Biology 1001- Section 10: Prokaryotes- Archaea and Bacteria

Tailings

Toxic waste from oil sands extraction that harms most plants and animals but provides a food source for microbes

Methanogens

Prokaryotes that break down organic carbon and release methane gas

Metagenomics

A method of using random sequences of DNA from a specific environment to identify and study the microorganisms living there

Hypersaline Environments

Places with extremely high salt levels, where only salt-loving organisms can survive.

Examples: Great Salt Lake, Utah, 32% more saline than seawater (Water is pink due to high Halobacterium levels)

Cold Environments

Very low-temperature habitats such as glaciers, where only cold-adapted microbes can function.

Example: Glaciers of Canadian Arctic

Hot Environments

Extremity hot places like hot springs or hydrothermal vents where heat-tolerant microbes live

Acidic Environment

Habitats with extremely low PH (very acidic), such as volcanic fumeroles where only acid-resistant microbes like Picrophilus ashimae can survive.

Cocci

Spherical bacteria; they can appear alone, in pairs, in chains, or in clusters

Bacilli

Rod-Shaped bacteria; usually solitary but sometimes form chains

Spiral

Bacteria with curved or corkscrews shapes, including loose spirals (spirilla), and tightly coiled forms (spirochètes)

Cell Wall

A protective outer layer that maintains a cell’s shape, prevents it from bursting (lysis) in hypotonic environments, and provides a surface for important molecules to attach.

Peptidogylcan

Makes up bacteria cell walls. It is a strong structure of sugar chains cross-linked by short peptides

Polysaccharides and Proteins

Make up archaeal walls (No peptidoglycan)

Gram Stain

A lab technique used to distinguish between gram-positive and negative cells. It separates bacteria into two groups based on their cell walls structure using a series of dyes

Gram-Positive Bacteria

Have simple structures for their cell wall, a think peptidoglycan layer and stain purple

Gram-Negative Bacteria

Have a thinner peptidoglycan layer plus an outer membrane with lipopolysaccharides (carbohydrates bound to lipids), making them a more complex structure, and stain red.

Capsule

A thick, sticky coating of polysaccharides or proteins around a prokaryote’s cell wall that prevents dehydration, protects against the host’s immune system, and helps the cell stick to surfaces; a thinner, less defined version is called a slime layer.

Fimbriae

Hairlike appendages. They allow the prokaryote to stick to substrate or other cells, contain protein, and are shorter and more in number than pili.

Neisseria Gonorrhoeae

Uses fimbriae to attach to mucous membranes of the host

Endospore

a tough, thick-coated, dormant cell some bacteria form when conditions become harsh; it loses water, shuts down metabolism, and can survive extreme heat, pressure, and dryness for years until conditions improve and it becomes active again.

Taxis

Directed movement, can move toward or away from the stimulus. Half of prokaryotes and 50um/sec.

Chemotaxis

Movement in response to chemicals

Flagella (Flagelllum)

Main structure for motility for prokaryotes; they are structurally different from eukaryotic flagella and are powered by protons flowing back into the cell after being pumped out.

Nucleoid Region

The area in a prokaryotic cell where the DNA is located but it is not enclosed by a membrane

Plasmids

Small, circular DNA molecules separate from the main chromosome that carry only a few genes (often helpful ones, like antibiotic resistance)

Binary Fission

a simple form of cell division in which a prokaryotic cell splits into two identical cells; under ideal conditions

Generation Time

How long cells take to divide

Sources that lead to high genetic Diversity

• Rapid reproduction

• Mutation

• Genetic recombination

Mutation

Unrepaired DNA damage or error during DNA replication

Genetic Recombination

Combing DNA from different sources to create new genetic combinations

Three mechanisms:

• Transoformation

• Transduction

• Conjugation

Transformation

A prokaryote takes up DNA fragments from it’s environment

Transduction

Viruses transfer DNA from one prokaryote to another

Conjugation

DNA is passed directly from one prokaryotic cell to another through a mating bridge (temporarily joined)

Horizontal Gene Transfer

The moment of genes between different species

Vertical Gene Transfer

Passing genes from parent to offspring

Recombinant Cell

Chromosomes have DNA from 2 different cels

F-Factor

Fertility factor. It is a piece of DNA (either a plasmid or part of the chromosome) that contains genes—about 25 in E. coli—which allow a cell to form a pilus and transfer DNA to another cell.

F-Plasmid

The F-factor in plasmid form

F+ cells

Cells having the F-plasmid and act as DNA donors during conjugation

F- Cells

Cells lacking the F-plasmid and act as DNA recipients

R-Plasmid

A plasmid that carries genes for antibiotic resistance, allowing bacteria to survive antibiotic treatment; these plasmids can hold resistance genes for many antibiotics and may also function as F plasmids, enabling them to spread resistance through conjugation.

Four Major Modes of Nutrition

1. Autotroph

2. Heterotroph

3. Phototroph

4. Chemotroph

Autotroph

An organism that gets its carbon from inorganic sources like CO2

Heterotroph

An organism that gets its carbon from organic molecules like glucose

Phototroph

An organism that gets its energy from light

Chemotroph

An organism that gets its energy from chemicals

Obligate Aerobes

Organisms that must have oxygen to survive and grow.

Example: many bacteria found on skin or in ocean water.

Obligate Anerobes

organisms which oxygen is toxic for. They survive through fermentation or anaerobic respiration using nitrate or sulfate as final electron acceptors. Example: Bacteria in the gut or deep sediments.

Facultative Anaerobes

Can use oxygen but can also function without oxygen

Nitrogen Fixation

a process done by certain prokaryotes (like cyanobacteria and methanogens) that converts atmospheric nitrogen (N₂) into ammonia (NH₃), which can then be turned into usable nitrogen products for other organisms. In symbiosis, Rhizobium provides fixed nitrogen to legume plants while the plant supplies nutrients and protection.

Heterocysts

Specialized cells that carry out nitrogen fixation. They have thick cell walls to restrict O2 entry and intercellular connections allows them to donate the created fixed nitrogen to surrounding cells and receive carbohydrates(Don’t perform photsynthesis to produce them themselves)

Biofilm

Surface-coating colony of one or more species of prokaryotes that in engage in metabolic cooperation.

Phylogeny

Diagram (like a tree) that shows evolutionary relationships among taxa (organisms or groups), based on phenotypic data and molecular data

Phenotypic Data

Observable traits. Such as shape, movement, nutrition type, or Gram stain results—used to classify organisms.

Molecular Data

Genetic information (like rRNA sequences or entire genomes) used to determine evolutionary relationships.

Monophyletic Group

A group of organisms that all descend from a single common ancestor.

Archaea

Group of prokaryotes more closely-related to Eukarya than bacteria as look similar to bacteria but are genetically more closely related to eukaryotes.

Metagenomics

A technique that allows scientists to recover complete prokaryotic genomes directly from environmental samples, without needing to culture the organisms.

Proteobacteria

A large and diverse group of Gram-negative bacteria that includes many important species, such as those involved in nitrogen fixation, disease, and environmental processes.

Alpha Proteobacteria

A subgroup of Proteobacteria that includes many species involved in symbiosis (like Rhizobium in plant roots) and some important pathogens; they are also thought to be the bacterial ancestors of mitochondria.

Beta Proteobacteria

A subgroup of Proteobacteria that includes nutritionally diverse species, such as bacteria involved in nitrogen recycling and some pathogens like Neisseria (which causes gonorrhea and meningitis).

Gamma Proteobacteria

A diverse subgroup of Proteobacteria that includes many well-known pathogens, such as E. coli, Salmonella, Vibrio cholerae, and Pseudomonas species.

Delta Proteobacteria

A subgroup of Proteobacteria that includes bacteria with unique behaviors, such as myxobacteria (which form slime-producing swarms and fruiting bodies) and bdellovibrios (predatory bacteria that attack other bacteria).

Epsilon Proteobacteria

A subgroup of Proteobacteria that includes many species found in animal digestive tracts, including important pathogens like Helicobacter pylori (causes ulcers) and Campylobacter (causes food poisoning).

Chlamydias

Group of bacteria that live only inside host cells and include species that cause infections in humans, such as the sexually transmitted infection Chlamydia trachomatis.

Spirochetes

long, spiral-shaped gram-negative bacteria that move with a twisting motion through internal, flagellum-like filaments; some species cause diseases such as Lyme disease and syphilis.

Cyanobacteria

Gram-negative photosynthetic bacteria that produce oxygen, with their plantlike photosynthesis and are important for ecosystems; they were the first organisms to release oxygen into Earth’s atmosphere.

Extreme Halophiles

Microorganisms that survive—or even require—very salty environments; for example, Halobacterium cannot function below about 9% salt.

Extreme Thermophiles

Microorganisms that thrive in extremely hot environments because their proteins and DNA are adapted to high temperatures; examples include Strain 121 (can grow at 121°C) and Pyrococcus furiosus, whose heat-resistant DNA polymerase is used in PCR.

Archea- Methanogens

Archaea that release methane as a by-product of obtaining energy. Uses CO2 to oxidize H2 producing methane.

Eucryachaeota

A major group of Archaea that includes many extreme halophiles and all known methanogens.

Crenarchaeota

A major group of Archaea that contains most of the extreme thermophiles.

TACK Supergroup

A recently identified group of Archaea (found through metagenomics) that is related to Crenarchaeota and includes species not previously classified.

Lokiarchaeotes

Archaea discovered in deep Arctic hydrothermal vents that share genes with eukaryotes for cell shape and movement, making them a possible “missing link” between prokaryotes and eukaryotes.

Chemical Recycling

The process by which prokaryotes and other organisms break down dead material and waste, returning essential elements (like carbon, nitrogen, and sulfur) back into the environment so they can be reused by living organisms.

Chemeoheterotrophs

Decomposing organisms that get energy and carbon from organic material; they break down dead organisms and convert organic compounds back into inorganic forms, returning elements like carbon and nitrogen to the soil.

Photoautotrophs

Organisms that use light, CO2, and water to make organic molecules like glucose, releasing oxygen as a by-product.

Example: Cyanobacteria

Nitrogen-fixing prokaryotes

Bacteria that convert atmospheric nitrogen (N2) into usable nitrogen compounds for plants

Example: Rhizobium

Cerenarchaeota

In the ocean. Archaea involved in nitrification, a key step in the nitrogen cycle where ammonia is converted into nitrite/nitrate

Symbiosis

Two species living in close contact with each other

Host

Larger organism

Symbiont

Smaller organism

Mutualism

Both species benefit

Commensalism

One benefits, the other neither benefits nor is harmed

Example: Your skin bacteria

Parasitism

One benefits, the other is harmed

Parasites

Organisms that benefits and does the harm

Pathogen

Disease-causing parasites

Endosymbionts

Prokaryote organisms that live inside the cells or body of another organism in a mutually beneficial relationship.

Human Microbiome

Community of microorganisms living in and on human body.

Intestines

500 to 1000 species bacteria

Exotoxins

Poisons proteins released by bacteria that cause illness even if the bacteria are no longer present.

Examples: Vibrio cholerae (cholera), Clostridium botulinum (botulism).

Endotoxins

toxic molecules (lipopolysaccharides) in the outer membrane of Gram-negative bacteria that are released only when the bacteria die and their cell walls break down.

Examples: Salmonella typhi (typhoid), Salmonella species (food poisoning)

Antibiotic resistance genes

Genes that allow bacteria to survive antibiotics and can spread to other cells or species through horizontal gene transfer.

Example: Conjugation of R plasmid

Horizontal Gene Transfer

The movement of genes between organisms that are not parent and offspring, allowing bacteria to quickly share traits like antibiotic resistance.

Virulence Factors

Traits that increase a bacterium’s ability to infect or damage a host

Genetic Engineering in Bacteria

Using modified bacteria to produce useful substances like vitamins, antibiotics, and hormones.

E. coli in gene cloning

E. coli is commonly used as a host cell where scientists insert foreign genes into plasmids; as the bacteria grow, they copy the inserted gene or make the protein it encodes (e.g., human insulin).