Question 1

Microbiome:

Accepted Answer

The community of microorganisms—bacteria, fungi, viruses, and others—and their genes living in a specific environment, including their interactions and activities.

Question 2

Three Key Concepts for Understanding the Microbe:

Accepted Answer

evolution, diversity, and ecology.

Question 3

Evolution:

Accepted Answer

how did life get started on Earth? How does life change and diversify over time?

Question 4

Diversity:

Accepted Answer

phylogenetic diversity-evolutionary relationships, metabolic diversity-cellular processes, ecological diversity-microbial interactions.

Question 5

Ecology:

Accepted Answer

interactions among organisms, interactions between organisms and their environment.

Question 6

Three Grand “Flows” in Microbiology:

Accepted Answer

information flow, energy flow, and carbon flow.

Question 7

Information Flow (Fidelity vs. Mutation):

Accepted Answer

Genetics: Information passes from parent cells to daughter cells. Evolution: Information passes from ancestral species to descendant species

Question 8

Energy Flow (Electron transfer):

Accepted Answer

Electrons flow from donors to acceptors. Results in ATP production. Generates reducing power (NADH, NADPH)

Question 9

Carbon Flow:

Accepted Answer

Inorganic carbon → organic carbon (carbon fixation). Organic carbon → organic carbon (metabolism, biosynthesis). Organic carbon → inorganic carbon (respiration, mineralization).

Question 10

The Bacterial Perspective (Scale):

Accepted Answer

500 bacteria can fit in the space of a single period (.) 2mm for bacteria = 2km for humans (1000× scale difference).

Question 11

Remarkable Capabilities of Bacteria:

Accepted Answer

they can sprint 50–60 body lengths per second, swim through water as if it were honey, use molecular motors strong enough to pack DNA into viral capsids, and possess such high relative strength that, if scaled to human size, they could lift an airliner.

Question 12

Early Evidence of Life:

Accepted Answer

The Earth is 4.5 billion years old, liquid water — which is required for life — first appeared 4.3 billion years ago, fossilized remains from 3.45-3.86 billion years ago can be found in rocks.

Question 13

Microfossils:

Accepted Answer

Evidence of ancient microorganisms. 3.45-billion-year-old rocks from Barberton, South Africa, show bacterial structures. 1-billion-year-old microfossils from central Australia include primitive filamentous cyanobacteria and green algae.

Question 14

Stromatolites:

Accepted Answer

Ancient (3.5 billion years old) and relatively recent (1.6 billion years old) examples exist. Layered structures created by microbial mat communities.

Question 15

Isotope Fractionation:

Accepted Answer

Organisms preferentially use light isotopes (e.g., ¹²C over ¹³C), creating distinct isotopic signatures. Carbon isotope patterns can indicate past biological activity, preserved in ancient plants and petroleum deposits.

Question 16

Oldest Evidence of Life (Hematite Tubes):

Accepted Answer

Hematite tubes and filaments discovered in the Nuvvuagittuq rocks of Canada (reported in 2017) may represent some of the oldest signs of life.

Question 17

Hematite Tubes & Biological Origins:

Accepted Answer

Tubes and filaments in Nuvvuagittuq rocks resemble iron-feeding vent bacteria. Their attachment structures and organic carbon suggest a biological origin, unlikely to form without life.

Question 18

Advantages for Hydrothermal Vents as the Site for Life's Origin:

Accepted Answer

Vents provide stable, UV-protected environments with chemical energy from H₂ and H₂S. Their geochemistry forms prebiotic molecules, and mineral structures concentrate molecules, stabilize reactions, and conserve energy, supporting life’s emergence.

Question 19

Hydrothermal Mounds:

Accepted Answer

Mineral pores concentrate nutrient-rich fluids, enabling abiotic biomolecule formation, energy-coupled reactions, and replication, eventually leading to lipid membranes and the first cells.

Question 20

Evidence that RNA Came First:

Accepted Answer

Backbone of ATP, NADH, CoA

Binds nucleotides & amino acids

Catalytic activity (ribozymes)

Self-replication

Supports protein synthesis and gene regulation

Question 21

Transition from RNA to Cellular Life:

Accepted Answer

Proteins eventually replaced RNA as primary catalysts (more efficient). DNA replaced RNA as the genome (more stable for long-term storage).

Question 22

Earliest cells probably had:

Accepted Answer

— DNA (genetic storage)
— RNA (intermediary)
— Proteins (catalysts and structures)
— Membrane systems for energy conservation

Question 23

Last Universal Common Ancestor (LUCA):

Accepted Answer

LUCA, the first cellular organism, existed 3.7-3.8 billion years ago, then Bacteria and Archaea diverged.

Question 24

Metabolic Evolution After LUCA:

Accepted Answer

LUCA used chemolithotrophy for energy from inorganic compounds. Later, organisms evolved heterotrophy, phototrophy (oxygenic photosynthesis), and respiration, shifting from anaerobic to aerobic metabolism.

Question 25

Horizontal Gene Transfer (HGT):

Accepted Answer

Genetic material transferred between organisms (not just parent to offspring). Major force in early evolution. Continues to drive microbial evolution today.

Question 26

Prebiotic Chemistry:

Accepted Answer

Composed mostly of biological building blocks (amino acids, nucleosides, and sugars).

Question 27

Precellular Life:

Accepted Answer

Started with the RNA world (catalytic and self-replicating RNA), then protein synthesis (RNA-templated translation), DNA (replication & transcription).

Question 28

Early Cellular Life Composition (Right Before LUCA):

Accepted Answer

composed of lipid bilayers, early cells likely had high rates of HGT.

Question 29

Evolutionary Diversification (Right After LUCA):

Accepted Answer

divergence of bacteria and archaea, components of DNA replication, transcription, and translation all in one place.

Question 30

Genetic Chimera:

Accepted Answer

Modern eukaryotic cells contain both bacterial and archaeal genes. Evidence of endosymbiotic origins.

Question 31

LUCA Structural Characteristics:

Accepted Answer

distinctly eukaryotic features, such as a nucleus, mitochondria (respiring O₂), various organelles, cytoskeleton, spliceosomal machinery, introns.

Question 32

LUCA Gene Percentages:

Accepted Answer

— >70% of genes are uniquely eukaryotic
— ~2/3 of shared genes come from Bacteria (mostly metabolic functions)
— ~1/3 of shared genes come from Archaea (mostly information processing)

Question 33

Endosymbiotic Theory:

Accepted Answer

Eukaryotic cells originated when one prokaryote engulfed another, and the engulfed cell became a mitochondrion or chloroplast, providing energy or photosynthesis capabilities.

Question 34

Endosymbiosis Evidence:

Accepted Answer

Mitochondria and chloroplasts resemble bacteria in size, replicate independently, have circular genomes, bacterial-type ribosomes and 16S rRNA, are antibiotic-sensitive, and the nucleus contains genes derived from them.

Question 35

Serial Endosymbiosis Hypothesis (Slide 33):

Accepted Answer

Eukaryotic cells evolved through multiple, separate endosymbiotic events, with the nucleus forming first, then mitochondria, and later chloroplasts in plant lineages.

Question 36

Symbiogenesis Hypothesis (Slide 33):

Accepted Answer

Eukaryotic complexity evolved because of an early endosymbiosis between an archaeal host and the mitochondrial ancestor, with the nucleus forming afterward; chloroplasts were acquired later in plants.

Question 37

Carl Woese’s Universal Tree of Life:

Accepted Answer

Carl Woese used DNA and RNA sequence comparisons—"living fossils" acting as molecular clocks—to construct the first universal tree of life. This work revealed the domain Archaea.

Question 38

Small Subunit rRNA (SSU rRNA) as a Molecular Chronometer:

Accepted Answer

SSU rRNA—16S in Bacteria/Archaea, 18S in Eukaryotes—traces evolution because it is universal, functionally conserved, slowly evolving, and contains both conserved and variable regions, allowing easy sequencing and comparison across organisms.

Question 39

Small Subunit rRNA Gene Organization (Slide 37):

Accepted Answer

The SSU rRNA gene is part of an rRNA operon with 23S and 5S rRNAs and tRNAs. Transcribed as a single long RNA with spacers, which are removed during processing to produce mature rRNAs for ribosome assembly.

Question 40

According to SSU rRNA comparative analysis, the three domains of life are:

Accepted Answer

bacteria, archaea, and eukaryotes.

Question 41

Supporting Evidence from Genomics for Three Domains of Life:

Accepted Answer

Comparative SSU rRNA analysis revealed that all life falls into three domains with genomic evidence showing that 60+ core genes for transcription, translation, and DNA replication were inherited from a universal ancestor.

Question 42

Key Relationships Between the Three Domains:

Accepted Answer

Eukaryotic and Archaeal genes share more similarity, Bacteria and Archaea likely diverged before Eukarya existed.

Question 43

Timeline of Divergence:

Accepted Answer

Bacteria and Archaea likely split around 3.7 billion years ago, while Eukarya branched from within Archaea between roughly 1.5–2.7 billion years ago; after these splits, each lineage developed and fixed its own defining traits.

Question 44

Systematics:

Accepted Answer

Study of diversity of organisms and their relationships. Links phylogeny with taxonomy. Characterizes, names, and classifies organisms

Question 45

The Polyphasic Approach to Taxonomy (Three Integrated Methods):

Accepted Answer

phenotypic analysis, genotypic analysis, and phylogenetic analysis.

Question 46

Phenotypic analysis:

Accepted Answer

Morphological characteristics, Metabolic capabilities, Physiological properties, Chemical characteristics.

Question 47

Genotypic analysis:

Accepted Answer

Genome composition, DNA sequences, Genetic markers.

Question 48

Phylogenetic analysis:

Accepted Answer

Evolutionary relationships, Based on molecular data

Question 49

Phylogeny:

Accepted Answer

evolutionary history of related DNA sequences.

Question 50

Phylogenetic Trees:

Accepted Answer

Diagrams showing evolutionary history by comparing DNA sequences. The number of mutations between homologous genes indicates how long ago organisms shared a common ancestor, helping infer relationships among Bacteria, Archaea, and Eukarya.

Question 51

Building Phylogenetic Trees – Methodology:

Accepted Answer

PCR: Amplify 16S rRNA gene.

Clone & Sequence: Obtain sequences.

Alignment: Identify homologous positions.

Tree Construction: Calculate distances and build the tree.

Question 52

Homology:

Accepted Answer

Inheritance from a common ancestor, Phylogenetic analysis requires homologous sequences

Question 53

Sequence Similarity:

Accepted Answer

Percentage of nucleotides shared between sequences, Can be used to infer homology, Can be calculated regardless of function or ancestry

Question 54

Orthologs (Types of Homologous Genes):

Accepted Answer

Have the same function, Originate from a single ancestral gene in a common ancestor, Result from speciation events, Phylogenetic analyses typically focus on orthologs

Question 55

Paralogs (Types of Homologous Genes):

Accepted Answer

Have evolved different functions, Result from gene duplication within a genome, Can complicate phylogenetic analysis

Question 56

Making a Phylogenetic Tree Yourself (Slide 46):

Accepted Answer

the first step to making a tree is to align sequences. Then, a distance matrix is calculated from the number of sequence differences. Finally, the tree is constructed by adding nodes to join lineages that have the fewest differences.

Question 57

Genomic Evolution:

Accepted Answer

evolution is the accumulation of DNA sequence changes over time, an increase in genetic diversity of time. The flow of genetic information from old species to new species.

Question 58

Evolution & Alleles:

Accepted Answer

an allele is a sequence variant of a given gene. Alleles are different versions of the same gene. Evolution is a change in allele frequencies in a population over time.

Question 59

What causes evolution:

Accepted Answer

Random DNA changes and selection.

Question 60

The Evolution of Interdependence in Microbial Communities:

Accepted Answer

initially, all cells can make all products. Genes with redundant functions are lost over time. Individual cells are dependent on functions provided by the community.

Question 61

Horizontal Gene Transfer (HGT)

Accepted Answer

The transfer of DNA between organisms outside of parent-to-offspring inheritance. Allows genes to move between distantly related species, significantly impacting microbial evolution by enabling rapid acquisition of new traits.

Question 62

Recombination in HGT

Accepted Answer

The process where donor DNA is passed to a recipient cell and becomes integrated into the recipient's genome. Unlike sexual recombination, HGT is unidirectional, involves small amounts of DNA, and can occur across species boundaries.

Question 63

Transformation

Accepted Answer

A mechanism of HGT where bacteria take up free DNA directly from their environment and incorporate it into their genome.

Question 64

Transduction

Accepted Answer

A mechanism of HGT where viruses transfer bacterial DNA from one cell to another during viral infection.

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Evolution & Taxonomy