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Bacteria & Archaea (Ch 27) (Comparison & Contrast of Prokaryote…
Bacteria & Archaea (Ch 27)
Structure and Functions of Prokaryotes
Prokaryotes were the first organisms to inhabit the Earth
Most are unicellular, although some species form colonies
Prokaryotic cells have a variety of shapes
Spherical prokaryotes (Cocci)
Rod-shaped prokaryotes (Bacilli)
Spiral prokaryotes (Spirilla or spirochetes)
Prokaryotic cell walls
Their cell wall maintains:
Cell shape
Protects the cell
Prevents it from bursting in a hypotonic environment
Most bacterial cell walls contain
peptidoglycan,
a network of sugar polymers cross-linked by polypeptides
Archaea 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 contains lipopolysaccharides (carbohydrates linked to lipids)
Gram staining can determine if a patient's infection is due to
gram negative
or to
gram positive
bacteria
Many antibiotics target peptidoglycan and damage bacterial cell walls
Gram positive
bacteria are particularly susceptible to this type of antibiotics
Gram-negative
bacteria also tend to be more resistant than gram-positive species b/c of their outer membrane impedes entry of the drugs
Prokaryotic functions of their features
Capsule
This capsule enables adherance to their substrate or to other individuals
Can shield pathogenic bacteria from their host's immune system
The cell wall of many prokaryotes are surrounded by a sticky outer layer of polysaccharide or protein called a
capsule
Endospores
They can become metabolically inactive and resume when their environment improves
Can remain viable in harsh conditions for centuries
In order to withstand harsh conditions certain bacteria develop resistant cells called
endospores
when they lack water or essential nutrients
Fimbriae
Fimbriae are usually shorter and more numerous than a
pili
Some prokaryotes have hairlike appendages called
fimbriae
that allow them to stick to their substrate or other individuals in a colony
Pili
A
pili
(singular pilus) are longer than fimbriae and allow prokaryotes to exchange DNA
Pili
is sometimes referred as sex pili
Nucleoid
The
nucleoid
, is a region of cytoplasm that is not enclosed by a membrane
Chromosomes are located in the
nucleoid
region
Plasmid
Prokaryotic also have smaller rings of independently replicating DNA molecules called
plasmids
Most carrying only a few genes
Motility
About half of all prokaryotes exhibit
taxis
, the ability to move toward or away from a stimulus
For Example: chemotaxis is the movement toward or away from a chemical stimulus
Flagella
are the most common structures used by prokaryotes fro movement
Flagella
may be scattered about the surface or concentrated at one or both ends of the cell
Bacterial & Archaeal flagella are similar in size & rotational mechanism but they are composed of entirely different & unrelated proteins
Bacterial flagella has 3 main parts the (motor, hook, & filament) they are themselves composed of 42 different kinds of proteins
Most of the proteins in the flagella are modified versions of bacterial proteins with different functions
Flagella likely evolved as existing proteins were added to an ancestral secretory system
This is an example of an
exaptation
, where structures adapted fro one function take on new functions through descent with modification
Internal organization & DNA
Cells of prokaryotes are simpler than those of eukaryotes in both their internal structure & the physical arrangement of their DNA
Prokaryotic cells usually lack the complex compartmentalization associated with the membrane-enclosed organelles found in eukaryotic cells
Some prokaryotes do have specialized membrane that perform metabolic functions
These are usually infoldings of the plasma membrane
The genome of a prokaryotic cell is structurally different from a eukaryotic genome and in most cases has less DNA
For prokaryotes most of the genome consists of circualar chromosomes
For eukaryotes they have a linear chromosome
There are some differences between between prokaryotes & eukaryotes in DNA replication, transcription & translation
These differences allow people to use certain antibiotics to inhibit bacterial growth without harming themselves
Certain antibiotics bind to ribosomes and block protein prokaryotes but not in eukaryotes
Prokaryotic ribosomes are slightly smaller than eukaryotic ribosomes & differ in their protein & RNA content
Reproduction
Many prokaryotes can reproduce quickly by binary fission and can divide every 1-3 hours under optimal conditions
Key features of prokaryote biology:
They are small
They reproduce by binary fission
They have short generation times
3 factors contribute to this genetic diversity:
(prokaryotes have considerable genetic variation)
Rapid Reproduction
Prokaryotes reproduce asexually; offspring cells are generally identical (to original parent cell)
Genetic variation can result from a combination of rapid reproduction & mutation
For Example: Escherichia coli cells reproduce using binary fission
Mutation
Mutation rates are low but, can increase genetic diversity quickly in species with short generation times & large populations
Prokaryotes have simpler cells than eukaryotes but their rapid adaptation to environmental change indicates that they are highly evolved
Genetic Recombination
Additional source of variation in prokaryotes also arise from
genetic recombination
, the combining of DNA fro the two sources (contributes to diversity)
Prokaryotic DNA from different cells can be brought together by:
Transformation
A Prokaryotic cell can take up & incorporate foreign DNA from the surrounding environment in a process called
transformation
The cell is now a recombination: Its chromosome contains DNA derived from 2 different cells
Cell surface proteins recognize DNA from closely related species & transport it into the cell. Once inside the cell, the foreign DNA can be incorporated into the genome by homologous DNA exchange
Transduction
In
transduction
, phages(from "bacteriophages") carry prokaryotes genes form one host cell to another (donor -> the recipient)
It results from accidents during the phage replicative cycle
If crossing over occurs after the transfer, genes from the donor may be incorporated into the recipients genome
Conjugation
In a process called
conjugation
, DNA is transferred between 2 prokaryotic cells
In bacteria, the DNA transfer is always one way
(One cell donates DNA, the other receives it)
A donor cell attaches to a recipient by a pilus, pulls it closer, and transfers DNA through a structure called the "mating bridge"
A particular piece of DNA called the
F factor
is required for the production of pili and the ability to donate DNA during conjugation
F factor in its plasmid form makes
F plasmid
Cells containing the
F plasmid
function as DNA donors during conjugation (F+ cells)
Cells without the F factor function as DNA recipients during conjugation (F- cells)
The F factor is transferrable during conjugation (F+ cell converts F- cell to F+ cell)
Provided some of the
F plasmids
DNA is transferred, the recipient cell becomes a recombinant cell
F factor
in the chromosome
A cell with the F factor built into its chromosome functions as a donor during conjugation
Such cells are called
Hfr cell
(for high frequency of recombination)
The recipient becomes a recombinant bacterium, with DNA from 2 different cells
R plasmids & Antibiotic Resistance
R plasmids
carry genes fro antibiotic resistance
Antibiotics kill sensitive bacteria, but not bacteria with specific
R plasmids
Through natural selection, the fraction of bacteria with genes for resistance increases in population exposed to antibiotics
Many
R plasmids
have genes that encode pili, making it possible for resistance genes to be transferred b/w bacterial cells
Some
R plasmids
carry genes for resistance to multiple antibiotics
Antibiotic resistant strains of bacteria are becoming more common, and the infections they cause are now harder to treat
Movement of genes among individuals from different species is called
horizontal gene transfer
Prokaryotes nutrition & metabolic adaptations
Prokaryotes are categorized by how they obtain energy & carbon. (There are 4 major modes of nutrition)
Phototrophs
obtain energy energy from light
Chemotrophs
obtain energy from chemicals
Autotrophs
require CO2 or related compounds as a carbon source
Photoautotrophy (#1 nutrition mode)
Energy source:
Light
Carbon source:
CO2
HCO3, or related compound
Types of Organisms:
Photosynthetic prokaryotes (for example, cyanobacteria); plants; certain protists (for example, algae)
Chemoautotrophy (#2 nutrition mode)
Energy source:
Inorganic chemicals
(such as H2S, NH3, or Fe)
Carbon source:
CO2
HCO3, or related compound
Types of Organisms
:
Unique to certain prokaryotes
(for example,
Sulfolobus
)
Heterotrophs
require an organic nutrient to make organic compounds
Photoheterotrophy (#3 nutrition mode)
Energy source
:
Light
Carbon source
:
Organic compounds
Types of Organisms
:
Unique to certain aquatic and salt-loving prokaryotes
(for example,
Rhodobacter
,
Chlorofelxus
)
Chemoheterotrophy (#4 nutrition mode)
Energy Source
:
Organic compounds
Carbon source
:
Organic compounds
Types of Organisms
:
Many prokaryotes (for example,
Clostridium
) and protists; fungi; animas; some plants
Metabolic adaptations
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 live by fermentation or use substances other than O2 known as
anaerobic respiration
Facultative anaerobes
can use O2 if it is present or carry out fermentation or anaerobic respiration if it
is not
Nitrogen Metabolism
:
Nitrogen is essential for the production of amino acids and nucleic acids in all organisms
Prokaryotes can metabolize nitrogen in a variety of ways
For Example: Some prokaryotes covert atmospheric nitrogen (N2) to ammonia (NH3) in a process called
nitrogen fixation
Metabolic Cooperation:
Cooperation between prokaryotes allows them to use environmental resources they could not use as individual cells
This cooperation takes place between specialized cells of a filament
For instance: in the cyanobacterium
Anabaena
, photosynthetic cells and nitrogen-fixing cells called
heterocysts
(or heterocytes) exchange metabolic products
Metabolic cooperation occurs between different prokaryotic species in surface-coating colonies called
biofilms
Another example of cooperation:Sulfate-consuming bacteria and methane-consuming bacteria on the ocean floor use each other’s waste products
Prokaryotic Diversity
Prokaryotes now inhabit every environment known to support life
Advances in genomics are beginning to reveal the extent of prokaryotic diversity
Genetic analysis led to the division of prokaryotes into two domains:
Bacteria & Archaea
Archaea
Archaea share certain traits with bacteria and other traits with eukaryotes
They also have many unique characteristics
Some archaea live in extreme environments and are called
extremophiles
Extreme halophiles
live in highly saline environments
Extreme thermophiles
thrive in very hot environments
Bacteria
Bacteria include the vast majority of prokaryotic species familiar to most people
Diverse nutritional types are represented among bacteria
Characteristics of the 3 Domains of Life:
Bacteria
Archaea
Eukarya
Nuclear Envelope
:
Bacteria: Absent
Archaea: Absent
Eukarya: Present
Membrane-enclosed organelles:
Bacteria: Absent
Archaea: Absent
Eukarya: Present
Peptidoglycan in cell wall:
Bacteria: Present
Archaea: Absent
Eukarya: Absent
Membrane lipids:
Bacteria: Unbranched hydrocarbons
Archaea: Some branched hydrocarbons
Eukarya: Unbranched hydrocarbons
RNA polymerase:
Bacteria: One kind
Archaea: Several kinds
Eukarya: Several kinds
Initiator amino acid for protein synthesis:
Bacteria: Formyl-methionine
Archaea: Methionine
Eukarya: Methionine
Response to the antibiotics strep-tomycin & chloramphenicol:
Bacteria: Growth usually inhibited
Archaea: Growth not inhibited
Eukarya: Growth not inhibited
Histones associated with DNA:
Bacteria: Absent
Archaea: Present in some species
Eukarya: Present
Circular chromosome:
Bacteria: Present
Archaea: Present
Eukarya: Absent
Growth at temperatures >100C:
Bacteria: No
Archaea: Some species
Eukarya: No
The use of polymerase chain reaction (PCR) has allowed for more rapid sequencing of prokaryote genomes
Horizontal gene transfer between prokaryotes obscures the root of the tree of life (evolution of prokaryotes)
A few taxonomic groups are monophyletic, but others are scattered throughout several lineages
Prokaryotes roles in the biosphere
Prokaryotes are important that if they were to disappear the prospects for any other life surviving on Earth would be dim
Chemical Recycling
Atoms that make up the organic molecules in all living things were at one time part of inorganic substances in soil, air, and water
Prokaryotes play a major role in the
recycling of chemical elements
between the living and nonliving components of the environment
For example: Some Some chemoheterotrophic prokaryotes function as
decomposers
, breaking down dead organisms and waste products
Decomposers therefore unlock supplies of carbon, nitrogen, and other elements
Prokaryotes can convert some molecules to forms that can be taken up by other organisms
For example: under some conditions, prokaryotes can
increase
the availability of nutrients required for plant growth
Prokaryotes can also “immobilize” or
decrease
the availability of nutrients by using them in their own cells
Ecological Interactions
Prokaryotes play a central role in ecological interactions
Symbiosis
is an ecological relationship in which 2 species living in close contact with each other: the larger organism is known as the
host
and the smaller is known as
symbiont
Prokaryotes often form symbiotic relationships with larger organisms
In many cases the prokaryote and its host participate in
mutualism
, an ecological interaction where both organism benefit
Other interactions take the form of
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
Many of which are prokaryotic
Prokaryotes beneficial & harmful impacts
Mutualistic Bacteria
People depend on mutualistic prokaryotes, including hundreds of species that live in our intestines and help digest food
Different species live in different portions of the intestine, and they vary in theier ability to process different foods
Many of these species are mutualists and break down food that is undigested by our intestines
Pathogenic Bacteria
Pathogenic prokaryotes known to date are bacteria
Bacteria cause about half of all human diseases
Some bacterial diseases are transmitted by other species
For example: Lyme disease is caused by a bacterium and carried by ticks
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
Antibiotics are currently evolving in many bacterial strains
Giving the ability of resistant genes to be able to spread to other species via horizontal gene transfer
Horizontal gene transfer can spread genes associated with virulence
For Example: Pathogenic strains of of
E. coli
contain genes that were acquired through transduction
Prokaryotes in Research & Technology
Experiments using prokaryotes have led to important advances in DNA technology
For example, E. coli is used in gene cloning
For example, the prokaryotic CRISPR-Cas system can alter genes in other organisms
Prokaryotes can be used in the production of plastics, vitamins, antibiotics, and other products
Bacteria are also being engineered to produce ethanol from agricultural and municipal waste biomass, switchgrass, and corn
Prokaryotes can also be used in
bioremediation
, the use of organisms to remove pollutants from the environment
Comparison & Contrast of Prokaryote & Eukaryote
Prokaryotic
A prokaryotic cell is 0.5-5 qm much smaller
Prokaryotic flagella are one-tenth the width and typically are not covered by an extension of plasma membrane
Prokaryotic genome has less DNA
Genome consists of circular chromosomes
Lack a nucleus
Has a nucleoid region with no surrounding membrane
Prokaryotic ribosomes are slightly smaller
Meiosis and fertilization do not occur in prokaryotes
Nutritional diversity (how they obtain energy) is much broader along with having nutritional modes unique to prokaryotes
Eukaryote
A Eukaryotic cell is 10-100 qm
Eukaryotic genome has more DNA
Genome consists of linear chromosomes
Have a nucleus
Has nucleus with surrounding membrane
Eukaryotic ribosomes are larger
In eukaryotes the sexual process of meiosis and fertilization combine DNA from 2 individuals in a single zygote
Every type of nutrition observed in eukaryotes is represented among prokaryotes
Flagella of prokaryotes & eukaryotes differ in structure, mechanism of propulsion, and molecular composition
Prokaryotic cells usually lack the complex compartmentalization associated with the membrane-enclosed organelles found in eukaryotic cells
Prokaryotic and Eukaryotic ribosomes differ in their protein & RNA content
Unlike eukaryotes, prokaryotes can metabolize nitrogen in many different forms
