BIOLOGICAL SCIENCE 6TH EDITION FREEMAN

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Notes to Instructors
Chapter 26 Bacteria and Archaea

What is the focus?

Relatively recent studies indicate that prokaryotes are incredibly diverse—so diverse that
they have been split into two domains: the Archaea and the Eubacteria. It is likely that
early life-forms were more like the Archaea. In other words, life on the early Earth was
very different from what we see today.

Activity 26.1 What Are the main Characteristics of Bacteria

and Archaea?

What is this activity designed to do?

This activity is designed to help students discern the characteristics of bacteria in
comparison to archaea, and compare and contrast their form and functions in light of their
extreme diversity. This activity also requires students to think about why the first forms
of life on Earth were likely similar to prokaryotes.

Activity 26.2 How Has small size Affected prokaryotic diversity?

What is this activity designed to do?

This activity is designed to help students understand how small size has limited
morphological diversity but promoted biochemical (metabolic) diversity among the
prokaryotes.

What misconceptions or difficulties can this activity reveal?

We often state that the prokaryotes are more diverse metabolically and the eukaryotes are
more diverse morphologically. Then we go on to indicate that a wide variety of metabolic
types exists in the prokaryotes. As instructors, we understand that any single species
of prokaryote has a specific type of metabolism. When we talk about the variety of
metabolic types, we mean that different species of prokaryotes can display very different

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 types of metabolism. Some students don’t have this same understanding, however. They
have the impression that a single species can display many different types of metabolism.

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 Answers

Activity 26.1 What Are the main Characteristics of Bacteria

and Archaea?

1. Based on DNA sequence analysis, three major domains of life have been proposed.
What are the three major domains of life? What sets of characteristics place
organisms into one domain versus another?

Major domains of life Key characteristics

Bacteria The bacteria and archaea both display the
prokaryote cell structure.
Most bacteria have a circular chromosome.
Bacterial cell walls contain peptidoglycan
with muramic acid.
All bacterial species use the same type
of RNA polymerase.
Bacteria use formylmethionine as their
initiator amino acid to start protein synthesis.
Archaea Archaeal cell walls do not contain peptidoglycan or
muramic acid.
Archaea have a circular chromosome.
Several types of RNA polymerase can be found
among the different archaeal species.
Archaea use methionine as the initiator amino
acid in translation.
Eukarya Eukaryotes have the eukaryotic cell structure, which
includes a double-membrane-bound nucleus and
membrane-bound organelles.
Eukaryotes have linear chromosomes.
Eukaryotic cell walls when present (for example, around
plant cells) generally contain cellulose of chitin.
Methionine is the initiator amino acid in translation.

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 2. The Bacteria are divided into six major groups. What characteristics are used to
place organisms into each of these groups?

Bacterial group Characteristics

Firmicutes Gram-positive; DNA contains low percentage of
guanine and cytosine; rod- or sphere-shaped; some
can fix N; some can photosynthesize; some
metabolize via fermentation; some metabolize via
cell respiration; members of this group cause
anthrax, botulism, tetanus, etc.; some are used to
ferment milk products
Spirochaeles Corkscrew shape and flagella contained within an
outer sheath; metabolize via fermentation; some
species can fix N; syphilis and Lyme disease are
both caused by spirochetes; many are anaerobic
Actinobacteria DNA contains high percentage of guanine and
cytosine; Gram-positive; rod and filamentous
shapes; heterotrophic and parasitic species; source
of many antibiotics; cause of tuberculosis and
leprosy; some are abundant soil decomposers
Chlamydiales Spherical shape and very small; all known species
are parasitic and live inside host cells; causes STD
Chlamydia, most common cause of blindness in
humans
Cyanobacteria Solitary or colonial forms; dominate mass of
aquatic environments; all are photosynthetic;
some can fix N; some live in association with
fungi—called lichens
Proteobacteria Has five major subgroups; rod, sphere, or spiral
shape; have a wide metabolic diversity; can cause
Legionnaire’s disease, cholera, dysentery,
gonorrhea, ulcers, diarrhea, etc.; used to produce
vinegar; genus Rhizobium live in or on plant roots
and fix N

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 3. The Archaea are divided into two major groups: the Euryarchaeota and the
Crenarchaeota. What characteristics are used to place organisms into each of these
groups?

Archaean group Characteristics

Euryarchaeota This group includes the methanogens, many extreme
halophiles, and some extreme thermophiles. The
methanogens are strictly anaerobic. The extreme
halophiles are aerobic and require high environmental
salt concentrations (720%). Many nonextremophile
species of Euryarchaeota have also been discovered.
Crenarchaeota This group is thought to be similar to the oldest archaeans.
Most of the thermophilic species of archaea fall into this
category. As with the Euryarchaeota, many nonextremophile
species of Crenarchaeota have also been discovered.

4. There is great diversity in the ways different species of microbes

• obtain energy for metabolic functions, and
• obtain carbon for building the macromolecules of life.

Fill in the chart to indicate how these characteristics are used to describe the
nutritional type or nutritional classification of organisms. (Refer also to Table 26.2
on page 529 in Biological Science, 6th edition.)

Prokaryotes

Energy Light Inorganic Light Organic Organic Inorganic

source chemicals compounds compounds chemicals
Carbon CO2 CO2 Organic CO2 Organic Organic
source compounds compounds compounds
Mode of Photo Chemo- Photo- Autotrophic Chemoorga- Chemo-
nutrition autotroph lithotroph heterotroph organotroph notroph lithotrophic
heterotrophs

5. Bacteria first appear in the fossil record about 3.5 billion years ago. Humans
appeared in the fossil record only a few million years ago. Given this information,
which group would you say is more highly evolved?

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 Answers to this question depend a great deal on how one defines evolved. Many
kinds of comparisons can be made. We provide one example below.

a. What kinds of arguments or evidence would you use to support the idea that
bacteria are more highly evolved?
If we consider organisms that are closely fit (in their metabolism, for example)
to their environment as more highly evolved, then many of the species of bacteria
are more highly evolved than humans.

b. How would you support the idea that humans are more highly evolved?
If we use the term evolved to indicate major changes in morphology that allow
organisms to survive in a number of different habitats, then humans are more
highly evolved.

6. Given what you know about the origin of life on Earth, you want to look for life on
other planets.

a. What characteristics of the planet’s environment would you look for? Explain
your reasoning.
Although we know that life can exist in the absence of oxygen, to the best of our
knowledge it cannot exist in the absence of water. Therefore, one of the first tests
would be for the presence of free water.

b. What kind(s) of life would you look for? Explain your reasoning.
To the best of our knowledge, free oxygen is not present on other planets.
Therefore, it would be best to look for life-forms that have characteristics similar
to those of anaerobic archaeal species.

c. What tests or probes would you use to find the kind of life you proposed in part a?
Explain your reasoning.
To answer this question, you need to make the assumption that life on other
planets may have evolved similar to life on Earth. This assumption is supported
by Miller’s experiments, which indicated that key organic compounds present
on Earth can be produced under reducing atmospheric conditions. Given that
assumption, we could look for some of the compounds we know are common
to life (we could analyze soil or other samples for the presence of polymers of
carbon, e.g., carbohydrates, proteins, lipids or nucleic acids).

Based on the assumption that the life-forms have DNA or RNA as their genetic
material, you could use radioactive DNA or RNA probes. Making these similar
to highly conserved genes in archaea and other organisms would give you a
better chance of finding possible homology.

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 Activity 26.2 How Has small size Affected prokaryotic diversity?

It is often said that bacteria tend to be more diverse biochemically and eukaryotes
tend to be more diverse morphologically.
Answer questions 1–7. Then write a summary argument (question 8) to support the
statement above. In other words, write an argument describing how small size has limited
morphological diversity but promoted biochemical (metabolic) diversity among the
prokaryotes.

1. All living organisms must maintain a relatively constant internal environment.

Maintaining this environment means that a certain concentration of each substance
must be maintained per unit volume of the cell. The cell’s ability to maintain a
specific concentration of a substance is affected by

• the ability of the substance to diffuse through the membrane,

• the overall size and shape of the cell, and
• the maximum amount of the substance a given area of membrane can transport
per unit time.

a. How do surface-area-to-volume (SA/V) ratios change as the size and shape of

cells and organisms change? To answer this, calculate the SA and V of a cube that
is 1 mm on a side. Then do the same for cubes that are 2 mm and 4 mm on a side,
and compare their SA/V ratios.

Cubes: 1-mm square 2-mm square 4-mm square

Linear dimension 1 mm 2 mm 4 mm
Surface area (SA) 6(1 mm2) = 6 mm2 6(2 mm2) = 24 mm2 6(4 mm2) = 96 mm2
Volume (V) (1 mm)3 (2 mm)3 = 8 mm3 (4 mm)3 = 64 mm3
SA/V ratio 6 mm2/1 mm3 24 mm2/8 mm3 96 mm2/64 mm3
= 3 mm2/1 mm3 = 1.5 mm2/1 mm3

b. In general, how does surface area change as linear dimensions increase twofold?
Surface area increases as a function of the square of the increase in linear
dimension. For example, the surface area of a 1-mm square is 6 mm2. The
surface area of a 2-mm square is 24 mm2.

Two millimeters in linear dimension is two times 1 mm. The increase in surface
area should then be 22 (the number of times bigger 2 mm is compared with
1 mm). In fact, 24 mm2 is four times greater than 6 mm2. Similarly, the 4-mm

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 square is two times the linear dimensions of the 2-mm square, and its surface
area (96 mm2) is four times the surface area (24 mm2) of the 2-mm square. On
the other hand, the 4-mm square is four times the linear dimensions of the 1-mm
square. Therefore, its surface area should be 42, or 16 times that of the 1-mm
square, and it is (96/6 = 16).

c. In general, how does volume change as linear dimensions increase twofold?

Volume changes as the cube of the difference in linear dimension. If linear
dimensions double, the volume increases by 23, or 8 times.

The volume of the 1-mm cube is 1 mm3, the volume of the 2-mm cube is 8 mm3,
and the volume of the 4-mm cube is 64 mm3. Each doubling in linear dimensions
produces an eightfold (23) increase in volume. If you quadruple the linear
dimensions from 1 mm to 4 mm, the volume increases by 43, or 64 times.

d. In general, how do SA/V ratios change as linear dimensions increase twofold?

If you compare the SA/V ratios among the cubes, you can see that as linear
dimension increases twofold (two times), the SA/V ratio is halved. (Note: This
assumes that the “organisms” under consideration retain the same general
shape—in this case, square.)

2. Assume a bacterium is 10 μm in linear dimension. Fill in the chart.

a. If modeled as a cube, what would its SA, V, and SA/V ratio be?
b. If modeled as a sphere, what would its SA, V, and SA/V ratio be?
c. What are the SA and V values and the SA/V ratios for a cube-shaped eukaryotic
cell that is 100 μm in linear dimension?

a. 10-μm bacterium b. 10-μm bacterium c. 100-μm eukaryote,

as a cube as a sphere cube-shaped
SA 6(10 μm)2 = 600 μm2 4πr2 = 3.14(5 μm)2 6(100 μm)2
= 314 μm2 = 6 3 104 μm2
V (10 μm)3 = 1,000 μm3 4/3 πr3 = 523.3 μm3 (100 μm)3
= 1,000,000 μm3
SA/V ratio 6 μm2/10 μm3 314 μm2/523.3 μm3 6 μm2/100 μm3
= 6.2 μm2/10 μm3

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 3. Assume that every cell requires a minimum of 1 unit of oxygen per μm3 per second
to stay alive. Fill in the chart.

a. How much oxygen must cross each μm2 of surface area per second in the 10-μm
bacterium versus the 100-μm eukaryote to keep each alive?
b. What effects might this difference have on metabolic rates in these organisms?

10-μm bacterium 100-μm eukaryote

a. Oxygen/μm of SA/second
2
10 units/6 μm /second
2
100 units/6 μm2/second
b. Possible effect(s) on The metabolic rate can be If there is any difficulty
metabolic rate relatively high. supplying oxygen at this
rate, the metabolic rate
would be lower
(compared to that of
the 10-μm bacterium).

4. Given what you know about cell membranes, is there likely to be a maximum upper
limit on the number of molecules of a substance that can cross a given area of
membrane per unit time? If so, what factors would be involved in determining the
maximum upper limit?

Because oxygen can diffuse through the phospholipid bilayer, its movement into the
cell would be limited only by its rate of diffusion and the total surface area available.
If we assume a finite maximum rate of diffusion, then aerobic cells would be limited
in their maximum size by this maximum rate.
If a substance requires a transport protein to facilitate its movement across the
membrane, then its maximum rate of movement into (or out of cells) would also be
limited by the total number of available transport proteins in the membrane.

As you answer questions 5, 6, and 7, fill in the chart on the next page.

5. (a) On average, how large is a prokaryotic genome? (b) On average, how many
times larger is a eukaryotic genome? (c) Are these genomes haploid or diploid?
(Hint: See Section 20.4 on pages 405–407 in Biological Science, 6th edition.)

(a) Prokaryotic genomes can contain from 500 to several thousand genes.

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 (b) In contrast, a eukaryotic genome can contain tens of thousands of genes. For
example, A. thaliana (plant) contains 28,000 genes; the human genome contains
approximately 25,000 genes.

(c) Many eukaryotic genomes are diploid. Prokaryotic genomes are haploid.

6. Under ideal conditions, many bacterial cells can reproduce or duplicate themselves
within an hour. Some species (for example, E. coli) can reproduce every 20 minutes
under ideal conditions. If you inoculate 1 liter of culture medium with one bacterium
per milliliter (of medium) at time t = 0, how many bacteria will be present in
1 milliliter of the culture medium after 10 hours?

In the first 20 minutes, the one bacterium will become two. The number will double
every 20 minutes over the next 9 hours and 40 minutes, or it will double during each
of the next 29 twenty-minute intervals. As a result, at the end of 10 hours, there will
be 229 bacteria in the flask (229 is approximately equal to 108).

(Note: This calculation assumes no limitations are placed on the ability of the
bacteria to grow and replicate as the number of bacteria increases over time.)

7. Assume the mutation rate of bacterial cells in culture is 10–6 to 10–8. This means
that in every 1 million to 100 million cells produced from a single original cell,
you would expect to find at least one mutation. How many mutations would you be
likely to find in 1 liter of the 10-hour culture of the cells you grew in question 6?

Prokaryote Eukaryote
Genome size 500–5000 genes ~30,000 genes
Haploid versus diploid Haploid Diploid
Maximum reproduction rate Every 20 minutes One hour to many hours
8
Mutation rate per hour If 10 bacteria contain one The mutation rate for
mutation, then 1000 ml of eukaryotic cells would
culture containing 108 be three to many times
bacteria per milliliter less.
would yield about 103 or
1000 mutations every
10 hours, or 100 per hour
on average.

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 8. Using all of the information in this activity, write an argument entitled: “How
small size in prokaryotes played a role in limiting their morphological diversity and
promoting their biochemical (metabolic) diversity.”
There are many possible ways to make this argument. All arguments should
mention that the genome of prokaryotes is haploid. As a result, any mutations have
immediate effects on the phenotype of the organism. High surface-area-to-volume
ratios mean metabolic rates can also be very high. High metabolic rates support
rapid reproduction (cell growth and fission), so the apparent rate at which mutations
show up in the population is much higher in prokaryotes.

Note: The metabolic rate depends a great deal on whether the prokaryote is aerobic
or anaerobic and on its other characteristics.

Arguments should also consider how the absolute mass or volume of an organism
can limit its morphology. A single cell 1 μm in diameter can assume only a
limited number of different shapes. Multicellular organisms, in contrast, are much
less limited in their morphology. Of course, they have many more cells and a
considerably greater volume per cell to work with.

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 Notes to Instructors
Chapter 27 protists

What is the focus?

This activity provides students with an overview of the early evolution of eukaryotic,
single-celled organisms. The first eukaryotes appear in the fossil record around
2.1 billion years ago. Current evidence indicates that eukaryotic cells arose as a result
of endosymbiosis (sometimes multiple endosymbioses) among ancestral prokaryotes.
The early eukaryotic cells that resulted underwent great diversification to become the
seven major groups of eukaryotes (see Figure 27.6 on page 545 in Biological Science,
6th edition).

Activity 27.1 How Has endosymbiosis Contributed to the diversity of

organisms on earth today?

What is this activity designed to do?

This activity is designed to help students begin to understand the vast diversity of the
protists as well as some of the evidence and thought processes that were involved in the
development of the endosymbiotic theory.

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 Answers

Activity 27.1 How Has endosymbiosis Contributed to the

diversity of organisms on earth today?

1. The protists have been called a “catch-all group.” What does this mean? Explain.
This is a paraphyletic group including all eukaryotes except those assigned to the
fungi, animal, or plant kingdoms. The protists range in size from microscopic
to macroscopic. Some of the large brown algae can be 60 m long. Many protists
have a characteristic overall form, organelles with distinctive features, or
both. All eukaryotes alive today, including all living protists, have a nucleus
and endomembrane system, mitochondria or genes that are normally found in
mitochondria, and a cytoskeleton.

2. There are more than 100,000 recognized species of protists. Even though the
organisms in this group are so diverse, we can recognize some common themes
in their evolution, including the evolution of complex cell structure, novel genetic
recombination strategies, and complex life cycles. In addition, this group as a whole
has great ecological importance. Provide at least two examples of protists from
Chapter 27 in Biological Science, 6th edition, that illustrate each theme.

Note: Any number of different examples can be used to answer the following questions.

Theme Examples

a. Complex cell Euglenida Contains light detector, eyespot, contractile

structure vacuole, pyrenoids, and chloroplast.
Paramecium Contains contractile vacuole, oral groove and cell
mouth, micro- and macronuclei, and cilia.
b. Novel genetic Paramecium Has micro- and macronuclei. The micronuclei
recombination function in sexual recombination and reproduction. The
strategies macronuclei function in growth, maintenance, and asexual
reproduction.
Laminaria Displays alternation of generations between
gametophyte (haploid) and sporophyte (diploid) multicellular
forms.
(Continued )

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 Theme Examples

c. Complex Plasmodium Has a two-host life history and causes malaria.

life cycles It reproduces asexually in its human host and sexually in its
mosquito host.
Cellular slime molds (e.g., Dictyostelium) Have a life cycle
that includes single-celled feeding amoebae (n). In the sexual
phase, haploid amoebas can fuse to form a zygote, which
immediately undergoes meiosis. Amoebae can also aggregate
to form colonies. The aggregate can develop into a stalked,
asexual fruiting body that gives rise to spores, which can
survive unfavorable environments.
d. Ecological All the species of photosynthetic protists (in association with the
importance cyanobacteria) provide the basis for the food webs of freshwater and
marine environments.
The absorptive or fungus-like protists aid in the decomposition
and recycling of organic matter (carbon compounds).

3. In the late 1960s (and since), Lynn Margulis provided considerable evidence for the
endosymbiotic theory of the origin of various organelles in eukaryotic cells.

a. What is the endosymbiotic theory?

The endosymbiotic theory proposes that eukaryotes originated when ancestral
prokaryotes (most likely archaeal species) engulfed formerly free-living prokaryotic
cells and enclosed them in vacuoles. These endosymbionts became major eukaryotic
organelles.

b. Which two eukaryotic organelles c. What evidence did Margulis present

were proposed to have arisen as to support each organelle as an
endosymbionts? endosymbiont?
Mitochondria Mitochondria are bounded by two
membranes. In addition, they contain their
own circular DNA (with no associated
histones) and 70s ribosomes. Some of the
inner membrane proteins are more similar
to those of prokaryotes than eukaryotes.

(Continued )

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 Chloroplasts Chloroplasts are also bounded by two
membranes. They also contain their own
circular DNA (with no associated histones)
and 70s ribosomes. Some of their inner
membrane proteins are more similar to those
of prokaryotes than eukaryotes.

4. The chloroplasts of the Discicristata, Chromalveolates, and Rhizaria are all thought
to have arisen as a result of secondary endosymbiosis.

a. What is secondary endosymbiosis?

Secondary endosymbiosis is said to occur when a heterotrophic eukaryote
engulfs a photosynthetic eukaryote, which then becomes an endosymbiont.

b. What evidence supports this idea of secondary endosymbiosis?

Evidence includes the following: The chloroplast is surrounded by four
membranes; it carries out photosynthesis in its own plastids.

5. Structurally, Giardia lamblia lacks complete mitochondria and was once thought to
be an example of what the earliest living eukaryotes may have looked like.
a. If Giardia is similar in structure to the earliest living eukaryotes, what does this
imply about the order of evolution of the various eukaryotic organelles (that is,
nucleus, cytoskeleton, mitochondria, chloroplasts)?
Giardia has several flagella and a double nucleus. However, it contains no
plastids and no functional mitochondria. Giardia’s structure indicates that the
double nucleus in eukaryotes evolved prior to the endosymbiosis of mitochondria
or chloroplasts.

b. We have since discovered that the diplomonads (e.g., Giardia) and the
parabasalids (the other group of excavates) have modified mitochondria.
• What types of mitochondria do they have?
Excavates contain nuclear genomes containing genes that are normally
found in mitochondria or unusual organelles that appear to be vestigial
mitochondria.
• What does this evidence indicate about the evolution of the various
eukaryotic organelles?
These observations support the hypothesis that the ancestors of excavates
had mitochondria, but that these organelles were lost or reduced over time.

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 6. The metabolic pathways of organisms living today evolved over a long period of
time—undoubtedly in a stepwise fashion because of their complexity. Considering
everything you have learned to date about the evolution of life on Earth, put
numbers 1–5 in the following blanks to indicate the order in which these organisms
might have evolved, and explain your arrangement. (Note: Some steps happen at the
same time and will be part of the same stage.)
3 prokaryotes capable of performing the Krebs cycle
4 eukaryotes capable of performing the Krebs cycle
2 prokaryotes capable of performing electron transport
4 eukaryotes capable of performing electron transport
1 prokaryotes capable of performing glycolysis
2 prokaryotes capable of performing photosynthesis
5 eukaryotes capable of performing photosynthesis

1—First, glycolysis in prokaryotes. It is found in all eukaryotes and many

prokaryotes. It takes place in the cytoplasm and can occur in the absence of oxygen.
Because eukaryotes arose as endosymbionts with prokaryotes, the prokaryotes
capable of photosynthesis and oxidative respiration must have evolved after the
prokaryotes capable of these processes.

2—Second, prokaryotic photosynthesis requires electron transport and produces

oxygen as a by-product. Neither the Krebs cycle nor electron transport can occur in
the absence of oxygen.
Electron transport is required to convert NADH to NAD+. Because glycolysis
produces 2 ATP (net) and 2 NADH, the addition of electron transport represents
an advantage. Organisms can then gain 8 ATP (net) from glycolysis plus electron
transport.

3—The Krebs cycle in prokaryotes cannot occur without a mechanism to convert

NADH to NAD+. Electron transport must have evolved before the Krebs cycle.

4—Eukaryotes capable of glycolysis, Krebs cycle, and electron transport (as

oxidative phosphorylation) are thought to have evolved due to endosymbiosis of an
amitochondrial organism and an aerobic bacterium.

5—Some of the eukaryotes with mitochondria are thought to have undergone

another endosymbiosis with a cyanobacterium to produce chloroplasts in
photosynthetic eukaryotic cells.

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