*L3 Bacteria + Archeae

Prokaryote

Informal term for a tiny, single-celled organism with no nucleus and no membrane-bound organelles. Refers to Bacteria + Archaea together.

How old are the oldest fossil traces of prokaryotic life?

At least 3.5 billion years old, including fossil stromatolites.

How abundant and diverse are prokaryotes?

They are the most abundant and the most biochemically diverse organisms on Earth, and are found in every environment capable of supporting life.

Three major clades of Life

Bacteria, Archaea, Eukarya.

Which two major clades are most closely related?

Archaea and Eukarya — they are sister groups, and each is more closely related to the other than to Bacteria.

Why is "prokaryotes" NOT a clade?

A clade must contain a common ancestor and ALL of its descendants. Grouping Bacteria + Archaea leaves out Eukarya, even though Archaea are more closely related to Eukarya than to Bacteria. "Prokaryote" is defined by an absence (no nucleus), which is a shared-ancestral trait.

Typical size of prokaryotic cells

Mostly very small: about 0.5-5 μm.

Three basic prokaryotic cell shapes

Spherical, rod-shaped, spiral.

How can prokaryotic cells be arranged?

As individual cells, or in pairs, chains, or clusters.

Structure of the prokaryotic genome

No nucleus

• One large chromosome loop

• Smaller plasmid loops

Bacterial chromosome

The large loop of DNA carrying the cell's primary genetic information.

Plasmid

A small loop of DNA separate from the main chromosome; often carries accessory genes (including antibiotic-resistance genes) and can be transferred between cells.

Peptidoglycan

The material making up bacterial cell walls — sugars cross-linked by short amino acid chains, like a chain-link fence around the cell.

• Provides structure and resists environmental stress

Gram-positive bacteria

Have a THICK peptidoglycan cell wall and only one membrane.

Gram-negative bacteria

Have a THIN peptidoglycan cell wall PLUS a second outer membrane.

Antibiotic

A compound that kills bacteria or limits bacterial growth.

Why can antibiotics selectively target bacteria?

They attack structures bacteria have that our cells do not, such as peptidoglycan and bacterial ribosomes.

Why are Gram-negative bacteria often more resistant to treatment?

Their extra outer membrane makes it harder for drugs to reach the cell wall or get inside the cell.

Why can Gram-negative bacteria be more dangerous?

Their outer membrane can be toxic to the body, and it also makes them harder to treat.

How do prokaryotes reproduce?

By binary fission (splitting) — rapid asexual division, roughly every 20 minutes to 3 hours under favorable conditions.

What factors limit bacterial population growth?

• Nutrient supply

• Buildup of toxic metabolic waste

• Competition

• Being consumed by other organisms

What two things must all organisms acquire?

A source of energy and a source of carbon.

Phototroph

Gets energy from light.

Chemotroph

Gets energy from chemicals.

Autotroph

Gets carbon from CO2.

Heterotroph

Gets carbon from organic molecules (food).

Photoautotroph

Energy from light + carbon from CO2. Ex: cyanobacteria, plants

Chemoautotroph

Energy from chemicals + carbon from CO2. Ex: deep-sea sulfide-oxidizing bacteria

Photoheterotroph

Energy from light + carbon from organic molecules.

Chemoheterotroph

Energy from chemicals (food) + carbon from organic molecules. Ex: E. coli, animals, fungi

An organism oxidizes sulfide compounds for energy and gets carbon from CO2. What is it?

A chemoautotroph — "chemo" because energy comes from chemicals, "auto" because carbon comes from CO2.

Nitrogen fixation

Some prokaryotes convert atmospheric nitrogen gas (N2) into NH4+ or NO2-, forms of nitrogen that organisms can actually use.

Why is nitrogen fixation important?

It converts inert atmospheric N2 into nutrients required by ALL living organisms — it is the entry point of nitrogen into the biosphere.

Relationship between legumes and nitrogen-fixing bacteria

Legumes (clover, peas, beans) house nitrogen-fixing bacteria in root nodules — a mutualism.

How does nitrogen fixation benefit agriculture?

Legume-associated nitrogen fixers fertilize the soil naturally, which is why legumes are valuable in crop rotation and reduce the need for synthetic fertilizer.

Extremophile

An organism adapted to live in extreme conditions — extreme salt, heat, cold, pressure, and/or oxygen-deprived environments.

Are only Archaea extremophiles?

NO. Archaea are famous for it, but Bacteria can be extremophiles too.

Desulforudis

A bacterium living ~2 miles underground that indirectly uses the radioactive decay of uranium as its energy source.

Deinococcus

The "world's toughest bacterium"

— massive radiation resistance, and also withstands cold, acid, vacuum, and dehydration.

Endoparasite

A parasite that lives inside its host.

Lecture example: Chlamydia, which can only live inside animal cells.

About what proportion of prokaryotes can move in response to stimuli?

About one-half (~50%), using whip-like flagella.

Why are the flagella of Bacteria, Archaea, and Eukarya convergent structures?

They evolved independently in all three clades, with different structures and mechanisms

— they were not inherited from a shared flagellated ancestor.

Same function, different origin.

Endospore

A durable, dehydrated capsule formed by some bacteria that lets them survive harsh conditions for years.

• Emergency response structure, not reproduction

Which bacteria form endospores, and what do they cause?

• Clostridium → botulism, tetanus, C. diff

• Bacillus → anthrax, food poisoning

Biofilm

A surface-coating community formed when prokaryotes cooperate and share nutrients.

• Common example: dental plaque

• Biofilms strongly resist antibiotics

Why are prokaryotes important to ecosystems?

They act as decomposers, nitrogen fixers, and recyclers of chemicals and nutrients; photoautotrophic bacteria also produce a large share of atmospheric oxygen.

How can prokaryotes benefit human health?

Mutualistic bacteria of the human microbiome support digestion, nutrient supply, and defense against pathogens.

How are prokaryotes used in food production?

As cultures to make cheese and yogurt and to sour/ferment foods and drinks.

How are prokaryotes used to make medical products?

They can be genetically engineered to produce useful proteins, such as insulin.

Bioremediation

The use of microorganisms to break down or remove pollutants

— for example oil spills and plastics.

What role do bacteria play in human infectious disease?

They cause roughly one-half of human infectious diseases.

How have bacterial diseases affected human history?

Outbreaks such as plague, typhus, and cholera have shaped history and even human physiological evolution.

Leading infectious-disease killer worldwide (from lecture)

Tuberculosis (TB).

MRSA fact from lecture

MRSA causes about 10x more infections than all multi-drug-resistant Gram-negatives combined.

How does antibiotic resistance ORIGINATE?

Through random mutation.

Why does antibiotic resistance arise so quickly in bacteria?

High mutation rates + enormous population sizes + very short generation times mean rare beneficial mutations appear often.

What happens to resistant bacteria when antibiotics are present?

Resistance becomes a huge survival advantage, so resistant cells survive, reproduce, and quickly dominate the population (natural selection).

Three basic modes of bacterial gene transfer

1. Direct uptake 2. Viral transfer (transduction) 3. Conjugation

Direct uptake

Stray DNA — free fragments or plasmids — is picked up from the environment.

Viral transfer

A virus (bacteriophage) carries a gene from a donor bacterium to a recipient bacterium.

Conjugation

Direct DNA donation between bacteria through a temporary bridge; sometimes called "bacterial mating." The MOST COMMON route of resistance spread.

Why can antibiotic resistance spread so rapidly?

Mutation generates resistance, and gene transfer (especially conjugation) spreads it horizontally

— even between unrelated species

— so resistance does not have to be re-invented in each lineage.

How does inappropriate antibiotic use worsen resistance?

Using antibiotics when they are not needed (e.g., for viral infections) adds selection pressure that favors resistant bacteria without any benefit.

How can antibiotic resistance be slowed?

• Do not use antibiotics for viral infections

• Complete the full prescribed course

• Prescribe the narrowest-spectrum drug appropriate

• Reduce antibiotic use in livestock

LAB: Serial dilution

A stepwise series of dilutions in which the product of one step becomes the sample for the next, used to reduce a dense culture to a countable concentration.

LAB: Dilution factor of ONE step

Total volume ÷ volume of sample transferred.

Ex: 1 mL of sample into 9 mL of diluent = 10 mL total → 1/10 dilution (10^-1).

LAB: Total (final) dilution factor

The PRODUCT of the individual dilution factors. Ex: three 1/10 steps = 1/10 × 1/10 × 1/10 = 1/1,000 (10^-3).

LAB: How do you back-calculate the original concentration?

Original concentration = (number of colonies counted) ÷ (volume plated in mL × total dilution factor).

Equivalently: colonies ÷ volume plated × (1/dilution factor).

LAB: Worked example

Three 1/10 steps (total 10^-3), plate 0.1 mL, count 54 colonies. 54 ÷ (0.1 mL × 10^-3) = 54 ÷ 10^-4 = 5.4 × 10^5 CFU/mL.

LAB: Why dilute at all?

Undiluted cultures produce a lawn of overlapping colonies that cannot be counted.

Plates with roughly 30-300 colonies are countable and statistically reliable.

LAB: Common mistakes

• Forgetting the plated volume is not 1 mL

• Adding dilution factors instead of multiplying them

• Using the dilution of one step instead of the cumulative dilution

ESSAY: Explain how antibiotics work selectively, and why Gram-negatives are more dangerous and resistant

Antibiotics exploit structures unique to bacteria — peptidoglycan cell walls and bacterial ribosomes — so they can kill bacteria without destroying human cells. Gram-positive cells have a thick, exposed peptidoglycan wall, making them easier targets. Gram-negative cells have a thin wall plus an additional outer membrane that blocks many drugs from reaching the wall or entering the cell, so fewer antibiotics work on them. That same outer membrane can also be toxic to the human body, worsening the illness itself.

ESSAY: Describe the mode and rate of prokaryotic reproduction and the factors that limit growth

Prokaryotes reproduce asexually by binary fission, dividing roughly every 20 minutes to 3 hours under good conditions, which produces exponential growth. Growth does not continue indefinitely because nutrients run out, toxic metabolic wastes accumulate, competitors use the same resources, and predators/phages consume the population. Rapid division plus huge population size is also why beneficial mutations, including resistance, appear so quickly.

ESSAY: Explain how antibiotic resistance originates and how it spreads

ORIGIN: random mutation. Because bacteria have high mutation rates, enormous populations, and short generation times, resistance mutations arise constantly. When antibiotics are present, resistance confers a major survival advantage, so resistant cells survive and rapidly dominate. SPREAD: horizontal gene transfer by (1) direct uptake of free environmental DNA or plasmids, (2) viral transfer by bacteriophage, and (3) conjugation, direct transfer through a temporary bridge — the most common route. Because transfer can cross species lines, resistance genes move between unrelated bacteria instead of being confined to one lineage. Inappropriate prescribing and livestock use intensify the selection pressure.

ESSAY: Explain nitrogen fixation and its importance

Certain prokaryotes convert inert atmospheric N2 into NH4+/NO2-, forms usable by living things. This matters because nitrogen is required by ALL organisms (proteins, nucleic acids) but atmospheric N2 is unusable to nearly everything else, so nitrogen fixers are the gateway for nitrogen into the biosphere. Agriculturally, legumes house nitrogen-fixing bacteria in root nodules, so legume crop rotation fertilizes soil and reduces fertilizer demand.

PRACTICE (do on paper)

Draw a cladogram for Bacteria, Archaea, Eukarya and label which two are sisters; then explain in one sentence why "prokaryotes" fails the clade test. Then work three serial-dilution problems with different plated volumes.