Deck 17: Origins and Evolution

Question 1

Isotope analysis of $\delta$ ¹³C % value has found biosignatures to exist in which of the following?

A) igneous rock
B) mantle rock
C) carbonate rock
D) sedimentary rock
E) supernovas

Answer 1

sedimentary rock

Question 2

__________ results in a loss of genes encoding for unselected traits.

A) Random mutation
B) Natural selection
C) Reductive evolution
D) Clade evolution
E) Random recombination

Answer 2

C

Question 3

Horizontal gene transfer can occur by all EXCEPT for which of the following?

A) plasmid acquisition
B) transposable genetic elements
C) bacteriophage infection
D) transformation processes
E) parent to offspring

Answer 3

E

Question 4

Spikes in __________ often indicate that a horizontal gene transfer has occurred in the genome.

A) GC content
B) AC content
C) GT content
D) AT content
E) CU content

Question 5

Which of the following did early methanogens use from the early atmosphere to generate energy?

A) CO₂ and H₂
B) H₂O and O₂
C) CH₄ and CO₂
D) N₂ and O₃
E) O₂ and H₂

Question 6

Chemical indicators of life left in the geological fossil record are known as:

A) biosignatures
B) genetic markers
C) abiotic artifacts
D) enzyme markers
E) molecular weight markers

Question 7

The mineral __________, precipitated by mucus in ancient cyanobacteria biofilms, resulted in the formation of fossils that resemble today's ____________.

A) hydroxyapatite; Nautilus shells
B) FeO; banded iron formations
C) CaCO₃; stromatolites
D) all of the above
E) none of the above

Question 8

Oparin, in the former Soviet Union, and Miller and Urey, in England, performed some of the first experiments to prove:

A) organic macromolecules can arise from abiotic conditions
B) micelle formation generated the first membranes
C) RNA was the catalytic molecule of early Earth
D) TCA cycle generates amino acids
E) iron band formations were caused by photoferrotrophy

Question 9

Which of the following is a bacterial molecule that has been used as a biosignature in analysis of the geological record?

A) RNA
B) hopanoid
C) ribosomal proteins
D) flagellin
E) DNA

Question 10

Microbial life appeared on Earth as early as:

A) 10.4 billion years ago
B) 3.8 billion years ago
C) 1.2 billion years ago
D) 58 million years ago
E) 29 million years ago

Question 11

Based on their highly divergent genomic sequences, which group is thought to have had an early evolutionary start?

A) cyanobacteria
B) lithotrophs
C) thermophilic bacteria
D) methanogenic archaea
E) aerobic phototrophs

Question 12

A molecular clock is best defined as:

A) the information contained in DNA or protein sequences that shows changes over time
B) genes that under selective pressure show a higher rate in mutation frequencies
C) organisms in favorable environments that have greater offspring potential
D) the time between Earth's creation and the beginnings of life in an RNA world
E) a monophyletic group of organisms that replicate in synchrony

Question 13

Which of the following is NOT correct about endolithic microorganisms:?

A) They have been found as deep as 3 km in gold mines.
B) Their discovery elicited interest in NASA scientists seeking life on Mars.
C) They can grow in the Earth's core.
D) The term endolithic means living "within rocks."
E) They metabolize by oxidizing e^- donors generated through decay of radioactive metals.

Question 14

Early metabolism most likely consisted of:

A) the ability to form microbial mats
B) the ability to grow on silica matrices
C) bacteriorhodopsin-mediated photosynthesis
D) UV-driven oxidation-reduction reactions
E) oxygenic phototrophy

Question 15

The elements that formed initial microbial life originated from:

A) oceans
B) lightning
C) supernovas
D) the sun
E) ozone

Question 16

The temperature of water cannot drop below freezing and sustain life because:

A) macromolecules will break down
B) nutrients would be trapped in the environment
C) metabolic precursors will become crystalline
D) plasma membrane will freeze
E) metabolic reactions cannot be maintained

Question 17

Based on small subunit rRNA phylogeny studies, the current view is that there are __________ domains of life.

A) 2
B) 3
C) 4
D) 5
E) none of the above

Question 18

The sum of all of Earth's life is called:

A) lithosphere
B) mantle
C) core
D) atmosphere
E) biosphere

Question 19

The theory that life originated elsewhere and seeded life on Earth is called:

A) meteorite evolution
B) panspermia
C) extraterrestrial ecology
D) exobiology
E) Martian origin

Question 20

The earliest catalytic components present in early life can still be found in which subcellular structure?

A) chromosomes
B) carboxysomes
C) vacuole
D) plasmids
E) ribosomes

Question 21

Mycobacterium tuberculosis and H1N1 could both be placed in the same category in some classification systems based on the fact that they both:

A) are prokaryotes
B) can be visualized in the laboratory after acid-fast stain
C) create energy using aerobic respiration
D) have similar SSU rRNA
E) cause lung infection

Question 22

Operational genes found within the genome of an organism govern:

A) translational needs (e.g., elongation factor and peptidyl tranferase)
B) conditional needs (e.g., fermentation and toxin production)
C) ribosomal needs (e.g., rRNA and tRNA)
D) replication needs (e.g., DNA polymerase and DNA helicase)
E) transcriptional needs (e.g., RNA polymerase and sigma factor)

Question 23

Which of the following is the organizing body that sets the rules for naming a new prokaryotic species or taxa?

A) Bergey's Manual of Determinative Bacteriology
B) International Committee on Systematics of Prokaryotes
C) International Journal of Systematic and Evolutionary Microbiology
D) American Society for Microbiology
E) World Microbiological Organization

Question 24

Which of the following would NOT be considered a species trait based on ecotype?

A) Gram-positive cell wall structure
B) fermentative metabolism
C) Streptococcus structure
D) nucleoid sequence of orthologs
E) psychrotrophic growth

Question 25

In the domains of life, Archaea and Bacteria differ from each other in that:

A) Archaea contain membrane bound organelles; Bacteria do not
B) Bacteria can be extreme thermophiles; Archaea cannot
C) Archaea contain ester-linked membrane fatty acids; Bacteria do not
D) Bacteria start protein production with formylmethionine; Archaea do not
E) Bacteria have introns; Archaea do not

Question 26

A clade could best be described as a:

A) random but neutral DNA mutation
B) hypothesis that early evolution happened faster than later evolution
C) series of related organisms producing a monophyletic group
D) hypothesis of how life began on Earth
E) group of genes unselected for in evolution

Question 27

In the study of adaptive evolution through exposure to strongly selective environments, what is the energy cost to an organism that emerges as the fittest?

A) slow growth as a result of disabling gene regulation of the stress response
B) slow growth as a result of decreasing respiratory activities
C) slow growth as a result of impaired DNA replication
D) uncontrolled growth due to an inability to regulate mRNA translation
E) uncontrolled growth due to an inability to regulate binary fission

Question 28

The term __________ indicates that the members of a clade share a common ancestor, one not shared by any group outside the clade.

A) monogamy
B) monophyletic group
C) polyphyletic group
D) monoploid
E) polyploid

Question 29

Evidence in the study of adaptive evolution can be obtained from:

A) comparisons of gene sequences within a genome or across genomes
B) experimental evolution
C) the study of microorganisms growing in strongly selective environments
D) all of the above
E) none of the above

Question 30

Molecular clocks use genes that:

A) code for TCA cycle enzymes
B) are found primarily on plasmid DNA
C) are involved in transcription and translation
D) are acquired though transduction
E) encode enzymes for glycolysis

Question 31

In the domains of life, Archaea and Eukarya differ from each other in that:

A) Archaea contain membrane-bound organelles; Eukarya do not
B) Eukarya undergo methanogenesis; Archaea do not
C) Eukarya contain membrane-bound organelles; Archaea do not
D) Archaea are pathogenic to humans; Eukarya are never pathogenic
E) Eukarya have introns; Archaea do not

Question 32

Taxonomy can be defined as the:

A) description of distinct life-forms and their organization into different categories
B) recognition of the class of a given microbe isolated in pure culture
C) identification of new species into existing classes
D) recognition of different classes of life
E) naming of the different classes

Question 33

Calibration of phylogenic trees with respect to time since divergence is based on:

A) fossil and/or geological records
B) the frequency of mutations
C) the number of nodes and branches
D) whether the tree is rooted or unrooted
E) "housekeeping" genes

Question 34

Which of the following is NOT one of the standard assumptions made when using molecular clocks to determine phylogeny?

A) The best alignment between homologous sequences always encompasses the least number of mutational changes.
B) Mutations incorporated by PCR artifacts are high.
C) Nucleotides in the position of third codon show more random mutation.
D) Sequences that encode for essential catalytic portions of a protein change more slowly than portions without essential function.
E) All of the above.

Question 35

Which branch of taxonomy deals with the recognition of all the different classes of life?

A) identification
B) classification
C) nomenclature
D) biogeography
E) ethnology

Question 36

Which of the following is NOT used as a criterion to define a prokaryotic species?

A) phylogenetic relatedness
B) that members of different species cannot interbreed
C) the average nucleotide identity (ANI) of orthologs95%
D) DNA hybridization70%
E) SSU rRNA similarity97%

Question 37

In organisms selected for loss of genes through reductive evolution, energy is saved by:

A) acquiring the ability to exploit new ecological niches
B) becoming pathogens
C) dependence on a symbiotic partner's resources
D) both B and C
E) none of the above

Question 38

The term "pan-genome" can best be defined as:

A) the world DNA genomic databank
B) the sum of all expected genetic sequence variations found within a given species
C) genomic islands found in pathogenic organisms
D) the entire genomic sequence of all known organisms
E) differences in RNA transcription between species

Question 39

Experimental evolution consists of which three basic processes?

A) fixing, staining, and decolorizing
B) disabling gene expression and regulation, leading to slow cell growth
C) potentiation, actualization, and refinement
D) gene amplification, purification, and subcloning
E) restriction digestion, agarose gel electrophoresis, and staining

Question 40

Which of the following would be considered a gene product of an "informational gene"?

A) Staphylococcus toxic shock toxin
B) siderophore transport protein
C) hexokinase enzyme for glycolysis
D) O157:H7 attachment pili
E) 16S ribosomal RNA

Question 41

Rhizobial bacteroids and their plant hosts have evolved to have what type of symbiotic relationship?

A) mutalistic
B) parasitic
C) commensal
D) ectosymbiotic
E) naturalistic

Question 42

Human diseases caused by defective mitochondrial DNA include all of the following EXCEPT:

A) sickle cell anemia
B) forms of ataxia
C) motor neuron disease
D) Parkinson's disease
E) All of the above are caused by defective mitochondrial DNA.

Question 43

Explain how studying the evolutionary rate of RNA viruses in comparison to DNA viruses can help explain the evolutionary rate in the early Earth?

Question 44

The disease filariasis is caused by ___________, which harbors Wolbachia endosymbionts.

A) the flatworm Taenia solium
B) the ciliate protist Paramecium bursaria
C) the flagellate protist Guilladia theta
D) the bacterium Staphylococcus aureus
E) the nematode Brugia malayi

Question 45

The coevolved symbiosis between an alga and a fungus is called:

A) a heterocyst
B) a stromatolite
C) rhizobia
D) lichen
E) mycorrhiza

Question 46

Which of the following is an example of an endosymbiotic relationship?

A) parasitic fungus on leaf cutter ants
B) Staphylococcus sp. on the skin
C) Enterobacter sp. in intestinal microbiota
D) human ringworm infection
E) lichen formations

Question 47

How do membrane compartments spontaneously arise from the properties of fatty acid glycerol esters?

Question 48

All life on Earth has been categorized into three domains: Bacteria, Archaea, and Eukarya. There are many differences within each of these domains but all share some similarities. List four features that all cells of Earth share, regardless of which domain they belong to.

Question 49

You have amplified four unique sequences using PCR of the SSU rRNA gene from unknown microorganisms. Calculate the percent relatedness of each in comparison with the known sequence given to determine which strain(s) is/are most phylogenetically related.

Question 50

Mitochondria maintained which essential genes from the ancestral endosymbiont they evolved from?

A) NADH dehydrogenase, cytochrome oxidase, and ATP synthetase
B) pyruvate dehydrogenase, citrate synthase, and fumarase
C) hexokinase, phosphoglucose isomerase, and phosphofructokinase
D) photosystem I and II, ATP synthetase
E) catalase, superoxide dismutase, and peroxidase

Question 51

Explain how banded iron formations could arise in the geologic record due to photoferrotrophy.

Question 52

If you performed a $\delta$ ¹³C isotope analysis on an unknown geological sample and determined a negative $\delta$ ¹³C % value, would you conclude that life had existed or not in that sample and why?

Question 53

The ancestral organism that gave rise to the modern-day chloroplast was:

A) a lichen
B) a cyanobacterium
C) Wolbachia
D) a rhizobial bacteroid
E) a methanogen

Question 54

The most likely ancestor for today's mitochondria according to the endosymbiosis hypothesis is:

A) a species of the genus Bacillus
B) a cyanobacterium
C) a member of the clostridia
D) an enterobacterium
E) a rickettsial

Question 55

In the "RNA world," how could RNA molecules form spontaneously and how did that formation give rise to the protein enzymes of today?

Question 56

Eukaryotic organelle structures that are thought to have arisen from endosymbiotic relationships include:

A) rough and smooth endoplasmic reticulum
B) vacuoles and Golgi apparatuses
C) nuclei and lysosomes
D) mitochondria and chloroplasts
E) carboxysomes and chloroplasts

Question 57

Why and how is the small subunit ribosomal RNA (SSU 16S rRNA) used to determine molecular phylogeny?

Question 58

What effect does the bacterium Wolbachia pipientis have on the fruit fly Drosophilia?

A) It halts egg production.
B) It feminizes infected males.
C) It masculinizes infected females.
D) It halts sperm production.
E) It atrophies both male and female reproductive organs.

Question 59

How could catalytic activity in enzyme proteins have evolved from catalytic RNA?

Question 60

Why was the discovery of endolithic bacteria of great interest to NASA scientists seeking life on Mars?

Question 61

How can plants be so efficient photosynthetically if the chloroplast genome has fewer genes when compared with free-living cyanobacteria?

Question 62

You have just isolated four homologous sequences through PCR amplification of specific glycolytic enzymes genomic sequence from four separate bacterial cultures that you proved to be Escherichia coli through morphological and biochemical laboratory analysis. Unknown 3 colonies look different from the other three. Is this still an Escherichia coli? How can you explain this difference and what can you deduce about the gene product in comparison with the other three samples?

Question 63

Why do bacterial antibiotics have a greater effect on diminishing the effects of nematode infection caused by Brugia malayi (the etiologic agent of filariasis) than current antinematode agents?

Question 64

Describe the intracellular endosymbiosis between algae of the genus Chlorella and Paramecium. Why is this symbiosis considered reversible?

Question 65

What type of laboratory medium and conditions would you need in order to culture the secondary symbiont alga Guillardia theta?

Question 66

Describe how the genome of the Escherichia coli enterohemorrhagic strain O157:H7 differs from the harmless enteric E. coli K12 and how this difference relates to O157:H7 pathogenicity.

Question 67

Studies on the genome of Bacillus species have revealed that Bacillus anthracis has a closed pan-genome, whereas Bacillus cereus has an open pan-genome. What does this mean and why did these two species evolve in this manner?

Question 68

Define the term "metagenomics" and explain why growth in this field has led to an increase in SSU rRNA species designations.

Question 69

Special Topic 17.1 in the textbook discussed the discovery of bacterial species in a "soap scum" biofilm on a shower curtain. If you could perform a phylogenetic analysis of a sample, what would you test? Briefly describe how you would go about the testing. What would you expect to find?

Question 70

What criteria need to be met in order to prove that two bacterial strains belong in the same species?