27 - Bacteria and Archaea

8/12/2019 27 - Bacteria and Archaea

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27 - Bacteria and Archaea

Prokaryotic Structural and Functional AdaptationsBasic Characteristics of Prokaryotes

Most are unicellular (some remain attached after cell division)

Cells typically .5-5 micrometers in diameter (much smaller than eukaryotes) Well organized - all life's functions in one cell

Cell-Surface Structures

Cell wall - protects cell, maintains shape, prevents bursting in hypotonic environments(hypertonic causes plazmolyzation, inhibiting reproduction)

Bacterial cell walls contain peptidoglycan (polymer composed of modified sugars cross-linked by short polypeptides)

"molecular fabric" encloses entire bacterium and anchors other molecules thatextend from its surface

Archaeal cell walls contain various polysaccharides and proteins, but no peptidoglycan Gram stain - classifies bacterial species into two groups based on cell wall composition

Process: Sample stained with crystal violet dye

Sample rinsed with alcohol

Sample stained with red dye (like safranin)

Gram positive - simpler walls with lots of peptidoglycan, which traps crystal violetin the cytoplasm - masks red safranin, appears purple

Gram negative - complex walls with lipopolysaccharides and very littlepeptidoglycan, so crystal violet is easily rinsed - red safranin shows, appears

pink/red

Medical applications: Gram negative bacteria - lipopolysaccharides are toxic (cause

fever/shock), outer-membrane protects from body's defenses, tend to be

more resistant to antibiotics than Gram-positive bacteria Gram positive bacteria - some virulent strains are multi-drug resistant Effectiveness of some antibiotics (penicillin) derives from their ability to

inhibit peptidoglycan cross-linking - decreases cell wall functionality Does not harm most human cells (which have no peptidoglycan)

Prokaryote cell wall surrounded by a capsule - sticky layer of polysaccharide or proteinwhich is dense and well defined

Called a slime layer if it is less well organized

Enable adherance to their substrate or other individuals in a colony

Can protect against dehydration and the host's immune system

Fimbriae - hairlike appendages that allow prokaryotes to stick to substrate or each other(shorter and more numerous than pili)


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Pili (sometimes called sex pili) - appendages that pull two cells together prior to DNAtransfer from one cell to the other

Motility

Taxis - directed movement toward or away from a stimulus (1/2 of all prokaryotes arecapable)

Chemotaxis - changes movement pattern in response to chemicals

Flagella - most common motile element, either scattered over the body or concentratedat one end

1/10 width of eukaryotic flagella; not covered by an extension of membrane

Flagella of prokaryotes are different in molecular composition and mechanism ofpropulsion than eukaryotic flagella

Bacterial and archaeal flagella are similar in size and mechanism, but arecomposed of different proteins

Flagella of eukaryotes, bacteria, and archaea are most likely analogous Bacterial flagella probably evolved through exaption (was a secretory system,

and other proteins were added over time that made it a flagellum)

Internal Organization - DNA

Prokaryotes lack the complex compartmentalization of eukaryotics

Some prokaryotic cells do have specialized membranes that perform metabolic functions

Prokaryotic genome is structurally different and usually has much less DNA

Genome is usually a circular chromosome with far fewer proteins than eukaryotes

Nucleoid - region of the cytoplasm that appears lighter than the surrounding cytoplasm inelectron micrographs; contains the chromosomes

May also have plasmids - smaller rings of independently replicating DNA; generally carryonly a few genes

Prokaryotic ribosomes tend to be smaller and differ in protein and RNA content

Reproduction and Adaptation

Binary fission - allows prokaryotes to reproduce very quickly in favorable environments

Reproduction is limited by nutrient supply, the toxicity of their own metabolic waste,competition from other microorganisms, and consumption by other organisms

Key features: Small

Reproduce by binary fission

Short generation times

Can exist as large populations (in the millions)

Biochemical and/or structural adaptations allow some prokaryotes to withstand harshenvironments


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Endospores - resistant cells developed by some bacteria when they lackessential nutrients; original cell hides copy of chromosome in endospore, which

lies dormant until conditions improve

High generation rate allows fast evolution and adaptation

Genetic Diversity in ProkaryotesRapid Reproduction and Mutation

New mutations are rare (and generally occur by errors in DNA replication) but canincrease genetic diversity quickly in species with short generation times and large

populations

Diversity can lead to rapid evolution

Genetic Recombination

In eukaryotes, sexual process of meiosis and fertilization foster genetic recombination

Prokaryotes use transformation, transduction, and conjugation Transformation - genotype (and possibly phenotype) of a prokaryotic cell one

altered by the uptake of foreign DNA from the surroundings Many bacteria have cell-surface DNA-recognizing proteins

Transduction - phages carry prokaryotic genes from one host cell to another Phage infects donor cell

Phage DNA replicates; phage proteins halt host cell's protein synthesis

and host cell's DNA may be fragmented

New phages assemble, perhaps carrying host cell alleles in a phage

capsid

Phage carrying donor allele infects recipient cell; recombination betweendonor and recipient DNA occurs

Genotype of resulting recombinant cell differs from donor and recipient

Conjugation - DNA is transferred between two prokaryotic cells (usually of thesame species) that one temporarily joined

In bacteria, DNA transfer is always one way In E. coli(best understood):

Pilus of the donor cell attaches to recipient cell

Pilus retracts, pulling the cells together

Possible formation of "mating bridge" - DNA is transferred

Ability to form pili and donate DNA due to the F (fertility) factor (piece of

DNA)

F plasmid - F factor in plasmid form; F+

cells have F plasmid and

donates DNA to F-cells (which lack the F factor); if F plasmid

copy is transferred, F-cell becomes an F

+cell

Hfr (high frequency recombination) cell - F factor is built into


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chromosome, so chromosomal genes may be transferred

Hfr cell acts like F+

cell

When chromosomal DNA from an Hfr cell enters an F-cell,

homologous regions of Hfr and F

-

chromosomes may align- DNA can be exchanged

R plasmids - carry antibiotic-resistant genes

Antibiotics kill many, but not all, bacteria

Natural selection supports proliferation of bacteria with R plasmids

Many can also form pili and enable conjugation

Any are multi-antibiotic resistant

Nutritional and Metabolic AdaptationsTrophic Types

Phototrophs - obtain energy from light

Chemotrophs - obtain energy from chemicals

Autotrophs - need only CO2in some form as a carbon source

Heterotrophs - require at least 1 organic nutrient (ex: glucose)

Combinations lead to 4 major nutritional modes

Mode Energy source Carbon source Type of organism

Photoautotroph LightCO2, HCO3

-, etc

Photosynthetic prokaryotes

Chemoautotroph Inorganic

chemicalsCO2, HCO3

-, etc

Some prokaryotes

Photoheterotroph Light Organic

compounds

Some aquatic and salt-loving

prokaryotes

Chemoheterotroph Organic

compounds

Organic

compounds

Many prokaryotes

Oxygen and Metabolism

Obligate aerobes - must use O2for cellular respiration Obligate anaerobes - poisoned by oxygen

Some live exclusively by fermentation

Anaerobic respiration - substances other than oxygen act as oxidizing agents inETCs

Facultative anaerobes - use oxygen when present but carry out fermentation or


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anaerobic respiration in an anaerobic environment

Nitrogen Metabolism

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

Nitrogen fixation - bacteria convert atmospheric nitrogen to ammonia

Some cyanobacteria and some methanogens (archaea) are very good - self-sufficient

Important to other organisms (plants, particularly)

Metabolic Cooperation

Cells work together to perform metabolic functions not otherwise possible; generallytakes place in specialized cells of a filament

Cyanobacteria Anabaena: some photosynthesize, others fix nitrogen

Heterocysts - fix nitrogen; surrounded by thickened cell wall to protect from

oxygen Intercellular connections transfer fixed nitrogen and carbohydrates

Biofilms - surface coating prokaryotic colonies that often exhibit cooperation

Cells secrete signaling molecules to recruit other cells

Cells produce proteins and polysaccharides that let them stick to substrate andeach other

Channels allow transport of nutrients and waste

Molecular Systematics

Genetic diversity of prokaryotes is immense Entire prokaryotic genomes can be obtained from environmental samples using

metagenomics

Horizontal gene transfer is significant in prokaryotic evolution

Comparing the Three Domains of Life

Characteristic Bacteria Archaea Eukarya

Nuclear envelope +

Membrane-enclosed

organelles

+

Peptidoglycan in cell wall + -

Membrane lipids Unbranched HCs Some branched

HCs

Unbranched

HCs

RNA polymerase One kind Several kinds Several kinds


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Initiator amino acid for protein

synthesis

Formyl-methionine Methionine Methionine

Introns in genes Very rare Present in some Present in many

Response to some antibiotics Inhibited Not inhibited Not inhibited

Histones associated with DNA In some +

Circular chromosome + + -

Growth at >100degrees

Celsius In some -

Archaea

Extremophiles - can survive in extreme environments

Extreme halophiles - live in highly saline environments; some tolerate the salt,others (Halobacterium) require it

Extreme thermophiles - thrive in very hot environments

Have adaptations in DNA and proteins that prevent denaturing

Methanogens - release methane as a byproduct of their metabolism

Strict anaerobes

Live in extreme and moderate environments; swamps, guts of animals

Decompose sewage in waste-treatment facilities

Euryarchaeota - includes all methanogens, many extreme halophiles, and some extreme

thermophiles Crenarchaeota - contains most extreme thermophiles

Korarcheota - discovered in a 1996 sample in Yellowstone park

Nanoarchaeota - very small; originally found clinging to a crenarchaeote

Bacteria

Proteobacteria - all gram-negative, and includes photoautotrophs, chemoautotrophs, andheterotrophs; includes anaerobes and aerobes; 5 recognized subgroups:

Alpha proteobacteria - closely associated with eukaryotic hosts: endosymbiotic

theory maintains that mitochondria evolved from aerobic alpha proteobacteria

Beta proteobacteria - nutritionally diverse group including nitrogen-recyclingNitrosomonas

Gamma proteobacteria - include sulfur-producing bacteria, Salmonella,

Legionella, Vibrio cholerae, and E. coli

Delta proteobacteria - include slime-secreting myxobacteria and offensive

bdellovibrios

Epsilon proteobacteria - most are pathogenic to humans and other animals;

includes Campylobacter (blood poisoning, intestinal inflammation) and


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Helicobacter pylori (ulcers)

Chlamydias - can only survive within animal cells; gram-negative, lack peptidoglycan Chlamydia trachomatis - most common cause of blindness; most common STD

in the US

Spirochetes - helical heterotrophs that travel by rotation; most are free living but someare pathogenic parasites

Treponema pallidum - syphilis Borrelia burgdorgeri - Lyme disease

Cyanobacteria - photoautotrophs; only prokaryotes with plant-like oxygen-generatingphotosynthesis

Endosymbiotic theory: chloroplasts likely evolved from cyanobacteria

Gram-positive bacteria - rival proteobacteria in diversity Actinomycetes - most decompose organic matter in soil (some cause leprosy or

TB) Bacillus anthracis - anthrax Clostridium botulinum - botulism Also includes Staphylococcus and Streptococcus Mycoplasmas - very small; only bacteria known to lack cell walls

Prokaryotes and the BiosphereChemical Recycling

Decomposers - break down dead organisms and waste products

Chemoheterotrophic prokaryotes and fungi

Prokaryotes can convert molecules to forms other organisms can use

Cyanobacteria - use carbon dioxide to make sugars; produce oxygen Variety of prokaryotes fix atmospheric nitrogen into usable forms

Prokaryotes can increase and decrease availability of resources for plant growth(nitrogen, phosphorus, potassium, etc)

Ecological Interactions

Symbiosis - two species live in close contact with each other

Prokaryotes (symbionts) often form symbiotic relationships with larger organisms(hosts)

Mutualism - both species benefit

Commensalism - one species benefits, the other is not helped or harmed Parasitism - parasite eats cell contents, tissues, or body fluids of the host

Parasites harm but usually do not kill the host (immediately)

Pathogens - parasites that cause disease; many are prokaryotic

Chemoautotrophic bacteria harvest energy from thermal vents to support communitieson the ocean floor, where sunlight does not reach


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Prokaryotes and HumansMutualistic Bacteria

Many kinds live in intestines, helping to digest various foods

Bacterium digests food and synthesizes carbohydrates, vitamins, and other nutrients

Signals from bacterium activate human genes which build the network of intestinal blood

vessels necessary to absorb nutrients

Other signals induce production of antimicrobial compounds to kill competitors

Pathogenic Bacteria

All known pathogenic prokaryotes are bacteria

Some carried by pests (ex: ticks and Lyme disease

Usually cause illness by producing poisons

Exotoxins - proteins secreted by certain bacteria and other organisms

Vibrio cholerae secretes exotoxin causing cholera - stimulates intestinalcells to release chloride ions; water follows by osmosis, leading to violent

diarrhea and dehydration

Clostridium botulinum - secretes exotoxin causing botulism as it fermentsin food

Endotoxins - lipopolysaccharide components of the outer membrane of gram-negative bacteria (ex: Salmonella)

Improved sanitation and antibiotics have reduced threat, but antibiotics may also helpcreate super-bacteria

Horizontal gene transfer can make normally harmless bacteria into pathogens O157:H7 - very dangerous strain of E. coli, probably introduced by transduction

Prokaryotes in Research and Technology

E. coli used to clone genes

Agrobacterium tumefaciens - helps produce transgenic crops

PHA (polyhydroxylalkanoate) harvested from bacteria can be used in bioplastics

Bioremidiation - use of organisms to remove pollutants from soil, air, or water

Treating sewage, cleaning oil spills, precipitating radioactive material out ofgroundwater

27 - Bacteria and Archaea

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