BIO 182 - Bacteria, Arachae, Protists, Fungi

Prokaryote

A cell that lacks a membrane-bound nucleus and membrane-bound organelles. Bacteria and Archaea are prokaryotes; their DNA is located in a nucleoid region.

Bacteria vs. Archaea

Both are unicellular prokaryotes, but they differ in cell wall and membrane chemistry. Bacteria usually have peptidoglycan cell walls; Archaea do not have typical bacterial peptidoglycan.

Gram-positive bacteria

Bacteria with a thick peptidoglycan cell wall and no outer membrane. They retain crystal violet during Gram staining and appear purple.

Gram-negative bacteria

Bacteria with a thin peptidoglycan layer plus an outer membrane. They do not retain crystal violet after decolorization and usually appear pink/red after counterstaining.

Why Gram-positive bacteria stain purple

Their thick peptidoglycan layer traps the crystal violet-iodine complex during Gram staining.

Why Gram-negative bacteria stain pink/red

Alcohol disrupts the outer membrane and the thin peptidoglycan cannot retain crystal violet, so the cells take up the pink/red counterstain.

Peptidoglycan

A strong mesh-like polymer of sugars and peptides that provides shape and structural support to bacterial cell walls.

Outer membrane of Gram-negative bacteria

An extra membrane outside the thin peptidoglycan layer. It can limit entry of some antibiotics and contributes to differences in antibiotic susceptibility.

Antibiotics and bacterial cell walls

Some antibiotics interfere with cell-wall synthesis. Their effectiveness can differ depending on whether a bacterium has thick peptidoglycan, an outer membrane, or no cell wall.

R plasmid

A plasmid carrying one or more antibiotic-resistance genes. Because plasmids can move between bacteria, resistance traits can spread rapidly.

Plasmid

A small, usually circular DNA molecule separate from the main bacterial chromosome. It may carry genes for antibiotic resistance or special metabolic abilities.

Nucleoid

The non-membrane-bound region of a prokaryotic cell where the main chromosome is located.

Capsule

A sticky outer coating outside the cell wall. It can help bacteria attach to surfaces, resist drying, and sometimes avoid host defenses.

Fimbriae

Short, numerous protein appendages used mainly for attachment to surfaces or host cells.

Pili

Longer, fewer surface appendages. Some pili help bacteria attach, while sex pili can transfer DNA during conjugation.

Flagellum in bacteria

A long appendage used for movement. Rotation of the flagellum propels the bacterium through its environment.

Heterocyst

A specialized cell in some filamentous cyanobacteria where nitrogen fixation occurs.

Endospore

A highly resistant dormant structure formed by some bacteria when conditions become unfavorable. It helps the cell survive heat, drying, chemicals, or lack of nutrients.

Purpose of an endospore

Survival, not reproduction. One cell forms one endospore, and that endospore can later return to an active cell.

Coccus

A spherical or round bacterial shape.

Bacillus shape

A rod-shaped bacterial form.

Spiral-shaped bacteria

Bacteria with curved, helical, or corkscrew-like forms, such as spirilla or spirochetes.

Transformation

A process in which a bacterium takes up free DNA from its environment. This can add new genetic variation.

Transduction

Transfer of bacterial DNA from one bacterium to another by a bacteriophage, which is a virus that infects bacteria.

Conjugation

Direct transfer of DNA between bacterial cells, often through a pilus. Plasmids are commonly transferred this way.

Transformation vs. transduction vs. conjugation

Transformation = DNA from environment; transduction = DNA carried by a virus; conjugation = direct DNA transfer between bacterial cells.

Genetic recombination in prokaryotes

Transformation, transduction, and conjugation introduce new DNA combinations and help maintain genetic variation.

Photoautotroph

Uses light as its energy source and CO2 as its carbon source. Cyanobacteria are a major example.

Chemoautotroph

Gets energy by oxidizing inorganic chemicals and obtains carbon from CO2.

Photoheterotroph

Uses light for energy but obtains carbon from organic compounds.

Chemoheterotroph

Uses organic compounds for both energy and carbon.

How to decode prokaryotic nutrition names

Photo = light energy; chemo = chemical energy; auto = carbon from CO2; hetero = carbon from organic compounds.

Obligate aerobe

Requires oxygen for cellular respiration and growth.

Obligate anaerobe

Cannot tolerate oxygen and carries out metabolism without it.

Facultative anaerobe

Can grow with or without oxygen. It uses oxygen when available but can switch to anaerobic metabolism when oxygen is absent.

Nitrogen fixation

Conversion of atmospheric nitrogen gas, N2, into biologically usable nitrogen compounds.

Why nitrogen fixation matters

Most organisms cannot use atmospheric N2 directly. Fixed nitrogen is needed to build amino acids, proteins, DNA, and RNA.

Cyanobacteria

Photosynthetic bacteria that perform oxygen-producing photosynthesis. Some species also fix nitrogen.

Proteobacteria

A very large and diverse group of mostly Gram-negative bacteria divided into several major subgroups.

Chlamydias

Bacteria that are obligate intracellular parasites, meaning they must live and reproduce inside host cells.

Spirochetes

Long, thin, spiral-shaped bacteria that often move with a twisting or corkscrew-like motion.

Mycoplasmas

Very small bacteria that lack a cell wall. Antibiotics that target cell-wall synthesis are ineffective against the missing wall target.

Archaea

A domain of unicellular prokaryotes distinct from Bacteria. Their cell walls do not contain typical bacterial peptidoglycan, and their membrane chemistry is unique.

Extremophile

An organism adapted to environmental conditions that are extreme for most life.

Halophile

An organism adapted to very salty environments. Many well-known halophiles are Archaea.

Thermophile

An organism adapted to very high temperatures. Some Archaea are thermophiles.

Methanogen

An archaeon that produces methane as a metabolic byproduct, usually in oxygen-free environments.

Are all Archaea extremophiles?

No. Some Archaea live in extreme environments, but many live in ordinary soils, oceans, and other non-extreme habitats.

Prokaryotes in chemical recycling

Bacteria and Archaea recycle elements such as carbon, nitrogen, and sulfur, making nutrients available to other organisms.

Mutualistic bacteria

Bacteria involved in relationships where both the bacterium and its partner benefit.

Pathogenic bacteria

Bacteria that cause disease in a host.

Protist

A diverse eukaryotic organism that does not fit neatly into the traditional animal, plant, or fungal groups.

Protist nutritional modes

Protists may be autotrophic, heterotrophic, or mixotrophic depending on how they obtain energy and carbon.

Autotrophic protist

A protist that makes organic molecules from inorganic sources, usually using photosynthesis.

Heterotrophic protist

A protist that gets organic nutrients by consuming, engulfing, or absorbing other organisms or organic matter.

Mixotroph

A protist that can combine autotrophic and heterotrophic nutrition.

Contractile vacuole

An organelle that collects and expels excess water from a cell. It is especially important in freshwater protists because water enters by osmosis.

Why freshwater protists need contractile vacuoles

Freshwater is hypotonic relative to the cell, so water tends to enter by osmosis. The contractile vacuole prevents excess swelling by pumping water out.

Primary endosymbiosis

A eukaryotic cell engulfed a photosynthetic cyanobacterium that eventually became a chloroplast.

Secondary endosymbiosis

A eukaryotic cell engulfed another photosynthetic eukaryote, helping explain the diversity of chloroplast types found in protists.

Excavates

A major protist group that includes diplomonads, parabasalids, and euglenozoans.

Diplomonads

Excavates with modified mitochondria; some have two similar nuclei and multiple flagella. Several species are parasitic.

Parabasalids

Excavates that often contain modified mitochondria called hydrogenosomes. Some are parasites or symbionts.

Euglenozoans

Flagellated excavates that include euglenids and kinetoplastids. Some euglenids are mixotrophic.

Stramenopiles

A major protist group including diatoms, golden algae, and brown algae.

Diatoms

Mostly photosynthetic unicellular stramenopiles with glass-like cell walls made largely of silica.

Golden algae

Mostly photosynthetic stramenopiles with yellow-gold accessory pigments.

Brown algae

Mostly multicellular marine stramenopiles, including kelps.

Alveolates

A major protist group characterized by membrane-bound sacs called alveoli just beneath the plasma membrane.

Dinoflagellates

Alveolates that usually have two flagella. Many are photosynthetic, and some can cause harmful algal blooms.

Apicomplexans

Mostly parasitic alveolates with specialized structures used to enter host cells.

Ciliates

Alveolates covered with cilia used for movement and feeding. Paramecium is a common example.

Rhizarians

A major protist group whose members often have thin, threadlike pseudopodia.

Pseudopodia

Temporary cytoplasmic extensions used by some protists for movement and feeding.

Foraminiferans

Rhizarians that often have porous shells, called tests, through which pseudopodia extend.

Radiolarians

Rhizarians with intricate internal skeletons often made of silica.

Cercozoans

A diverse rhizarian group, many of which use threadlike pseudopodia for feeding.

Archaeplastida

A major eukaryotic group that includes red algae, green algae, and land plants.

Red algae

Mostly marine photosynthetic organisms with accessory pigments that help them absorb light at different underwater depths.

Green algae

Photosynthetic organisms closely related to land plants. They contain chlorophyll a and b.

Unikonts in the study guide

The study guide includes slime molds, tubulinids, and Entamoebas within this group.

Plasmodial slime mold

A slime mold that forms a large multinucleate mass of cytoplasm.

Cellular slime mold

Usually exists as separate amoeboid cells. When food is scarce, many individual cells aggregate into a larger structure.

Plasmodial vs. cellular slime molds

Plasmodial slime molds form one multinucleate mass; cellular slime molds remain individual cells that aggregate together.

Tubulinids

Amoeboid protists that use pseudopodia for movement and feeding.

Entamoebas

Amoeboid parasites; some species live in the intestines of animals and can cause disease.

Ecological roles of protists

Protists can be primary producers, symbionts, pathogens, and nutrient cyclers in ecological communities.

Diatoms vs. radiolarians

Both can contain silica. Diatoms have silica-based cell walls; radiolarians have intricate silica skeletons.

Dinoflagellates vs. ciliates

Dinoflagellates usually have two flagella; ciliates are covered with many cilia.

Fungus

A eukaryotic heterotroph that absorbs nutrients from its environment. Most fungi are multicellular and have cell walls containing chitin.

Fungal nutrition

Fungi release digestive enzymes into their surroundings, break food down outside the body, and then absorb the resulting nutrients.

Chitin

A structural polysaccharide found in fungal cell walls.

Hypha

A thin filament that makes up much of a fungus’s body.

Mycelium

A network of hyphae that forms the main feeding body of most fungi.

Hypha vs. mycelium

A hypha is one fungal filament; a mycelium is a network of many hyphae.

Septate hyphae

Hyphae divided into compartments by cross-walls called septa.

Coenocytic hyphae

Hyphae that lack regular septa, producing a continuous cytoplasm containing many nuclei.

Septate vs. coenocytic hyphae

Septate hyphae have cross-walls; coenocytic hyphae are mostly continuous and multinucleate.

Mycorrhiza

A mutualistic association between a fungus and plant roots.

Benefit of mycorrhiza to plants

The fungus increases the plant’s access to water and mineral nutrients.