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CAMPBELL BIOLOGY IN FOCUS

2014 Pearson Education, Inc.

Urry Cain Wasserman Minorsky Jackson Reece

Lecture Presentations by

Kathleen Fitzpatrick and Nicole Tunbridge

24 Early Life and

the Diversification

of Prokaryotes


Earth formed 4.6 billion years ago

The oldest fossil organisms are prokaryotes dating back to 3.5 billion years ago

Prokaryotes are single-celled organisms in the domains Bacteria and Archaea

Some of the earliest prokaryotic cells lived in dense mats that resembled stepping stones

Overview: The First Cells


Prokaryotes are the most abundant organisms on Earth

There are more in a handful of fertile soil than the number of people who have ever lived

Prokaryotes thrive almost everywhere, including places too acidic, salty, cold, or hot for most other

organisms

Some prokaryotes colonize the bodies of other organisms


Concept 24.1: Conditions on early Earth made the origin of life possible

Chemical and physical processes on early Earth may have produced very simple cells through a sequence

of stages

1. Abiotic synthesis of small organic molecules

2. Joining of these small molecules into macromolecules

3. Packaging of molecules into protocells, membrane-

bound droplets that maintain a consistent internal

chemistry

4. Origin of self-replicating molecules


Synthesis of Organic Compounds on Early Earth

Earths early atmosphere likely contained water vapor and chemicals released by volcanic eruptions

(nitrogen, nitrogen oxides, carbon dioxide, methane,

ammonia, and hydrogen)

As Earth cooled, water vapor condensed into oceans, and most of the hydrogen escaped into space


In the 1920s, A. I. Oparin and J. B. S. Haldane hypothesized that the early atmosphere was a

reducing environment

In 1953, Stanley Miller and Harold Urey conducted lab experiments that showed that the abiotic

synthesis of organic molecules in a reducing

atmosphere is possible


However, the evidence is not yet convincing that the early atmosphere was in fact reducing

Instead of forming in the atmosphere, the first organic compounds may have been synthesized near

volcanoes or deep-sea vents

Miller-Urey-type experiments demonstrate that organic molecules could have formed with various

possible atmospheres

Organic molecules have also been found in meteorites

Video: Hydrothermal Vent Video: Tubeworms


Figure 24.3

Mass o

f

am

ino

acid

s (

mg

)

Nu

mb

er

of

am

ino

acid

s

1953 1953 2008

20

2008

10

0

200

100

0


Abiotic Synthesis of Macromolecules

RNA monomers have been produced spontaneously from simple molecules

Small organic molecules polymerize when they are concentrated on hot sand, clay, or rock


Protocells

Replication and metabolism are key properties of life and may have appeared together

Protocells may have been fluid-filled vesicles with a membrane-like structure

In water, lipids and other organic molecules can spontaneously form vesicles with a lipid bilayer


Adding clay can increase the rate of vesicle formation

Vesicles exhibit simple reproduction and metabolism and maintain an internal chemical environment


Figure 24.4

Vesicle boundary

Precursor

molecules only

1 m

Rela

tive t

urb

idit

y, a

n

ind

ex o

f vesic

le n

um

ber

(a) Self-assembly

Time (minutes)

0.4

0.2

0 0 20 40 60

Precursor molecules plus

montmorillonite clay

20 m

(c) Absorption of RNA (b) Reproduction


Self-Replicating RNA

The first genetic material was probably RNA, not DNA

RNA molecules called ribozymes have been found to catalyze many different reactions

For example, ribozymes can make complementary copies of short stretches of RNA


Natural selection has produced self-replicating RNA molecules

RNA molecules that were more stable or replicated more quickly would have left the most descendant

RNA molecules

The early genetic material might have formed an RNA world


Vesicles with RNA capable of replication would have been protocells

RNA could have provided the template for DNA, a more stable genetic material


Fossil Evidence of Early Life

Many of the oldest fossils are stromatolites, layered rocks that formed from the activities of prokaryotes

up to 3.5 billion years ago

Ancient fossils of individual prokaryotic cells have also been discovered

For example, fossilized prokaryotic cells have been found in 3.4-billion-year-old rocks from Australia


Figure 24.5

Time (billions of years ago)

10 m 30

m

5 c

m

Nonphotosynthetic bacteria

Cyanobacteria

Stromatolites

Possible earliest appearance in fossil record

4 3 2 1 0


The cyanobacteria that form stromatolites were the main photosynthetic organisms for over a

billion years

Early cyanobacteria began the release of oxygen into Earths atmosphere

Surviving prokaryote lineages either avoided or adapted to the newly aerobic environment


Concept 24.2: Diverse structural and metabolic adaptations have evolved in prokaryotes

Most prokaryotes are unicellular, although some species form colonies

Most prokaryotic cells have diameters of 0.55 m, much smaller than the 10100 m diameter of many eukaryotic cells

Prokaryotic cells have a variety of shapes

The three most common shapes are spheres (cocci), rods (bacilli), and spirals


Figure 24.6

3

m

(a) Spherical (b) Rod-shaped (c) Spiral

1

m

1

m


Cell-Surface Structures

A key feature of nearly all prokaryotic cells is their cell wall, which maintains cell shape, protects the cell, and

prevents it from bursting in a hypotonic environment

Eukaryote cell walls are made of cellulose or chitin

Bacterial cell walls contain peptidoglycan, a network of modified sugars cross-linked by polypeptides


Archaeal cell walls contain polysaccharides and proteins but lack peptidoglycan

Scientists use the Gram stain to classify bacteria by cell wall composition

Gram-positive bacteria have simpler walls with a large amount of peptidoglycan

Gram-negative bacteria have less peptidoglycan and an outer membrane that can be toxic


Figure 24.7

Peptido- glycan layer

Cell wall

Gram-negative bacteria

10 m

Gram-positive bacteria

(b) Gram-negative bacteria

(a) Gram-positive bacteria

Plasma membrane

Plasma membrane

Peptidoglycan layer

Cell wall

Outer membrane

Carbohydrate portion of lipopolysaccharide


Many antibiotics target peptidoglycan and damage bacterial cell walls

Gram-negative bacteria are more likely to be antibiotic resistant

A polysaccharide or protein layer called a capsule covers many prokaryotes


Figure 24.8

Bacterial cell wall

Bacterial capsule

Tonsil cell

200 nm


Some bacteria develop resistant cells called endospores when they lack an essential nutrient

Other bacteria have fimbriae, which allow them to stick to their substrate or other individuals in a

colony

Pili (or sex pili) are longer than fimbriae and allow prokaryotes to exchange DNA


Figure 24.9

Fimbriae

1 m


Motility

In a heterogeneous environment, many bacteria exhibit taxis, the ability to move toward or away

from a stimulus

Chemotaxis is the movement toward or away from a chemical stimulus


Most motile bacteria propel themselves by flagella scattered about the surface or concentrated at one

or both ends

Flagella of bacteria, archaea, and eukaryotes are composed of different proteins and likely evolved

independently


Figure 24.10

Flagellum

Filament 20 nm

Hook Motor Cell wall

Rod

Peptidoglycan layer

Plasma membrane


Figure 24.10a

20 nm

Hook

Motor


Evolutionary Origins of Bacterial Flagella

Bacterial flagella are composed of a motor, hook, and filament

Many of the flagellas proteins are modified versions of proteins that perform other tasks in bacteria

Flagella likely evolved as existing proteins were added to an ancestral secretory system

This is an example of exaptation, where existing structures take on new functions through descent

with modification


Internal Organization and DNA

Prokaryotic cells usually lack complex compartmentalization

Some prokaryotes do have specialized membranes that perform metabolic functions

These are usually infoldings of the plasma membrane


Figure 24.11

Respiratory membrane

0.2 m 1 m

Thylakoid membranes

(a) Aerobic prokaryote (b) Photosynthetic prokaryote


The prokaryotic genome has less DNA than the eukaryotic genome

Most of the genome consists of a circular chromosome

The chromosome is not surrounded by a membrane; it is located in the nucleoid region

Some species of bacteria also have smaller rings of DNA called plasmids


Figure 24.12

Plasmids

1 m

Chromosome


There are some differences between prokaryotes and eukaryotes in DNA replication, transcription,

and translation

These allow people to use some antibiotics to inhibit bacterial growth without harming themselves


Nutritional and Metabolic Adaptations

Prokaryotes can be categorized by how they obtain energy and carbon

Phototrophs obtain energy from light

Chemotrophs obtain energy from chemicals

Autotrophs require CO2 as a carbon source

Heterotrophs require an organic nutrient to make organic compounds


Energy and carbon sources are combined to give four major modes of nutrition

Photoautotrophy

Chemoautotrophy

Photoheterotrophy

Chemoheterotrophy


Table 24.1


The Role of Oxygen in Metabolism

Prokaryotic metabolism varies with respect to O2

Obligate aerobes require O2 for cellular respiration

Obligate anaerobes are poisoned by O2 and use fermentation or anaerobic respiration, in which

substances other than O2 act as electron acceptors

Facultative anaerobes can survive with or without O2


Nitrogen Metabolism

Nitrogen is essential for the production of amino acids and nucleic acids

Prokaryotes can metabolize nitrogen in a variety of ways

In nitrogen fixation, some prokaryotes convert atmospheric nitrogen (N2) to ammonia (NH3)


Metabolic Cooperation

Cooperation between prokaryotes allows them to use environmental resources they could not use as

individual cells

In the cyanobacterium Anabaena, photosynthetic cells and nitrogen-fixing cells called heterocysts (or

heterocytes) exchange metabolic products


Figure 24.13

20 m

Heterocyst

Photosynthetic cells


In some prokaryotic species, metabolic cooperation occurs in surface-coating colonies called biofilms


Reproduction

Prokaryotes reproduce quickly by binary fission and can divide every 13 hours

Key features of prokaryotic biology allow them to divide quickly

They are small

They reproduce by binary fission

They have short generation times


Adaptations of Prokaryotes: A Summary

The ongoing success of prokaryotes is an extraordinary example of physiological and

metabolic diversification

Prokaryotic diversification can be viewed as a first great wave of adaptive radiation in the evolutionary

history of life


Prokaryotes have considerable genetic variation

Three factors contribute to this genetic diversity

Rapid reproduction

Mutation

Genetic recombination

Concept 24.3: Rapid reproduction, mutation, and genetic recombination promote genetic diversity in prokaryotes


Rapid Reproduction and Mutation

Prokaryotes reproduce by binary fission, and offspring cells are generally identical

Mutation rates during binary fission are low, but because of rapid reproduction, mutations can

accumulate rapidly in a population

High diversity from mutations allows for rapid evolution

Prokaryotes are not primitive but are highly evolved


Figure 24.14 Experiment

0.1 mL (population sample)

Results

Daily serial transfer

Old tube (discarded after transfer)

New tube (9.9 mL growth medium)

Po

pu

lati

on

gro

wth

rate

(r

ela

tive t

o a

ncestr

al

po

pu

lati

on

)

Generation

10,000 20,000 15,000 5,000 0

1.8

1.6

1.4

1.2

1.0


Genetic Recombination

Genetic recombination, the combining of DNA from two sources, contributes to diversity

Prokaryotic DNA from different individuals can be brought together by transformation, transduction,

and conjugation

Movement of genes among individuals from different species is called horizontal gene transfer


Transformation and Transduction

A prokaryotic cell can take up and incorporate foreign DNA from the surrounding environment in a

process called transformation

Transduction is the movement of genes between bacteria by bacteriophages (viruses that infect

bacteria)


Figure 24.15-1

1 Phage infects bacterial donor cell with A and B alleles.

Donor cell

A B

Phage DNA


Figure 24.15-2

2


Phage DNA is replicated and proteins synthesized.

Donor cell

A B

A B

Phage DNA


Figure 24.15-3

3

2



Fragment of DNA with A allele is packaged within a phage capsid.

Donor cell

A

A

B

A B

Phage DNA


4

3

2




Phage with A allele infects bacterial recipient cell.

Recipient cell

Crossing over

Donor cell

A B

A

A

A

B

A B

Phage DNA

Figure 24.15-4


Figure 24.15-5

Phage infects bacterial donor cell with A and B alleles.

Incorporation of phage DNA creates recombinant cell with genotype AB.



Phage with A allele infects bacterial recipient cell.

Recombinant cell

Recipient cell

Crossing over

Donor cell

A B

A B

A

A

A

B

A B

Phage DNA

5

4

3

2

1


Conjugation and Plasmids

Conjugation is the process where genetic material is transferred between prokaryotic cells

In bacteria, the DNA transfer is one way

In E. coli, the donor cell attaches to a recipient by a pilus, pulls it closer, and transfers DNA


Figure 24.16

Sex pilus

1 m


The F factor is a piece of DNA required for the production of pili

Cells containing the F plasmid (F+) function as DNA donors during conjugation

Cells without the F factor (F) function as DNA recipients during conjugation

The F factor is transferable during conjugation


Figure 24.17-1

1 One strand of F cell plasmid DNA breaks at arrowhead.

Bacterial chromosome


F plasmid

Mating bridge

F cell (donor)

F cell (recipient)


Figure 24.17-2

2 1 One strand of F cell plasmid DNA breaks at arrowhead.



F plasmid

Mating bridge

F cell (donor)

F cell (recipient)

Broken strand peels off and enters F cell.


Figure 24.17-3

3 2 1 One strand of F cell plasmid DNA breaks at arrowhead.



F plasmid

Mating bridge

F cell (donor)

F cell (recipient)


Donor and recipient cells synthesize complementary

DNA strands.


Figure 24.17-4

4 3 2 1 One strand of F cell plasmid DNA breaks at arrowhead.



F plasmid

Mating bridge

F cell (donor)

F cell (recipient)

F cell

F cell


Recipient cell is now a recombinant F cell.

Donor and recipient cells synthesize complementary

DNA strands.


The F factor can also be integrated into the chromosome

A cell with the F factor built into its chromosomes functions as a donor during conjugation

The recipient becomes a recombinant bacterium, with DNA from two different cells


R Plasmids and Antibiotic Resistance

Genes for antibiotic resistance are carried in R plasmids

Antibiotics kill sensitive bacteria, but not bacteria with specific R plasmids

Through natural selection, the fraction of bacteria with genes for resistance increases in a population

exposed to antibiotics

Antibiotic-resistant strains of bacteria are becoming more common


Concept 24.4: Prokaryotes have radiated into a diverse set of lineages

Prokaryotes have radiated extensively due to diverse structural and metabolic adaptations

Prokaryotes inhabit every environment known to support life


An Overview of Prokaryotic Diversity

Applying molecular systematics to the investigation of prokaryotic phylogeny has produced dramatic

results

Molecular systematics led to the splitting of prokaryotes into bacteria and archaea

Molecular systematists continue to work on the phylogeny of prokaryotes


The use of polymerase chain reaction (PCR) has allowed for more rapid sequencing of prokaryote

genomes

A handful of soil may contain 10,000 prokaryotic species

Horizontal gene transfer between prokaryotes obscures the root of the tree of life


Bacteria

Bacteria include the vast majority of prokaryotes familiar to most people

Diverse nutritional types are scattered among the major groups of bacteria

Video: Tubeworms


Figure 24.19a

Alpha subgroup Beta subgroup

Gamma subgroup Delta subgroup Epsilon subgroup

Rhizobium (arrows) (TEM)

Nitrosomonas (TEM)

Thiomargarita namibiensis (LM)

Helicobacter pylori (TEM)

Chondromyces crocatus (SEM)

Proteo- bacteria

Alpha

Beta

Gamma

Delta

Epsilon

2.5

m

1

m

2

m

300

m

200

m


Proteobacteria are gram-negative bacteria including photoautotrophs, chemoautotrophs, and

heterotrophs

Some are anaerobic and others aerobic


Members of the subgroup alpha proteobacteria are closely associated with eukaryotic hosts in

many cases

Scientists hypothesize that mitochondria evolved from aerobic alpha proteobacteria through

endosymbiosis

Example: Rhizobium, which forms root nodules in legumes and fixes atmospheric N2

Example: Agrobacterium, which produces tumors in plants and is used in genetic engineering


Members of the subgroup beta proteobacteria are nutritionally diverse

Example: the soil bacterium Nitrosomonas, which converts NH4

+ to NO2


The subgroup gamma proteobacteria includes sulfur bacteria such as Thiomargarita namibiensis

and pathogens such as Legionella, Salmonella, and

Vibrio cholerae

Escherichia coli resides in the intestines of many mammals and is not normally pathogenic


The subgroup delta proteobacteria includes the slime-secreting myxobacteria and bdellovibrios, a

bacteria that attacks other bacteria


The subgroup epsilon proteobacteria contains many pathogens including Campylobacter, which

causes blood poisoning, and Helicobacter pylori,

which causes stomach ulcers


Figure 24.19b

Spirochetes Cyanobacteria


Chlamydias

Leptospira (TEM)

Oscillatoria

Streptomyces (SEM)

Chlamydia (arrows) (TEM)

Mycoplasmas (SEM)

2.5

m

40

m

5

m

2

m

5

m


Chlamydias are parasites that live within animal cells

Chlamydia trachomatis causes blindness and nongonococcal urethritis by sexual transmission


Spirochetes are helical heterotrophs

Some are parasites, including Treponema pallidum, which causes syphilis, and Borrelia burgdorferi,

which causes Lyme disease


Figure 24.19bb

Spirochetes

Leptospira, a spirochete (colorized TEM)

5

m


Cyanobacteria are photoautotrophs that generate O2

Plant chloroplasts likely evolved from cyanobacteria by the process of endosymbiosis


Figure 24.19bc

Cyanobacteria

Oscillatoria, a filamentous cyanobacterium

40

m


Gram-positive bacteria include

Actinomycetes, which decompose soil

Streptomyces, which are a source of antibiotics

Bacillus anthracis, the cause of anthrax

Clostridium botulinum, the cause of botulism

Some Staphylococcus and Streptococcus, which can be pathogenic

Mycoplasms, the smallest known cells


Figure 24.19bd


Streptomyces, the source of many antibiotics (SEM)

5

m


Figure 24.19be


Hundreds of mycoplasmas covering a human fibroblast cell (colorized SEM)

2

m


Archaea

Archaea share certain traits with bacteria and other traits with eukaryotes


Figure 24.UN02

Eukarya

Bacteria

Archaea


Table 24.2


Table 24.2a


Table 24.2b


Some archaea live in extreme environments and are called extremophiles

Extreme halophiles live in highly saline environments

Extreme thermophiles thrive in very hot environments

Video: Cyanobacteria (Oscillatoria)


Figure 24.20


Methanogens produce methane as a waste product

Methanogens are strict anaerobes and are poisoned by O2

Methanogens live in swamps and marshes, in the guts of cattle, and near deep-sea hydrothermal

vents


Recent metagenomic studies have revealed many new groups of archaea

Some of these may offer clues to the early evolution of life on Earth


Concept 24.5: Prokaryotes play crucial roles in the biosphere

Prokaryotes are so important that if they were to disappear, the prospects for any other life surviving

would be dim


Chemical Recycling

Prokaryotes play a major role in the recycling of chemical elements between the living and nonliving

components of ecosystems

Chemoheterotrophic prokaryotes function as decomposers, breaking down dead organisms

and waste products


Prokaryotes can sometimes increase the availability of nitrogen, phosphorus, and potassium for plant

growth

Prokaryotes can also immobilize or decrease the availability of nutrients


Figure 24.22

Seedlings growing in the lab

Soil treatment

Up

take o

f K

by p

lan

ts (

mg

)

Strain 1 Strain 2 Strain 3 No bacteria

1.0

0.8

0.6

0.4

0.2

0


Ecological Interactions

Symbiosis is an ecological relationship in which two species live in close contact: a larger host and

smaller symbiont

Prokaryotes often form symbiotic relationships with larger organisms


In mutualism, both symbiotic organisms benefit

In commensalism, one organism benefits while neither harming nor helping the other in any

significant way

In parasitism, an organism called a parasite harms but does not kill its host

Parasites that cause disease are called pathogens


The ecological communities of hydrothermal vents depend on chemoautotrophic bacteria for energy


Impact on Humans

The best-known prokaryotes are pathogens, but many others have positive interactions with humans


Mutualistic Bacteria

Human intestines are home to about 5001,000 species of bacteria

Many of these are mutualists and break down food that is undigested by our intestines


Pathogenic Bacteria

Prokaryotes cause about half of all human diseases

For example, Lyme disease is caused by a bacterium and carried by ticks


Figure 24.24

5 m


Pathogenic prokaryotes typically cause disease by releasing exotoxins or endotoxins

Exotoxins are secreted and cause disease even if the prokaryotes that produce them are not present

Endotoxins are released only when bacteria die and their cell walls break down


Horizontal gene transfer can spread genes associated with virulence

For example, pathogenic strains of the normally harmless E. coli bacteria have emerged through

horizontal gene transfer


Prokaryotes in Research and Technology

Experiments using prokaryotes have led to important advances in DNA technology

For example, E. coli is used in gene cloning

For example, Agrobacterium tumefaciens is used to produce transgenic plants


Bacteria can now be used to make natural plastics

Prokaryotes are the principal agents in bioremediation, the use of organisms to remove

pollutants from the environment

Bacteria can be engineered to produce vitamins, antibiotics, and hormones

Bacteria are also being engineered to produce ethanol from waste biomass


Figure 24.UN03


Figure 24.UN04

Fimbriae

Cell wall

Capsule

Flagella

Sex pilus

Internal organization

Circular chromosome


Figure 24.UN05

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