Deck 17: Origins and Evolution

Question 1

Early metabolism most likely was driven by:

A) mitochondria
B) DNA
C) chloroplasts
D) oxidation-reduction reactions
E) oxygenic phototrophy

Answer 1

D

Question 2

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

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

Answer 2

sedimentary rock

Question 3

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

A) nucleoid
B) hopanoid
C) ribosome
D) flagella
E) plasmid DNA

Answer 3

B

Question 4

Molecular clocks use genes found in organisms that are:

A) used for TCA cycle
B) found primarily on plasmid DNA
C) necessary for transcription and translation
D) inherited though transduction
E) provide enzymes for glycolysis

Question 5

The elements that formed initial microbial life originated from:

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

Question 6

All of Earth's life-forms are found in the:

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

Question 7

__________ are phototrophic biofilms that have interacted with calcium carbonate (CaCO₃) to form fossils.

A) Cyanobacteria
B) Sedimentary mats
C) Stromatolites
D) Microbial mats
E) Microfossils

Question 8

A molecular clock is best defined as:

A) 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 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 sync

Question 9

Which of the following are early microbial cells that individually decayed and filled with calcium carbonate or silica?

A) stromatolites
B) sedimentary mats
C) archaean cells
D) Hadean formations
E) microfossils

Question 10

Scientists today believe that the earliest catalytic components to be formed in early life can still be found in which cellular structure?

A) chromosomes
B) cell walls
C) flagella
D) plasmids
E) ribosomes

Question 11

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

A) biosignatures
B) rubisco
C) abiotic artifacts
D) enzyme markers
E) biotic matter

Question 12

Microbial life appeared on this planet 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 13

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

A) CO₂ and H₂
B) H₂0 and O₂
C) CH₄ and CO₂
D) N₂ and O₃
E) O₂ and H₂

Question 14

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) group of genes unselected for in evolution
D) theory of how life began on Earth
E) series of related organisms producing a monophyletic group

Question 15

The type of evolution that results in a loss of genes encoding for unselected traits is called:

A) random mutation
B) natural selection
C) reductive evolution
D) clade evolution
E) decreased replication

Question 16

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

A) DNA will fall apart
B) nutrient transport systems do not work
C) ATP will become crystalline
D) plasma membrane will freeze
E) enzymatic reactions cannot be maintained

Question 17

Which of the microbial populations listed below is thought to have evolved earliest based on metabolism studies of the geological record?

A) cyanobacteria
B) aerobic oxidation-reduction bacteria
C) algae
D) anaerobic oxidation-reduction bacteria
E) aerobic phototrophy

Question 18

Which of the following is NOT one 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) Sequences that encode for essential catalytic portions of a protein change more slowly than portions without essential function.
C) Nucleotides in the position of third codon show more random mutation.
D) Artifactual mutations incorporated by PCR are high.
E) All of the above.

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

Scientists Oparin, Miller, and Urey 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 21

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 22

Using traditional taxonomic rank, which of the following is a smaller rank than family?

A) order
B) domain
C) genus
D) phylum
E) subclass

Question 23

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 24

Based on SSU rRNA phylogeny studies, the current scientific dogma is that there is/are __________ domains of life.

A) 1
B) 2
C) 3
D) 4
E) 5

Question 25

In this phylogenetic tree, what does "A" represent? "B" represent?

A) A = branch; B = branch
B) A = node; B = branch
C) A= root; B = branch
D) A = node; B = root
E) A = branch; B = node

Question 26

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 27

Recently identified organism "A," has just been placed in the taxonomic grouping of Nitrobacter winogradskyi, this is an example of:

A) identification
B) classification
C) nomenclature
D) species differentiation
E) phylum designation

Question 28

Many phylogenic trees can be calibrated in time based on:

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

Question 29

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 protein

Question 30

A recently isolated microbe was determined to be a Gram + rod by dichotomous key testing and probabilistic testing was ordered for this bacteria. What is the probability score that this bacteria is a Bacillus species based on the results given in Tables 1 and 2 below?

A) 1.0 × 10^-1
B) 5.7 × 10^-1
C) 2.2 × 10^-2
D) 1.3 × 10^-6
E) 6.3 × 10^-6

Question 31

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

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

Question 32

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

Question 33

Eukaryotic species are designated by their ability to:

A) inhabit the same ecological niche
B) eat the same foods
C) interbreed
D) look alike
E) move with similar locomotive structures

Question 34

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

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

Question 35

Taxonomy is best described as the:

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

Question 36

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 37

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) Prokaryotic Society of America
E) World Microbiological Organization

Question 38

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

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

Question 39

Which of the following represents the correct taxonomic designation of a common ulcer-causing bacteria?

A) Helicobacter Pylori
B) Helicobacter pylori
C) helicobacter pylori
D) helicobacter Pylori
E) all the above are equally correct taxonomic designations

Question 40

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

A) identification
B) classification
C) nomenclature
D) genus
E) species

Question 41

Wolbachia pipientis bacteria have what effect on the Drosophilia fruit fly?

A) halt egg production
B) feminize infected males
C) masculinize infected females
D) halt sperm production
E) atrophy both male and female reproductive organs

Question 42

If you performed an $\delta$ ¹³C isotope analysis on an unknown geological sample and determined a negative $\delta$ ¹³C % value, what would you conclude about the existence of life in that sample and why?

Question 43

The disease filariasis is caused by which infectious organism?

A) alga: Chlorella sp.
B) protist: Paramecium bursaria
C) fungus: Escovopsis sp.
D) bacteria: Staphylococcus aureas
E) nematode: Brugia malayi

Question 44

Lichens are a coevolved symbiosis of what two organisms?

A) plants and bacteria
B) paramecium and bacteria
C) alga and paramecium
D) fungus and algae
E) animal and plant

Question 45

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

Question 46

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

Question 47

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

A) Bacillus sp.
B) Cyanobacteria
C) Clostridium sp.
D) Escherichia sp.
E) Rickettsia sp.

Question 48

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

Question 49

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 50

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 flora
D) human ringworm infection
E) lichen formations

Question 51

Why do membrane compartments spontaneously arise from the chemistry of fatty acid glycerol esters?

Question 52

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

Question 53

Mitochondria maintained which essential genes from the ancestral endosymbiont it 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 & II, ATP synthetase
E) catalase, superoxide dismutase, and peroxidase

Question 54

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

A) rough and smooth endoplasmic reticulum
B) vacuoles and Golgi apparatus
C) nucleus and lysosome
D) mitochondria and chloroplasts
E) carboxysomes and chloroplasts

Question 55

Rhizobia 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 56

Why was the discovery of endolithic bacteria of interest to NASA scientists studying Mars?

Question 57

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

A) lichen
B) cyanobacteria
C) Wolbachia
D) rhizobial bacteroids
E) methanogens

Question 58

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

A) sickle cell anemia
B) forms of ataxia
C) dystonia
D) Parkinsonism
E) motor neuron disease

Question 59

You have just isolated four unique sequences through PCR amplification of the SSU rRNA. Calculate the percent relatedness of each in comparison with the known sequence given to determine which stain(s) is most phylogenetically related.
Known: T T C G C C G G A C A T T A A G C A G T T A A C G G
Unknown #1: T T C C C C C G A C A A A A A G C A G T C A A C G G
Unknown #2: T A A G G C G G A C A T T T A G C G G T C A A C C G
Unknown #3: T A C G C C G G A C A T T A A G C G G T T A A C G G
Unknown #4: A T C G C C G C A C A A A A A G C A G T T A A C G G

Question 60

Below is a table of data collected in a lab on five unknown specimens recently isolated from water sample. Based on the data given, which unknowns are most related and would best fit the criteria necessary for molecular clock analysis? Why?

Question 61

All life on Earth has been categories 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 domain designation.

Question 62

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

Question 63

What type of laboratory medium and conditions would you need in order for a culture of the secondary symbiont algae, Guillardia theta, to generate energy?

Question 64

The common working definition of bacterial species by taxonomists includes what three parameters? (What three things need to be met in order to prove two bacteria are from the same species?)

Question 65

Leafcutter ants have coevolved with three other species including two fungi and one bacteria. Describe the four-way symbiosis between all parties involved.

Question 66

Studies on the genome of Bacillus species have revealed that Bacillus anthracis has a closed pan-genome but Bacillus cereus has an open pan-genome. What does this mean and why do you think these two species evolved this way?

Question 67

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

Question 68

You have just isolated four homologous sequences through PCR amplification of specific glycolysis protein genomic sequence from four separate bacterial cultures that you proved to be Escherichia coli through morphological and biochemical laboratory analysis. Unknown #3 looks 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?
Unknown #1: A A T T T A C G A T A A A T G G A A A A A T T T C G A T
Unknown #2: A A T T T A C G A T A A A T G G A A A A A T T T C G A T
Unknown #3: A A T G G C C G G C G C G C G G A A A A A T T T C G A T
Unknown #4: A A T T T A C G A T A A A T G G A A A A A T T T C G A T

Question 69

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

Question 70

Why would two organisms in the process of symbiogenesis undergo dramatic reduction evolution in genetic material of one of the organisms? Why isn't more always better in terms of genetics for the newly evolving endosymbiotic organism?