Bio II Prokaryotes CH 22

Conditions on earth during prehistoric times

• no free oxygen

• radiation

• volcanic activity

Origins of living cell : Hypotheses

• Deep see vents

• asteroids

  • panspermia- spreading seeds throughout the cosmsos

Early life: Microbial mats

• multilayers of prokaryotes carrying out different metabolic pathways — similar to those found around hydrothermal vents in the pacific ocean.

stromatolites

• first fossil evidence of prokaryotic life — 3.5 million years ago

• australia ( shark bay) layers of microbes separated by carbonate or silicate layers

  • ancient

  • sedimentary formations

  • hypersaline conditions

  • mats of cyanobacteria

  • evidence of prehistoric bacteria

role of prokaryotes: oxtgen producers

• Cyanobacteria- basic producers

• credited for changing early atmosphere ( ozone layer)

  • 2.3 billion years ago

• photoautographs

• symbionts with other organisms

  • (ex. fungi + cyanobacteria = lichen)

Bacteria vs. Archaea

• both prokaryotes but differ enough to be placed in separate domains

• an ancestor of modern archaea is believed to have given rise to eukarya, the third domain of life.

• Archae and bacteria phyla are shown ; the evolutionary relationship between these phyla is still open to debate

Prokaryotes

• bacteria and archaea are dominant life forms ( ½ words biomass)

• teaspoon od soil: billions of microbes

• marine archaea: over 10000 individuals per ml seawater

• 10000 species named : 700 species in human mouth, 1000 in gut

Characteristics

• are two of the three largest branches on the tree of life

• are unicellular

• lack a membrane-bound nucleus

• unique types of molecules that make up plasma membrane and cell walls

• machinry they use to transcribe DNA and translate mRNA into proteins

• ancient, diverse, abundant, and ubiquitous ( everywhere)

Prokaryotic diversity

• oldest, structurally simplest, and most abundant forms of life

• abundant for over a billion years before eukaryotes

• 90 to 99% unknown and undescribed

  • large scale sequencing of random samples indicates the vast majority of bacteria

• less that 1% cause disease

• fall into two domains

  • bacteria ( eubacteria)

  • archaea (archaebacteria

    • many archaeans are extremophiles ( live in extreme environments)

Bacteria

• No nuclear envelope

• no membrane bound organelles

• peptidoglycan in cell walls

• un-branched membrane lipids

• simple RNA polymerase

• protein synthesis initiated by formyl methionine

• growht inhibited by antibiotics streptomycin and chloramphenicol

• circular chromosomes

• no histone proteins

• not possible for growth above 100C

• no introns

archaea

• no nuclear envelope

• no membrane bound organelles

• no peptidoglycan in cell walls

• some branched membrane lipids

• several kinds of RNA polymerase e

• protein synthesis initiated by methionine (AA)

• growth is not inhibited by antibiotics

• circular chromosomes

• some with histone proteins

• growth above 100C

• some introns ( noncoding DNA)

Eukarya

• nuclear envelope

• membrane bound organelles

• absent peptidoglycan in cell walls

• unbranched membrane lipids

• several kinds of RNA polymerase

• protein synthesis initiated by methionine (AA)

• growth is not inhibited by antibiotics

• linear chromosomes '

• histone proteisn

• not possible for growth above 100 C

• introns in genes

Prokaryotic cell morphology

• smallest

  • most bacteria are about 1 micrometer in diamerter but some are much larger

• from rods to spheres to spirals. In some species, cells adhere to form chains

• some bacteria are non -motile, but swimminf and gliding are common

Newer molecular classification system

1. amino acid sequence of key proteins

2. percent guanine-cytosine content

3. nucleic acid hybridization

   • closely relted species will have more base pairing

4. gene and RNA sequencing

   • especially with rRNA

5. whole-genome sequencing

History of Microbiology

• Robert Koch studied anthrax and proposed four postulates to prove a casual relationship between a microorganisms and an individual

  1. The microorganisms must be present in every case of the disease and absent from healthy individuals

  2. the putative causative agent must be isolated and grown in pure culture

  3. the same disease must result when the cultured microorganism is used to infect a healthy host

  4. the same microorganism must be isolated again from the diseased host

The germ theory

• Infectious diseases spread in three main ways :

  1. passed from person to person

  2. transmitted by bites from insects or animals

  3. acquired by ingesting contaminated food or water, or exposure to microbes in surrounding environment

• Koch’s postulates are the causative link between a specific disease and a specific microbe ( not by bad air)

What makes some bacterial cells pathogenic

• virulence

  • heritable, variable trait

• some species have both pathogenic virulent strains and harmless strains

  • Escherichia coli: genomes of pathogenic strains are larger because they have acquired virulence genes

  • E.g, a gene that codes for a protein toxin.

pathogenic

ability to cause disease

virulence

degree to which a disease is spread or causes damage

Endospores

• tough, thick-walled, dormant structures formed during times of environmental stress

• produced by some pathogenic bacteria

• contain a copt of cell’s DNA, RNA, ribosomes , and enzymes

• metabolic activity stops and original cell breaks down

• resistant to high temperatures , UV radiation, and antibiotics

• resume growth as actively dividing cells in favorable conditions

• involved in transmiting disease to humans

Antibiotics

• molecules that kill bacteria or stop them from growing

• produced naturally by some soil bacteria and fungi

• discovered in 1928; widespread use by 1940s

• extensive use has led to evolution of drug-resistant strains of pathogenic bacteria

• Biofilms

Biofilms

bacterial colonies emeshed in polysaccharide - rich matrix that shield bacteria from antibiotics

Examples of human impact : bacteria

Dental caries ( tooth decay)

• plaque consists of bacterial biofilms

• steptoccus sobrinus ferments sugar to lactic acid

• tooth enamel degenerates

Peptic ulcers

• Helicobacter pyloric is the main cause

• treated with antibiotics

Other treatments for prokaryotes

• beauty treatments

• probiotics

• food production

• biological control agents

• Genetic engineering

• vaccine production

• Additives for dairy products

• additives for fermentation

• seeding (bioaumentation)

• fertilization (N2 fixation)

Prokaryote insights into life

• abilities of extremophiles

• origins of life

• extraterrestrial life

• comercial applications

• taq polymerase

Three domains of life

• Bacteria

• Archaea

• Eukarya

Role of Prokaryotes : Nitrogen fixers

• Nitrogen is an essential building block of proteins and nucleic acids

• N₂ is abundant but needs to be converted to ammonia or nitrate

• nitrogenase in a few bacteria and archaea ( anaerobic habitats)

• found as symbionts ( legumes) and free living cells (heterocysts )

• Drive the nitrogen cycle

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Role of prokaryotes: nitrates and bacteria pollutants

• Marine blooms

• anoxic dead zones in the ocean

Prokaryote: Genetic Variation

• asexual (binary fission) haploid cells (no meiosis)

• Genetic variation achieved

  • Transformation

  • Transduction

  • Conjugation

Transformation

• the cell takes up prokaryotic DNA directly from the environment

• The DNA ay remain separate as plasmid DNA or be incorporated into the host genome.

Transduction

• a bacteriophage injects DNA into the cell that contains a small fragment of DNA from a different prokaryote

Conjugation

• DNA is tranferred from one cell to another via a pilus that connects the two cells

Natural transformation

• Occurs in many bacterial species

• Dna that is released from a dead cell is picked up by another live cell

• proteins involved in transformation are encoded by bacterial chromosome

  • not an accident like plasmid or phage biology

Light

phototroph

chemicals

chemotroph

organic material ( electron source)

organotroph

inorganic material

lithotroph

organic material ( carbon source)

heterotroph

carbon dioxide

autotroph

How do biologists study microbes?

• enrichment cultures

• metagenomics and direct sequencing

Actinobacteria

• common in soil and freshwater habitats

• Morphology

  • Cells found as rods or filaments

  • some form chains or branching chains ( called mycelia)

• Metabolism

  • Chemoheterotrophs

  • us a variety of organic electron donors and oxygen as an electron acceptor

  • several are parasites

  • some fix nitrogen

• Relevance

  • member of this group cause tuberculosis and leprosy

  • produce hundreds of antibiotics

Chlamydiae

• Common in host cells of many vertebrates

• Morphology

  • spherical cells

  • found in clusters

  • very small ( as small as some viruses)

• Metabolism

  • Chemoheterotrophs

  • all species live as parasites inside host cells

  • can produce atp by electron transport

• Relevanve

  • The sexually trasmitted disease caused by chlamydia trachomatic can lead to ectopic pregnancy and infertility

Cyanobacteria

• common in lakes, rivers, oceans

• Morphology

  • Filaments, spheres, spirals.

  • individual cells, chains, or colonies

  • some contain heterocysts where nitrogen fixation occurs

• Metabolism

  • Photoautographs

  • involved in nitrogen fixation

  • form symbiotic relationships with fungi ( called lichens) and with protists, sponges, and legume plants

• Relevance

  • Responsible for the origin of earth’s oxygen rich atmosphere

  • some involved in harmful algae blooms

  • provide much of the nitrogen used by other organisms

Firmicutes

• Common in the human gut

• Morphology

  • Most are rods or spheres

  • many form chains of four cells

  • one group produces a cell wall made of cellulose

  • some produce a durable resting stage called an endospore

• Metabolism

  • chemoheterotrophs

  • some fix nitrogen

  • some perform anoxygenic photosynthesis

  • some can use hydrogen gas as an electron donor

• Relevance

  • Members of this group cause anthrax, boutilism, tetanus, gangrene, streo throat.

  • Bacillus thuringiensis produces BT toxin, an important insecticide

  • some are use in yogurt production and cheese production

Proteobacteria

• common in aquatic environments and as pathogens

• Morphology

  • diverse morphology

  • rods, spheres, spirals

  • some form colonies that agregate into a fruiting body and produces reproductive spores at their tips

• Metabolism

  • most are heterotrophs or chemoautotrophs

  • some contain bacteriochlorophyll and obtain energy through photosynthesis

• Relevance

  • Escherichia coli and agrobacteria are often used in biotechnology

  • members of this group cause cholera, food poisoning, plague, dysentery, typhus

Spirochaetes ( spirochetes)

• Common in the gut of animals and as pathogens

• Morphology

  • Cork-screw shaped

  • found as individual cells

  • Flagella are found inside cells and cause cells to move in a spiral fashion

• Metabolism

  • Chemoheterotophs

  • produce atp via fermentation

  • can thrive in anaerobic conditions

• Relevance

  • Members of this group are responsible for leotispirosis, syphilis, and lyme disease

  • corkscrew like movement enables cells to burrow into host tissue.

Crenarchaeota ( eocytes)

• Common in sulfur rich hot springs acidic environments, and deep ocean sediments

• Morphology

  • Rods, spheres, filaments, and discs

  • flagella are common

  • some use protein fibers that help attach to sulfur granules

  • one species produces a gycoprotein cell wall

• Metabolism

  • Chemoheterotrophs and chemolithoautotrophs

  • use sulfur, hydrogen gas, or Fe+ as electron donors

  • some make atp only by fermentation

• Relevance

  • May be the only life forms in etremely hot, high pressure, acidic environments

Euryarchaeota

• Diverse habitats ( human gut, highly acidic and alkaline enviroments, deep ocean sediments)

• Morphology

  • rods, spheres, filaments, spirals, and discs

  • found as clusters or chains

  • flagella are common

  • some lack cell wall

• Metabolism

  • chemoheterotrohs and chemolithoautotrophs

  • many produce methane as a by-product of repsiration

• Relevance

  • some members found near abandoned mnes and produce acids that pollute streams

  • Methanogens ( found in guts of mammals and swamps) add billions of tons of methane to the atmosphere each year

Thaumarchaeota

• common in fresh and saltwater habitats

• Morphology

  • rod shaped

  • found as individual cells

• Metabolism

  • Chemolithoautotrophs

  • use ammonia as a source of energy and produce nitrate as a by product

• Relevance

  • Only a few members of the group have been observed

  • very abundant in oceans

  • one member lives as an endosymbiont in marine sponges

How do the various "tree of life" models compare to each other? How were they built?

• Darwin’s Tree (1859)

  • Idea: All organisms descend from a common ancestor, branching over time.

  • Built from: Morphological (physical) similarities and fossil evidence.

  • Limitation: Couldn’t account for microbes well and had no genetic data.

• Traditional 5-Kingdom Model (Whittaker, 1969)

  • Kingdoms: Monera (bacteria), Protista, Plantae, Fungi, Animalia.

  • Built from: Morphology, cell structure (prokaryote vs. eukaryote), nutrition.

  • Limitation: Lumped all bacteria together and oversimplified microbes.

• Three-Domain System (Carl Woese, 1977)

  • Domains: Bacteria, Archaea, Eukarya.

  • Built from: Molecular data — especially ribosomal RNA (rRNA) sequences.

  • Key insight: Archaea are genetically closer to Eukarya than to Bacteria, even though they look like bacteria.

  • Strength: First tree based on molecular evidence, not just physical traits.

• Modern Phylogenomic Trees

  • Built from: Whole-genome sequencing and large datasets (proteins, DNA, RNA).

  • Features: Much more detailed, showing horizontal gene transfer (especially among microbes), not just vertical descent.

  • Limitation: Some branches are still debated because of gene swapping between organisms.

   What are some challenges to studying prokaryotes? 

• Microscopic size – Prokaryotes are extremely small, making them hard to observe without specialized equipment.

• Lack of distinctive features – Many look similar under a microscope, so morphology alone doesn’t tell species apart.

• Difficult to culture – The majority of prokaryotes cannot be grown in lab conditions (they may need very specific nutrients, temperatures, or environments).

• High diversity – They are extremely diverse and numerous, so it’s hard to identify and classify them all.

• Horizontal gene transfer (HGT) – Genes can move between unrelated species, blurring evolutionary relationships and making classification complex.

• Rapid evolution – Their short generation times and high mutation rates mean traits can change quickly, complicating long-term study.

• Extreme habitats – Some archaea live in places like boiling springs or salt flats, which are difficult for researchers to replicate in the lab.

Gram positive bacteria

• Thick peptidoglycan layer (20–80 nm).

• Contains teichoic acids, which provide structural support and help in ion transport.

• No outer membrane.

• Retains the crystal violet stain during Gram staining → appears purple under the microscope.

Gram negative bacteria

• Thin peptidoglycan layer (2–7 nm).

• Has an outer membrane outside the peptidoglycan, containing lipopolysaccharides (LPS) that can act as toxins.

• Contains a periplasmic space between the inner and outer membranes.

• Does not retain the crystal violet stain; instead takes up the counterstain (safranin) → appears pink/red under the microscope.

what makes prokaryotes so successful

• Simplicity & Efficiency – Small cell size and simple structure let them reproduce and adapt quickly.

• Rapid Reproduction – Binary fission allows fast population growth; mutations spread quickly.

• Genetic Flexibility – Horizontal gene transfer (via plasmids, transformation, transduction, conjugation) lets them share traits like antibiotic resistance.

• Metabolic Diversity – They can use a wide range of energy sources (light, chemicals, organic and inorganic compounds).

• Ability to Survive Extreme Environments – Many prokaryotes (especially archaea) live in boiling hot springs, salt flats, deep oceans, and even inside rocks.

• Protective Adaptations – Some form endospores to survive harsh conditions (heat, radiation, desiccation).

• Symbiotic Relationships – They live in close partnerships with other organisms (e.g., gut microbiome in humans, nitrogen-fixing bacteria in plants).

• Global Abundance – Found everywhere: soil, water, air, and inside other organisms — making them extremely adaptable.

Difference between the use of vaccines and antibiotics

• Vaccines 💉

  • Purpose: Prevent disease before it happens.

  • How they work: Contain weakened, killed, or parts of pathogens (like proteins or mRNA) that stimulate the immune system to produce memory cells.

  • Target: Viruses and bacteria (depending on the vaccine).

  • Effect: Long-term protection by preparing the immune system.

• Antibiotics 💊

  • Purpose: Treat bacterial infections after they occur.

  • How they work: Kill bacteria or stop them from reproducing (e.g., by blocking cell wall synthesis or protein production).

  • Target: Only bacteria (not viruses).

  • Effect: Short-term treatment; doesn’t provide immunity. Overuse can lead to antibiotic resistance.

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Eutrophication

• the process where a body of water (like a lake, river, or pond) becomes overly enriched with nutrients, especially nitrogen and phosphorus.

• Cause: Often comes from fertilizer runoff, sewage discharge, or industrial waste.

• Process:

  1. Excess nutrients enter the water.

  2. Algae grow rapidly (algal bloom).

  3. When algae die, decomposers break them down, consuming oxygen.

  4. Oxygen levels drop → hypoxia.

  5. Aquatic life (fish, plants, invertebrates) may die due to lack of oxygen.

• Effects

  • Algal blooms block sunlight from reaching underwater plants.

  • Oxygen depletion harms fish and other aquatic animals.

  • Can create dead zones (areas with little to no oxygen).

  • Harms water quality → unsafe for drinking or recreation.