Lecture 12: Prokaryotes and the Tree of Life

Comprehensive review flashcards covering prokaryotic phylogeny, structural comparisons with eukaryotes, bacterial and archaeal diversity, metabolisms, and evolutionary relationships based on Lecture 12.

Why is the term "prokaryotes" traditionally placed in quotation marks in modern phylogenetic classification?

Prokaryotes represent a paraphyletic grouping because Archaea share a more recent common ancestor with Eukarya than they do with Bacteria.

How do the flagellar structures of prokaryotes and eukaryotes differ?

Prokaryotes have simple flagella composed of a single fiber, whereas eukaryotes have complex flagella structured in a $9 + 2$ arrangement.

How do prokaryotes and eukaryotes differ in their chromosome structure and standard cell division mechanism?

Prokaryotes have a single, circular DNA chromosome (with possible plasmids) and divide by binary fission, whereas eukaryotes possess multiple linear chromosomes in a double-membrane-bound nucleus and divide by mitosis.

What cellular feature is labeled with the letter "n" in this transmission electron micrograph of two Neisseria gonorrhoeae cells?

The nucleoid region (containing the single circular chromosome).

What percentage of the genes in the bacterium Thermotoga maritima are estimated to have originated from Archaea via lateral gene transfer?

$$20\%$$

Based on the illustrated cross-sections, what are the primary structural differences between Gram-positive (A) and Gram-negative (B) bacterial cell walls?

Gram-positive bacteria possess a thick, uniformly dense cell wall composed primarily of peptidoglycan, whereas Gram-negative bacteria have a thin peptidoglycan layer surrounded by an outer membrane and periplasmic space, which together make up the cell envelope.

What are the three common morphological shapes of bacteria depicted from left to right in this scanning electron micrograph?

Cocci (spherical), bacilli (rod-shaped), and spirilla (spiral-shaped).

How does bacterial growth distribute across the oxygen concentration gradient in culture tubes for obligate aerobes, obligate anaerobes, facultative anaerobes, and aerotolerant anaerobes?

(a) Obligate aerobes grow only near the top where oxygen is high; (b) obligate anaerobes grow exclusively at the bottom away from oxygen; (c) facultative anaerobes grow throughout but concentrate near the top; (d) aerotolerant anaerobes show an even, uniform distribution throughout the entire tube.

What energy source, electron donor, and carbon source are utilized by photoheterotrophs such as purple sulfur bacteria?

They use light as an energy source (via bacteriochlorophyll), $H_2S$ as an electron donor (producing elemental sulfur), and organic compounds from other organisms as a carbon source.

How do chemoautotrophs obtain their energy and carbon?

They derive energy from inorganic chemical bonds and obtain carbon from carbon dioxide ($CO_2$) to produce sugars.

Which initiating amino acid is used for protein synthesis in Bacteria compared to Archaea and Eukarya?

Formyl-methionine is used in Bacteria, whereas Methionine is used in both Archaea and Eukarya.

How does membrane lipid structure differ between Archaea and the other two domains of life?

Archaea have branched membrane lipids, whereas both Bacteria and Eukarya have unbranched membrane lipids.

How do Bacteria, Archaea, and Eukarya compare regarding the number of RNA polymerases and their growth response to the antibiotic streptomycin?

Bacteria have one RNA polymerase and their growth is inhibited by streptomycin; Archaea and Eukarya each have several RNA polymerases and their growth is not inhibited by streptomycin.

Based on character-state analysis of fundamental features across the tree of life, how many evolutionary changes separate Archaea & Eukarya versus Bacteria & Eukarya?

Archaea & Eukarya are separated by 3 changes, while Bacteria & Eukarya are separated by 8 changes (Bacteria & Archaea differ by 5 changes).

What are the characteristic features of Hadobacteria, and what notable capability does Deinococcus radiodurans possess?

Hadobacteria are Gram-negative, extreme heat lovers (thermophiles); Deinococcus radiodurans has the ability to survive extreme radiation and consume nuclear waste.

What are two representative taxa of Hyperthermophilic bacteria mentioned in the lecture?

Thermotoga maritima and Aquifex sp.

What are the typical characteristics of the phylum Firmicutes, and what is unusual about Mycoplasmas?

Firmicutes are typically Gram-positive and many form durable endospores (e.g., Bacillus anthracis, botulism-causing species); Mycoplasmas are extremely small members of this group that have lost their cell walls.

What specialized dormant structure is visible within this Clostridium difficile cell?

An endospore.

What are the defining characteristics of Actinobacteria, and what are two medically important species in this group?

They are Gram-positive, filamentous bacteria that often produce antibiotics; notable members include Mycobacterium tuberculosis (causes tuberculosis) and Streptomyces sp. (produces streptomycin and other antibiotics).

What are the key physiological and structural features of Cyanobacteria?

Cyanobacteria are Gram-negative photoautotrophs that can grow as single cells, colonies, or filaments.

What distinctive structure facilitates motility in Spirochetes, and what two human diseases do they cause?

They possess axial filaments; Treponema pallidum causes syphilis and Borrelia burgdorferi causes Lyme disease.

What two distinct cellular stages make up the life cycle of the parasitic bacterium Chlamydia psittaci seen in this micrograph?

Infectious elementary bodies (taken into host cells by phagocytosis) and thin-walled reticulate bodies (which grow and divide within the host cell before reorganizing back into elementary bodies).

Why is the phylum Proteobacteria uniquely notable among all known bacterial groups?

It is the only known species group containing all four metabolic categories (photoautotrophy, photoheterotrophy, chemoautotrophy, and chemoheterotrophy); it also includes pathogens like Vibrio cholerae (cholera), Salmonella sp., and the causative agent of plague.

Where were the Lokiarchaeota discovered, and why is this Asgard archaean group significant to eukaryotic evolution?

They were discovered at Loki’s Castle (an undersea hydrothermal vent system east of Greenland); they contain genes for many eukaryotic traits including cell shape determination, cytoskeleton formation, and cell membrane functioning.

What extreme environmental conditions do many members of Crenarchaeota tolerate?

They include thermophilic (extreme heat), cryophilic (extreme cold), and acidophilic (extreme acid) species that maintain their internal pH, with some capable of carbon fixation.

Which major ecological and physiological types of archaeans are found within the phylum Euryarchaeota?

Methanogens (e.g., Methanopyrus), extreme halophiles (e.g., Halobacteria), and extreme thermophiles.

According to the endosymbiotic origin model, which bacterial lineages gave rise to eukaryotic mitochondria and chloroplasts?

An engulfed proteobacterium gave rise to the mitochondrion, and an engulfed cyanobacterium gave rise to the chloroplast.