EPSc 230 Introduction to Astrobiology
Spring 2006
Study Questions for Exam 2:
These questions are meant to help you go over your notes, clarify any concepts that might be fuzzy,
and think about the topics covered in class. If you can answer all of these questions, you will do very
well on the exam. Please feel free to set up an appointment with me or Tom if you need help with any
of the answers – we will not hand out an answer key, but will be happy to help you figure out the
answers. These questions are not a homework assignment, so you can choose whether or not you feel
like answering them, or even when you feel like answering them…. A good strategy might be to study
your notes, then try to answer the questions without looking at your notes, then go to your notes and
the textbook for help, and ask.
Lecture 13:
1. What does the impact frustration of life mean? How might have this phenomenon influenced the
timing of the origin of life?
2. In 1908 _______________________ was the first to develop a scientific framework of
Panspermia.
3. Where is the best place on Earth to find rocks from Mars (other than the Johnson Space Center!)?
Why is this the best place to find Mars rocks?
4. Does the theory of Panspermia solve the problem(s) of the origin of life? Why or why not?
5. What is the best way to get organisms from one body in the solar system to another? What does
the term ejecta mean? Whether ejecta actually makes it into space depends upon three main
parameters: impact energy, gravity of the parent body, and __________________________.
How do each of these effect whether ejecta makes it into space (consider small amounts of impact
energy and high amounts of impact energy, etc)?
6. What is escape velocity? List in order of lowest to highest escape velocity: Earth, Mars, Moon,
Venus. What effect does a thick atmosphere have on ejecta? Life in order of thinnest to thickest
atmosphere: Earth, Mars, Moon, Venus. Based on these parameters, is it easier to move material
from Earth to Mars or from Mars to Earth?
7. Based on the graph: what is the fate of Mars Ejecta? Where does most of it end up? Based on the
second graph: what is the fate of Earth Ejecta? Where does most of it end up? According to the
graphs below, is it easier to move material from Earth to Mars or from Mars to Earth?
8. If organisms are going to survive an interplanetary transfer, they have to survive space conditions.
What are four factors about space conditions that make this a harsh environment to
microorganisms?
9. About how long are interplanetary transfer times: few years/few hundred years/few
thousand years/few million years/few billion years
EPSc 230 Introduction to Astrobiology
Spring 2006
10. What are two different types of bacteria that might be able to survive the harsh conditions of
space, and what are their unique properties that might allow them to survive these conditions?
Hey is Heliobacillus "special"?
11. What are spores and name 5 things spores are highly resistant to.
Lecture 14:
1. To survive interplanetary transfer, organisms would have to survive re-entry onto a new body.
What are three harsh conditions associated with this process?
2. What are dark interstellar clouds? Radio telescopes show that __________________ compounds
are abundant in dark interstellar clouds? What are cool carbon stars? Carbon starts release
abundant ___________________. A polyyne is an organic compound that contain nitrogen and
carbon with alternating single and triple bonds. Are these compounds commonly found in
biological material? What does the acronym PAH stand for? Describe what PAHs are. PAHs
are abundant in the universe (easily detected using infrared telescopes), but are they commonly
found on Earth? If so, where are they found on Earth?
3. What are buckyballs? Are they made of polyynes or PAHs?
4. Name three extraterrestrial sources of organic carbon that may have been important in the origin
of life on early Earth. Name one source of organic carbon that might have been intrinsic to the
early Earth.
5. NASA's Deep Impact intentionally hit an 800-pound projectile into a comet to see what would
happen. What did they find about the porosity? The impact put lots of gas into space. What
types of gases? Name two types of organic compounds that were detected. Are these organic
compounds commonly found in biological material?
6. Carbonaceous chondrites are a unique type of meteorite. Provide three reasons why they are
unique. About how much water and organic compounds are found on carbonaceous chondrites?
What kind of organic compounds are found in carbonaceous chondrites? Are these organic
compounds commonly found in biological material?
7. What is interplanetary dust, and where does most of it originate from? A small proportion of
interplanetary dust is presolar. What does this mean, and where does most of this material
originate from? About ____% is organic carbon. What type of organic compounds are found in
IDPs?
8. Describe the Miller-Urey experiment. Diagram the apparatus and what each chamber of the
apparatus mimics. What were the results of the experiment? What type of organic compounds
are found in the experiment?
9. There is one serious "flaw" about how the Miller-Urey experiment was originally carried out.
What is this flaw, and what happens when we try to correct for the flaw? Does the experiment
work as well as it originally did?
Lecture 15:
1. Define the following words: prebiotic chemistry, prebiotic soup, heterotroph, autotroph.
2. Describe the concept of the prebiotic soup in the origin of life. If life began with the prebiotic
soup it would have started out being heterotrophic/autotrophic and then later on must
have had to evolve heterotrophic/autotrophic metabolisms. Why is that?
3. As with many origin of life theories, there are many problems with the prebiotic soup. Name two
major problems and describe why each is a problem. Is there a way to get around this problem?
4. The surfaces of minerals are thought to have had important roles in the origin of life. Name three
unique properties of surfaces that would have made them important in the origin of life. What are
two types of "good" surfaces? What is meant by the term "good" surfaces?
5. Gunter Wachtershauser, a patent lawyer, proposed in 1988 a theory for the origin of life that
involved pyrite. Why did he choose pyrite as a mineral surface? What type of chemical reactions
EPSc 230 Introduction to Astrobiology
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would have occurred initially in this "iron sulfur world"? These would have gradually been
replaced by a second generation of iron sulfur life that had what feature? Wachtershauser
proposes that pyrite surfaces could have reduced CO2 to organic compounds. Is this an
autotrophic/heterotrophic origin of life?
Clays are also proposed to have been important in the origin of life. What unique properties of
clays could have made them important in the origin of life? If you add amino acids to clays and
subject them to wetting and drying cycles (for example in a tidal pool), the amino acids will
_______________________. Is this something you normally find in a cell? If you add RNA
nucleotides, these RNA nucleotides will ______________________________. Is this something
you normally find in a cell? One issue with any origin of life theory is chirality. How do
surfaces like clays address the issue of chirality?
Some people suggest that the origin of life started out with lipids. From what solar system
objects can components of lipids be isolated from?
The RNA world was first proposed in 1988 by Nobel prize winner Wally Gilbert. In this RNA
world, early life was made of _______________________ reacting together. This RNA world
was then replaced by the _________________ world, and then gave rise to the familiar tree of
life. Compare DNA and RNA. Which is more stable, which is single-stranded, which is an
information carrier, and which is chemically reactive? The chemical reactivity in RNA/DNA
gives it a central role in the polymerization of DNA/protein. ATP is the energy currency of
the cell. Is ATP a normal component of DNA or RNA? To have an RNA world, RNA must have
had two activities, catalytic and templating. What do these terms mean? What is going on here?
There are many "problems" with the RNA world. What are three of these problems? Thought
question: Can you propose a way to get around each of these problems?
Lecture 16:
1. In 1866 Swedish biologist Ernst Haeckel drew the first conceptual tree of life in his textbook
"General Morphology", showing a linear progression from Monera (the old word for prokaryote)
at the bottom to man at the top. It wasn't until Nobel prize winner Linus Pauling began thinking
about the molecular basis of disease in the 1960's that the tree of life was put into a real scientific
framework. What was he studying at the time that spurred his thinking?
2. Describe briefly how a phylogenetic tree is
constructed using gene sequences. You can use the
diagram to aid your explanation.
3. Define the following: cladistics, taxa, traits,
synapomorphies, cladogram, ingroup, outgroup,
root, phylogenetic tree
4. Explain how a tree is constructed using cladistics.
What type of data do you use to construct the tree?
5. Why is it so important for us to have a phylogenetic
tree for microorganisms?
6. The tree of life is often constructed using the
_________________________________ gene.
Why is this gene often chosen (provide at least two reasons)?
7. The tree of life shows three major lineages of organisms. These are called
____________________________. The root is where the
______________________________________________ once existed. Where is the root of the
tree of life placed with respect to the three major lineages? This implies that
___________________________ are more closely related to ___________________________.
Why was this a big surprise when this was discovered?
EPSc 230 Introduction to Astrobiology
Spring 2006
8. What role does the ribosome have in the cell? What is the ribosome made of (what components
and about how many of each of these components)? What is the relative proportion of each of
these two major components?
9. Each of the domains of life share some unique characteristics that aren't found in other domains.
What are two characteristics that are different in Bacteria and Archaea?
10. The archaeal domain of life contains two major lineages that contain cultured species. What are
these lineages called? Most of the early branches in this group are
hyperthermophilic/mesophilic/psychrophilic. All cultured species of
Crenarchaeota are hyperthermophilic/mesophilic/psychrophilic, however about
30% of the biomass in the open oceans are uncultured
hyperthermophilic/mesophilic/psychrophilic Crenarchaeota. Is the tree of life, in
general hyperthermophilic/mesophilic/psychrophilic have short branches while
hyperthermophilic/mesophilic/psychrophilic have long branches. In general,
hyperthermophilic/mesophilic/psychrophilic tend to branch deep in the tree of life
while hyperthermophilic/mesophilic/psychrophilic tend to branch peripherally.
Many Euryarchaeota are _________________________, which produce methane. These
organisms are strict aerobes/anaerobes. What do the words aerobe and anaerobe mean?
11. What are three characteristics that are shared between Archaea and Bacteria?
12. What are three characteristics of Eukaryotes not found in Archaea and Bacteria?
Lecture 17:
1. Phylogenetic trees assume that lineages branch dichotomously (in two). Trees show
_____________________________________ between organisms and the branch length is
proportional to ______________________________________.
2. The tree of life shows that most evolutionary diversity is found
_______________________________________________. The tree can be used as a framework
to understand the evolution of traits. If we look at thermophily and hyperthermophily, where do
we find these lineages in the tree of life? Where do we find photosynthetic lineages (in what
group(s) and deep/shallow)? Where do you find mesophilic lineages? Where do you find
multicellular life?
3. If the last common ancestor of all known life on Earth was thermophilic, does this mean that the
origin of life happened at high temperatures also? Why or why not? Think about the nature of
the early Earth in terms of impact rates, heat sources, and Panspermia when constructing your
answer. Does this mean that Panspermia transferred hyperthermophilic life? Why or why not?
4. Using phylogenetic trees as frameworks, all kinds of information can be inferred about the
ancestors of modern microbial groups. For example, in the Cyanobacteria, we can reconstruct the
size of the cells. Paleontologists have used in the past cell size to identify Cyanobacteria in the
rock record. Why is that? What does the analysis of cell size on the cyanobacterial tree tell us
about the early cyanobacterial lineages. Cyanobacteria that live in microbial mats are often
filamentous, make gooey sheaths, and are motile (they move up toward the light when buried).
Are these traits found in the early cyanobacterial lineages? What does this infer about the early
Cyanobacteria? Would they have lived in microbial mats?
5. Similarly, most paleontologists have been looking for cyanobacterial fossils in marine rocks
(partly because they are so plentiful in the rock record). Does character mapping show that the
early cyanobacteria were living in the marine environment?
6. When examining the archaeal domain of life, which traits below are ancient in the Crenarchaeota
and which are not (notice: the dashed line means "don't know):
EPSc 230 Introduction to Astrobiology
Spring 2006
EPSc 230 Introduction to Astrobiology
Spring 2006
Lecture 18:
1. We pretty much find life on Earth just about everywhere. Name two environments that are
actually sterile.
2. You need to have 5 things in order to have life. What are these 5 things? Briefly describe and
give an example (or two) for each.
3. Liquid water is absolutely essential for life. So how are organisms able to live in ice in
Antarctica or on glaciers? What does this imply for the search for life on Mars, where it is very
cold?
4. Define the following: phototroph, autotroph, organotroph. How do each of these organisms
generate ATP?
5. What is the name for an organism that uses inorganic chemicals to gain energy and uses CO2 as a
carbon source? What is the name for an organism that uses light to gain energy and uses organic
carbon as a carbon source?
6. Write out the chemical reaction for an aerobic chemo(auto)trophic metabolism.
7. Write out the chemical reaction for an anaerobic chemo(auto)trophic metabolism.
8. Many inorganic and organic chemical reactions in the natural environment are carried out by
microorganisms generating energy in order to live. Each of these lives in a unique
microenvironment, and therefore microbes are responsible for almost all the biogeochemical
cycling of elements in the natural environment. Despite this, only ____________% of species of
microbes have been cultured in the lab.
9. Oxygen is sometimes considered to be both a blessing and a curse. Why is this? Explain.
10. Temperature is an important growth parameter, controlling what types of organisms are present in
an environment (it certainly controls where we like to live!). What happens to cellular
components when you put an organism in an environment that is too hot? Too cold?
11. The optimal growth temperatures for a:
a. psychrophile
_______________ to ________________________
b. mesophile
_______________ to ________________________
c. thermophile
_______________ to ________________________
d. hyperthermophile
_______________ to ________________________
12. pH is another important environmental factor that controls where organisms like to live.
Organisms that grow optimally between pH 5-9 are called ___________________________,
while organisms that grow optimally below pH 5 are called __________________________.
Organisms that grow optimally above pH 9 are called ______________________________.
EPSc 230 Introduction to Astrobiology
Spring 2006
13. Describe what water activity is. Is water activity high or low in a salt brine? Do cells tend to
shrink or swell when they are placed in a brine? Explain why this happens (using the concept of
water activity).
14. Organisms are evolutionarily adapted to living in the optimal water activity. Organisms that
grow in 3% salt (i.e., marine organisms) are called _______________________. Organisms that
like to grow in concentrated brines between 15-30% salt are called
__________________________________.
Lecture 19:
1. Where do Deinococcus, Cyanobacteria, and Bacillus branch in the bacterial domain of life (deep,
shallow, in what major group)? In what environments do you find each of these organisms?
2. The first branch of cultured bacteria lives in what kind of environments? Where does it get its
name, and what chemical reaction does it do to gain energy? These organisms are
chemoautotrophs/chemoorganotrophs/photoautotrophs/photoheterotro
phs.
3. Where do Thermotoga, Thermus, and Thermodesulfobacterium branch in the bacterial domain of
life (deep, shallow)? Name one unique trait for each of these organisms, and where do they live?
4. The Proteobacteria is a diverse group of Archaea/Bacteria. Two different kinds of
photosynthetic bacteria are found in this group. Are they oxygenic/anoxygenic. What
does oxygenic and anoxygenic mean? Where do these two kinds of photosynthetic organisms
live, and what are their preferred reductant (hint: the preferred reductant for Cyanobacteria is
water, H2O).
5. Sulfur oxidizers, which can be found in the Proteobacteria, are often acidophiles. Why is that?
6. Hydrogen oxidizers are also found in the Proteobacteria, but they aren't related to Aquifex. Where
do these organisms grow?
7. Describe what metabolism methanotrophs have. Where do these organisms grow?
8. Rickettsias are pathogenic Proteobacteria. What is unique about these organisms, and what are
they closely related to? How do we know they are closely related (name two reasons).
9. Some Proteobacteria are sulfate reducers. Where do these organisms live?
10. There are a number of Low G+C Gram Positive bacteria that we encounter in our everyday lives.
Streptococcus infects our throats in the winter, and Staphylococcus can cause skin infections.
Lactococcus is commonly found in __________________________ and ferments lactic acid
(milk sugar). The two spore-formers ____________________ and _______________________
are found in this group. Also found are sulfate reducers. Do these sulfate reducers also form
spores?
11. We also encounter High G+C Gram Positive bacteria in our daily lives. Mycobacterium causes
tuberculosis and leprosy, Ureaplasma causes urinary tract infections, and Mycoplasma causes
STDs (hopefully these organisms are not effecting our daily lives). Propionibacterium is a
fermenter that produces CO2. This organism is found in ________________________ and in
__________________________. When it rains, the organic compounds secreted by
________________________________ produce an earth odor. These organisms also produce
_______________________ which are very important in fighting infections.
12. Cyanobacteria are oxygenic/anoxygenic. Write out the reaction that these organisms
catalyze. Indicate what their source of carbon and their reductant is. Are these organisms
autotrophs or heterotrophs? What is the highest temperature you can find Cyanobacteria? Many
Cyanobacteria fix nitrogen. What does this mean, and why is this process so important?
13. Green Sulfur and Green Non-Sulfur Bacteria are oxygenic/anoxygenic. Are these
organisms Proteobacteria or Cyanobacteria? What is their favorite source of reductant, and where
do these organisms like to grow?
EPSc 230 Introduction to Astrobiology
Spring 2006
Lecture 20:
1. Methanogens in the rumen of a cow can produce as much as 100 liters of methane gas a day.
What other environments are methanogens found in? What roles to they play in lakes and other
sedimentary environments where there is a lot of organic carbon?
2. Besides methanogens, what are two other major types of organisms found in the Euryarchaeota.
Are they both thermophilic? Do these groups of organisms branch deep or late in the
Euryarchaeota tree? What is unique about Archaeoglobus? Where did it gain its unique ability to
reduce sulfate?
3. What are two different types of Crenarchaeota?
4. Name two common metabolisms found in thermophilic archaea (other than methanogenesis).
5. The Proterozoic is split into three major periods, the Paleoproterozoic, Mesoproterozoic, and
Neoproterozoic. The Paleoproterozoic/Mesoproterozoic/Neoproterozoic is a
time of stability, while the Paleoproterozoic/Mesoproterozoic/Neoproterozoic is
a time of sudden oxygen increase and major geologic change. When did oxygen first appear in
the atmosphere? How does this correspond with global "Snowball" glaciations, and the
disappearance of banded iron formation? Name two other major changes that occur during this
time period.
6. Around 2.4 Ga, you begin to see the evidence of microbial sulfate reduction in ancient sediments.
How is microbial sulfate reduction recorded in rocks (write out the reaction)? What mineral
records their presence? What needs to be present in the sediments to form this mineral?
7. It is generally thought that oxygen increased in three major stages. When did each stage exist,
about what were the oxygen levels at each stage? In which did you have stratification of the
oceans?
8. How are "Snowball" glaciations different from "regular" glacial events (like the one we just had
ending ~15,000 years ago)? These glacial events are associated with disruptions in carbon
isotopes. This is seen in carbonate rock, which will have positive carbon isotopic values
(normally carbonate rock has isotopic values of _______________). It is also recorded in organic
carbon generated by organisms which has carbon isotopic values that are unusually
negative/positive. Here the carbonate rock is enriched in 12C/13C and the organic carbon
is enriched in 12C/13C.
9. At about 1.8 Ga, banded iron formation disappeared from the Earth! Ocean sediments went from
being iron oxides (like magnetite, or Fe3O4, and hematite, or Fe2O3,) to being iron sulfides (like
pyrite FeS2). What might have caused this change?
10. Toward the end of the Paleoproterozoic, after the rise in oxygen, what do we start to see in the
fossil record?
Lecture 21:
1. Compare and contrast the basic architecture of the prokaryotic and eukaryotic cell.
2. In what domains of life do we find organelles? Describe the process of endosymbiosis. What
does the word endosymbiosis mean? What evolutionary pressures might drive this process to
occur? What is endocytosis, what types of organisms perform endocytosis, and how might it
have been important in endosymbiosis?
3. There is a significant body of evidence showing that mitochondria and chloroplasts were once
free-living bacteria. What were these organisms once, and name 4 pieces of evidence that this
was the case.
4. What is primary endosymbiosis? What is secondary endosymbiosis? Which organelles have
undergone primary and which secondary endosymbioses? What type of eukaryotes have
undergone primary endosymbiosis and name three that have undergone secondary
EPSc 230 Introduction to Astrobiology
Spring 2006
endosymbiosis. Which endosymbiosis event happened early in the evolution of eukaryotes and
which late?
5. What are lipids? How old are the first fossil/ancient lipids? What types of lipids are these
ancient lipids, and what organisms did they come from? Which ones require oxygen for them to
be formed? What does this tell us about the presence of oxygen at the time? Was oxygen present
in the atmosphere?
6. What are Acritarchs and when did they first appear in the fossil record? How do we know that
these were once fossil eukaryotes? The first macroscopic (big) fossil that you can see with the
naked eye is Grypania. This fossil is found in
Paleoproterozoic/Mesoproterozoic/Neoproterozoic rocks. The first fossil red
algae are seen in Paleoproterozoic/Mesoproterozoic/Neoproterozoic rocks.
Why do we think that these were once red algae?
Lecture 22:
1. Describe the fossils found from the beginning of the Vendian, and compare them with those
found at the end of the Vendian. About what time did this change take place? Do we know what
type of eukaryotes produced the Vendian fossils?
2. The Duoshantuo Formation is a very important record of late Vendian life. How old are these
rocks, and what is recorded in these rocks? What are two important early fossils found in these
rocks?
3. What fossils dominate the assemblages found at the end of the Proterozoic? What modern groups
of organisms do they correspond to?
4. Name three types of fossils found in the first ten million years of the Cambrian. Describe what
happened after the first 10 million years of the Cambrian. What happened in terms of diversity,
skeletal parts, and complexity/diversity of body forms?
5. What is the Burgess Shale, and why is it important? In general terms, describe what these
organisms were like. What modern groups of organisms do they correspond to?
6. At what age do we see the second major "Snowball" Earth event? We mentioned other
glaciations during this time frame. How many glaciations were there? What evolutionary events
correspond with these glaciations?
7. Describe 4 major factors that might have contributed to the Cambrian Explosion of animal life.
8. What type of organisms are the land plants related to, and how are they all related to green algae?
9. What are three general factors that an aquatic organism would have to deal with in order to
colonize land for the first time?
10. It took a long time for plants to colonize land. What are four traits that plants had to evolve prior
to their emergence on land? Briefly describe the role that each of these traits plays. Mosses are
early land plants. What type of environments do they live in? Do they have all the adaptations
needed to live fully on land like the true land plants?
11. Vertebrate animals faced similar problems to plants when they ventured on to land. Name four
traits vertebrate animals had to have prior to their emergence on land. Explain why each trait had
to be evolved for successful colonization of land.
Lecture 23:
1. Mass extinctions have occurred throughout Earth's history. At the end of what five time periods
are there mass extinctions in the fossil record?
2. Name two major groups of diverse organisms in the Ordovician.
3. Mostly terrestrial/marine organisms were affected by the Ordovician extinction. How
large was this extinction compared to others in Earth’s history? What might have been the cause
of this extinction?
EPSc 230 Introduction to Astrobiology
Spring 2006
4. After all the 5 major extinction events, what generally occurred?
5. During the Silurian many important things occurred in the evolution of life. What was the
dominant marine predator at the time, and what two things occurred in the evolution of fish?
6. When did plants first colonize land? Describe what the plants looked like (describe 4 attributes of
these early land plants). Did plants or animals first colonize land?
7. What two significant evolutionary changes occurred within the fish during the Devonian?
Describe three traits the Devonian freshwater fish had. What other types of animals began to
colonize land?
8. What groups of animals preferentially died off in the mass extinction at the end of the Devonian?
What are two possible causes of this extinction?
9. Most of the modern coal deposits were produced during the _____________________________
in _____________________________ environments. If plant material produced this coal, what
does this imply about the atmosphere of this time?
10. What were the two abundant types of plants in the Carboniferous? What were animals like
during the Carboniferous?
11. The Permian was a time of continued diversification in land plants and animals. At the end of the
Permian was mass extinction was devastating to many groups of organisms. What groups of
organisms went extinct during this extinction?
12. What are four proposed causes of the end Permian mass extinction? What was the configuration
of the continents at this time? Why is it so difficult for us to find out what caused the Permian
mass extinction?
13. What two major groups of tetrapods evolved and diverged in the Mesozoic? What major group
of plants evolved in the Mesozoic?
14. What groups of organisms went extinct at the end of the Cretaceous? Is this one of the largest
mass extinctions in the Phanerozoic? There is now abundant evidence suggesting that this
extinction was caused by a meteorite impact. List and describe five other pieces of evidence that
this was a meteorite impact.
15. The impact would have released gigatons of SO2 and water vapor into the atmosphere. What
effect would this have had on climate. It would also have vaporized
_____________________________. What effect would this have had on climate, the landscape,
and organisms? What organisms did really well soon after the impact event? Why did these guys
do so well?