ yR
4
YyRR YyRr yyRR yyRr
3/ 1/
4 4
1/
4 yr
Phenotypic ratio 3:1 YyRr Yyrr yyRr yyrr
9/ 3/ 3/ 1/
16 16 16 16
Phenotypic ratio 9:3:3:1

RESULTS 517
315 108 101 32 Phenotypic ratio approximately 9:3:3:1
• Using a dihybrid cross, Mendel developed
the law of independent assortment
• The law of independent assortment states
that each pair of alleles segregates
independently of each other pair of alleles
during gamete formation
• Strictly speaking, this law applies only to
genes on different, nonhomologous
chromosomes or those far apart on the
same chromosome
• Genes located near each other on the
same chromosome tend to be inherited
together 518
Concept 14.2: The laws of probability
govern Mendelian inheritance
• Mendel’s laws of segregation and
independent assortment reflect the rules of
probability
• When tossing a coin, the outcome of one
toss has no impact on the outcome of the
next toss
• In the same way, the alleles of one gene
segregate into gametes independently of
another gene’s alleles 519
Concept 14.3: Inheritance patterns are often
more complex than predicted by simple
Mendelian genetics
• The relationship between genotype and
phenotype is rarely as simple as in the pea
plant characters Mendel studied
• Many heritable characters are not determined
by only one gene with two alleles
• However, the basic principles of segregation
and independent assortment apply even to
more complex patterns of inheritance
520
Extending Mendelian Genetics for a Single
Gene
• Inheritance of characters by a single gene
may deviate from simple Mendelian patterns
in the following situations:
– When alleles are not completely dominant or
recessive
– When a gene has more than two alleles
– When a gene produces multiple phenotypes
521
Degrees of Dominance
• Complete dominance occurs when
phenotypes of the heterozygote and
dominant homozygote are identical
• In incomplete dominance, the phenotype
of F1 hybrids is somewhere between the
phenotypes of the two parental varieties
• In codominance, two dominant alleles
affect the phenotype in separate,
distinguishable ways
522
Figure 14.10-3
P Generation
Red White
CRCR CWCW
Gametes CR CW
F1 Generation
Pink
CRCW
1/
Gametes 1/2 CR 2 CW
Sperm
F2 Generation 1/ 1/
2 CR 2 CW
1/
2 CR
Eggs CRCR CRCW
1/
2 CW
CRCW CWCW 523
The Relation Between Dominance and
Phenotype
• A dominant allele does not subdue a

recessive allele; alleles don’t interact that
way
• Alleles are simply variations in a gene’s
nucleotide sequence
• For any character,
dominance/recessiveness relationships of
alleles depend on the level at which we
examine the phenotype
524
Multiple Alleles
• Most genes exist in populations in more
than two allelic forms
• For example, the four phenotypes of the
ABO blood group in humans are determined
by three alleles for the enzyme (I) that
attaches A or B carbohydrates to red blood
cells: IA, IB, and i.
• The enzyme encoded by the IA allele adds
the A carbohydrate, whereas the enzyme
encoded by the IB allele adds the B
carbohydrate; the enzyme encoded by the i
allele adds neither 525
Figure 14.11
(a) The three alleles for the ABO blood groups and their
carbohydrates
Allele IA IB i
Carbohydrate A B none
(b) Blood group genotypes and phenotypes
Genotype IAIA or IAi IBIB or IBi IAIB ii
Red blood cell

appearance
Phenotype
A B AB O
(blood group)
526
Polygenic Inheritance
• Quantitative characters are those that vary
in the population along a continuum
• Quantitative variation usually indicates
polygenic inheritance, an additive effect of
two or more genes on a single phenotype
• Skin color in humans is an example of
polygenic inheritance
527
Figure 14.13
AaBbCc AaBbCc
Sperm
1/ 1/ 1/ 1/ 1/ 1/ 1/ 1/
8 8 8 8 8 8 8 8
1/
8
1/
8
1/
8
1/
8
Eggs 1/
8
1/
8
1/
8
1/
8
Phenotypes: 1/
64
6/
64
15/
64
20/
64
15/
64
6/
64
1/
64
Number of
dark-skin alleles: 0 1 2 3 4 5 6 528
Nature and Nurture: The Environmental
Impact on Phenotype
• Another departure from Mendelian genetics
arises when the phenotype for a character
depends on environment as well as genotype
• The norm of reaction is the phenotypic range
of a genotype influenced by the environment
• For example, hydrangea flowers of the same
genotype range from blue-violet to pink,
depending on soil acidity
529
Figure 14.14
530
• Norms of reaction are generally broadest
for polygenic characters
• Such characters are called multifactorial
because genetic and environmental factors
collectively influence phenotype
531
Recessively Inherited Disorders
• Many genetic disorders are inherited in
a recessive manner
• These range from relatively mild to life-
threatening
532
The Behavior of Recessive Alleles
• Recessively inherited disorders show up
only in individuals homozygous for the
allele
• Carriers are heterozygous individuals
who carry the recessive allele but are
phenotypically normal; most individuals
with recessive disorders are born to
carrier parents
• Albinism is a recessive condition
characterized by a lack of pigmentation 533
in
Figure 14.16
Parents
Normal Normal
Aa Aa
Sperm
A a
Eggs
Aa
AA
A Normal
Normal
(carrier)
Aa
aa
a Normal
(carrier) Albino
534
• If a recessive allele that causes a
disease is rare, then the chance of two
carriers meeting and mating is low
• Consanguineous matings (i.e., matings
between close relatives) increase the
chance of mating between two carriers of
the same rare allele
• Most societies and cultures have laws or
taboos against marriages between close
relatives 535
• How many unique gametes could be produced through
independent assortment by an individual with the genotype
AaBbCCDdEE?
A) 32 B) 4 C) 64 D) 8 E) 16
• Which of the following is an example of polygenic inheritance

A) the ABO blood group in humans B) skin pigmentation in humans
C) white and purple flower color in peas D) pink flowers in snapdragons
.
536

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‫‪General Biology 102 Handouts‬‬

‫‪Dr . Sulaiman Alnaimat‬‬

‫علوم حياتية عامة‬

© 2011 Pearson Education, Inc.

Carbon and the Molecular

© 2011 Pearson Education, Inc.

Name and Molecular Structural Ball-and- Space-Filling

Hydrogen Oxygen Nitrogen Carbon

(a) Length (c) Double bond position

Ethane Propane 1-Butene 2-Butene

(b) Branching (d) Presence of rings

Butane 2-Methylpropane Cyclohexane Benzene

STRUCTURE Alcohols NAME OF

EXAMPLE • Is polar as a result FUNCTIONAL

STRUCTURE Ketones if the carbonyl NAME OF

EXAMPLE • A ketone and an FUNCTIONAL

STRUCTURE Carboxylic acids, or organic NAME OF

EXAMPLE • Acts as an acid; can FUNCTIONAL

• Found in cells in the ionized

STRUCTURE Amines NAME OF

EXAMPLE • Acts as a base; can FUNCTIONAL

• Found in cells in the

STRUCTURE Thiols NAME OF

EXAMPLE • Two sulfhydryl groups can FUNCTIONAL

STRUCTURE Organic phosphates NAME OF

EXAMPLE • Contributes negative FUNCTIONAL

STRUCTURE Methylated compounds NAME OF

EXAMPLE • Addition of a methyl group FUNCTIONAL

The Structure and Function of

© 2011 Pearson Education, Inc.

Aldose (Aldehyde Sugar) Ketose (Ketone Sugar)

Aldose (Aldehyde Sugar) Ketose (Ketone Sugar)

Aldose (Aldehyde Sugar) Ketose (Ketone Sugar)

Hexoses: 6-carbon sugars (C6H12O6)

Glucose Galactose Fructose

(a) Linear and ring forms

Glucose Glucose Maltose

Glucose Fructose Sucrose

Mitochondria Glycogen granules

(a)  and  glucose

(a)  and  glucose ring structures

(b) Starch: 1–4 linkage of  glucose monomers

(c) Cellulose: 1–4 linkage of  glucose monomers 60

Cell wall Cellulose

Chitin forms the exoskeleton

Chitin is used to make a strong and flexibl

(b) Fat molecule (triacylglycerol) 68

(b) Fat molecule (triacylglycerol)

(a) Structural formula 77

Side chain (R group)

Nonpolar side chains; hydrophobic

Glycine Alanine Valine Leucine Isoleucine

Methionine Phenylalanine Tryptophan Proline

Serine Threonine Cysteine

Tyrosine Asparagine Glutamine

Electrically charged side chains; hydrophilic

Acidic (negatively charged)

Aspartic acid Glutamic acid Lysine Arginine Histidine

Amino end Peptide

Primary structure of transthyretin

Secondary Tertiary Quaternary

 strand, shown as a flat

Normal protein Denatured protein