BIO 1120 EXAM 3

CH. 24, 25, 26

What Characteristics Have Enabled Prokaryotes to Thrive in Diverse Environments?

• Small size and rapid reproduction

• High genetic diversity through mutations (mutations dont occur as fast in euk, but short life span enable high genetic diversity)

• Rapid evolution of diverse adaptations

Conditions on early earth made the origin of life possible

• Earth formed 4.6 billion years ago, conditions were too volatile to support life

• first chemical signatures of life date back to 3.6 bya

• the earliest fossil evidence of organisms date to 3.5 bya (prokaryotes)

• prok were alone on earth until the first eukaryote cells appeared about 1.8 bya

Chemical and physical processes on early Earth could have produced simple cells in four stages

1. Abiotic synthesis of small organic molecules

2. Joining of small molecules into macromolecules

3. Packaging of molecules into protocells, droplets with membranes that maintain consistent internal chemistry

4. Origin of self-replicating molecules

Synthesis of organoc compounds on early earth

• Earths early atmosphere had little oxygen and likely contained water vapor and compounds released by volcanic erruptions

• As earth cooled, water vapor condensed into oceans and most hydrogen escaped to space

• Some evidence suggests that the early atmosphere was neither reducing nor oxidizing

Different models of early earth

• 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 showed experimentally that abiotic synthesis of organic moleculeswas possible in a reducing atmosphere

Abiotic synthesis of macromolecules

• small organic molecules (monomers0 can be produced spontaneously through abiotic synthesis

• amino acids and RNA nucleotides form macromolecules (polymers) without enzymes or ribosomes, when they are concentrated on hot sand, clay or rock

• such polymers may have functioned as weak catalysts for chemical reactions on early earth

protocells

• replication and metabolism are key properties of life that likely appeared together in early protocells

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

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

• Montmorillonite clay increases the rate of vesicle formation by concentrating molecules on its surface.

• Abiotically produced vesicles can “reproduce”, “grow”, and absorb molecules from their surroundings.

• Some vesicles have a selectively permeable bilayer and can perform metabolic reactions using external reagents.

Self-replicating RNA

• The first genetic material was likely RNA not DNA

• single stranded RNA molecules have three dimensional shapes, making catalytic function possible

• Ribozymes are RNA molecules that cna catalyze reactions, some are also self replicating

• Ribozyme copying errors could produce new faster repliacting shapes, those with more accurate self replication would leave more descendant molecules

• In 2013, researchers built a vesicle in which RNA self replication could occur, vesciles that could grow, divide, and pass on genetic material could produce protocells that evolvd by natural selection

RNA to DNA

• Life today was likely preceded by a RNA world

• Single-stranded RNA could have provided the template for DNA synthesis in protocells

• Double-stranded DNA is a more stable and accuratley replicated genetic material than RNA

Fossil evidence of early life

• Many of the oldest fossils are stromatolites, layered rocks that formed from theactivities of prokaryotes (earliest 3.5 bya)

• Stromatolites living today are frmed by cyanobacteria and other photosynthetic bacteria

• Stromatolites with distinct morphologies and habitats evolved 3.1 and 2.8 bya

• Stromatolites living today are formed by cyanobacteria and other photosyntheic bacteria

• The cyanobacteria were the main photosyntheic organisms for over a billion years

• Cyanobacteria transformed the atmosphere on early earth by reeasig oxygen produced by the photosynthesis

• surving prokaryote lineages either avodied or adapted to the newly aerobic environment

Diverse structural and metabolic adaptations have eviolved in prokayotes

• Most prokayotes are unicellular, some species form colonies

• Prokayotic cells typically have much smaller diameters than eukaryotic cells

• Prokayotes have a variety of cell shapes, including spheres (cocci), rods (bacilli), and spirals

Cell-surface structures

• Cells walls protect and maintain cell shape, prevent bursting in hypotonic environments, and cause plasmolysis in hypertonic environments

• Euk cell walls contain cellulose or chitin

• Bacterial cell walls contain peptidoglycan, a network of modififed sugars and polypeptides

• Archaeal cell wells contain polysaccarides and proteins but lack peptidogylcan

Gram positive bacteria

Bacteria have simpler cell walls compsed of a thick layer of peptidoglycan

(Biologists categorize bacteria based on cell wall composition determined by response to Gram stain)

Gram negative bacteria

Bacteria have less peptidoglycan and anouter membrane with lipopolysaccharides

Lipid portions of lipopolysaccharides can be toxic

capsule

• Many antibiotics target peptidoglycan and damage bacterial cell walls

• The outer-membrane protects gram-negative bacteria, increasing their antibiotic resistance

• Many prokaryotes also have a sticky, protective outer layer called a capsule that allows them to adhere to the substrate or each other

Endospores

When water or nutrients are lacking, some bacteria develop resistant cells called endospores

Endospores are dormant cells that can remian viable for centuries or survive extreme conditions

Prokaryotes sticking together

• Some prokaryotes stick to the substrate or each other using hairlike appendages called fimbriae

• Pili (or sex pili) are longer, less numerous appendages that are used to pull prokaryotes together during DNA transfer between cells

Motility

• About half of all prokaryotes exhibit taxis, the ability to move toward or away from a stimulus

• EX: chemotaxis- movement from or to a chemical stimulus

• Some species can move up to 50 times their body length per second

• Flagella the most common motility structure in prok, likeley eveolved independently in the 3 domains

• prok and euk flagella differ in structure, molecular composition, and mechanical function

• The flagella of bacteria and archaea are structurally similar, but composed of unrelated proteins

Evolutionary origins of bacterial flagella

• composed of three main parts (motor, hook, and filament) and 42 different proteins

• many of flagellas proteins are modified versions of proteins that preform other tasks in bacteria

• bacterial flagella are likely the examples of exaptation

Internal organization and DNA

• prokaryote cells lack the complex compartmentalization found in euk cells

• some prok have specialized infoldings of the plasma membrane that preform metabolic functions

• some store metabolic products in simple protein made compartments

• prok have less genomic DNA than euk, the DNA is in a singular circular chromosome in the nucleiod region

• some bacteria have small rings of DNA called plasmids

• prok and euk have differences in DNA replication, transcription, and translation

Nutritional and metabolic adaptations: Prokaryotes can be categorized by how they obtain energy and carbon

• Phototrophs obtain energy from light

• Chemotrophs obtain energy from organic compoundsor inorganic chemicals like H₂S

• Autotrophs use inorganic carbon sources like CO₂

• Heterotrophs obtain carbon from organic compounds

The role of oxygen in metabolism

• Prok metabolism varies with respect to O2

• Obligate aerobes require O2 for celluar respiration

• Obligate anaerobes are poisioned by O2 and will use fermentation or anaerobic respiration with other substances

• Facultative anaerobes can use O2 if present or not

Nitrogen Metabolism

Nitrogen is essential for the production of amino acids and nucleic acids in all organisms

• Eukaryotes cannot use atmospheric nitrogen N2

• Some prokaryotes use nitrogen fixation to convert atmospheric nitrogen N2 to ammonia NH3 that can be used by both prokaryotes and eukaryotes

Metabolic cooperation

• Some prok cells cooperate to make use of the otherwise unavailable resources (ex in anabaena, photosynthetic cells exchnage products with nitrogen fixing cells called heterocysts

• Cooperation between different prokaryotic species occurs in surface-coating colonies called biofilms

• Biofilms are common but can cause a wide range of problems for humans, including chronic infections, tooth decay, and contamination of medical devices

Three key features of their biology allow prokaryotes to reproduce rapidly in favorable environments

• Small cell size

• Binary fission

• Short generation times

Adaptations of prokaryotes: summary

• The ongoing success of prokaryotes is primarily the result of physiological and metabolic diversification

• Metabolic diversification of prokaryotes was the first great wave of adaptive radiation in the history of life

Prokaryotes have considerable genetic variation. Three factors contribute to this genetic diversity:

• rapid reproduction

• mutation

• genetic recombination

Rapid reproduction and mutation

• prok reproduce by binary fission, most offspring are identicial to parent

• mutations are rare, but bc generation times are so short, they accumulate quickly in a pop

• high genetic diversity allows for rapid evolution

• prok are not primitive, they are highly evolved

Genetic recombination

• genetic recombination is the combining of DNAs from two sources which contributes to diversity

• prok 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

• Transformation: prok cells alter their genotype with DNA taken up from the external environment

• Transduction: phages (viruses that infect bacteria) move prok genes from one host cell to another

Conjugation and plasmids

• Conjugation is a process by which genetic material is transfeerred directly between prok cells (E. coli exhibits this)

• In bacteria, DNA transfer is one way

• F factor genes can also be transferred between chromosomes during conjugation to form a recombinant bacterium

The F factor

• The F factor is a piece of DNA consisting of about 25 genes required for the production of pili

• it may be present in the chromosome or an f plasmid

• in conjugation, cells with the f plasmid (F+) donate DNA; cells without the F plasmid (F-) recieve DNA

• Transfer of the f plasmid converts an F- cell to a recombinant F+ cell

R plasmids and antibiotic resistance

• Antibiotic resistance genes can be carried in R plasmids

• Bacteria with resistance genes will survive exposure to antibiotics that kill bacteria without resistance genes

• Antibiotic treatment increases the frequency of resistant bacteria in the population by killing the sensitive bacteria

• Natural selection through widespread antibiotic use has made resistant strains of bacteria increasingly common

An overview of prokaryotic diversity

• Dramatic revision of the prokaryote phylogeny has resulted from molecular research started in the 1970s (molecular analysis led to split of proks into bacteria and archaea)

• New advances in molecular systematics have enabled the analysis of over 1,700 entire prokaryote genomes

• Metagenomics uses the polymerase chain reaction (PCR) to sequence DNA in environmental samples (reveals the huge diversity of prok)

• Molecular systematics has revealed the key role of horizontal gene transfer in the evolution of prok

Bacteria

• Include the majoirty of prok familiar to people

• every major mode of nutrition and metabolism is represented among bacteria, a wide variety of nutritional modes can be found even within small taxonomic groups

• about 16,000 known species (estimated unknown 700,000-1.4 million)

Proteobacteria

• Proteobacteria is a clade of gram-negative bacteria with diverse metabolic and nutritional modes

• Evidence indicates that mitochondria evolved by ensosymbiosis from a heterotrophic proteobacterium

Chlamydias

• Chlamydias are gram-negative parasites that can only live within animal host cells

Spirochetes

• Spirochetes are helical gram-negative heterotrophs

• They move in a spiral pattern by rotating internal, flagellum like filaments

• Many species are free-living but some are parasitic

Cyanobacteria

• Cyanobacteria are gram-negative photoautotrophs that generate O2 through plant-like photosynthesis

• Plant chloroplasts likely evolved from cyanobacteria by the process of endosymbiosis

• Cyanobacteria are abundant in freshwater and marina phytoplankton

Gram-positive bacteria

• Diverse group

• Actinomycetes are colony-forming bacteria composed mostly of soil decomposers and some pathogens

• Streptomyces are soil dwelling bacteria that are cultured as a source of antibiotics

• Other subgroups include pathogens such as Bacillus anthracis, which causes anthrax

Archaea

• Archaea have many unique traits, but they also share some traits in common woith bacteria and others with eukaryotes

• Some archaea are extremophiles that live in extreme environments

• Extreme halophiles either tolerate or require a highly saline environment

• Extreme thermophiles have adaptations that styablize DNA and proteins allowing them to thrive in extreme heat