Biology 200, Summer 2015
Exam 3
Name: ________________________________________
TA: __________________
Biology 200
Summer Quarter 2015
Exam #3
DO NOT OPEN EXAM UNTIL DIRECTED TO DO SO
 Make sure you have 6 pages, including this one. Print your name and
information on all pages.
 Please use a pen. Pen is much easier to read, even with extensive
crossing-out. Pencil-written exams are acceptable, but may not receive full
credit to penciled answers on regrades.
 When asked, provide concise and clearly written answers. We may deduct
points if you do not fully answer the question or if your answer is too
vague or too confusing for us to follow.
 Extra information, if incorrect, will lose points.
 Limit your answers to the space provided. If you need extra space, you
can use the bottom of this first page. Indicate “on first page” where
necessary.
Page
Points Awarded
2 ______ out of 21 points
3 ______ out of 20 points
4 ______ out of 20 points
5 ______ out of 20 points
6: Take
______ out of 19 points
home
Total ______ out of 100 points
Exam 3
[21 points] Video Analysis
Name:_____________________________
For this question, you will see a video on loop in the front of the classroom. This short video will show some
aspects of development in a particular embryo. Use this video to answer the following questions.
/7
1a) Which developmental processes (differentiation, apoptosis, etc.) are happening here? How
do you know? Be specific and as complete as possible in 4-5 sentences, maximum.
/5 1b) In the video, these elements are not shown:
Mark all correct answers.
_____ Apoptosis
_____ Cell migration
_____ Proliferation
_____ Pseudopodia
_____ Gastrulation
_____ Receptor proteins
_____ Caspase
_____ Body folding
_____ Differentiation
You do not need to explain your answers here for full credit, but if you are making any special assumptions that you want the graders
to understand then please briefly note them here.
/4 1c) At the anterior of the embryo, you can see formation of eyes. Which molecular interactions
might be occurring to allow eye formation (in the correct location only) in this embryo?
Choose the single best answer and explain your answer in 1-2 sentences, max.
_____ The cells that will become the eyes already have special molecules that no other cell has
_____ The cells near the eyes produce a combination of molecules found nowhere else in the embryo
_____ The tail cells are lost, providing molecules that are used in eye formation
/5 1d) Development of this embryo continues after this video is over. Explain how cellular
proliferation might be used to help the maturation of this organism. Be as specific as you can for
this particular embryo and explain in 1-2 sentences, max.
Total: _____
Page 2 of 6
Exam 3
Name:_____________________________
[20 points] Completing a Concept Map
Several different molecules or processes will be arrayed here. Your task is to correctly build and/or describe links
between those parts of the map.
Fertilization
Membrane
Protein
Hox Genes
(or homeotic genes)
Differentiation
Promoter
Transcription
Factor
Transposon
/4
2a) Place an appropriate note on an arrow between Differentiation and Transcription Factor.
/4
2b) Place an appropriate note on an arrow between Membrane proteins and Fertilization.
/4
2c) Place an appropriate note on an arrow between Promoter and Hox/Homeotic.
/4
2d) Build and correctly note two new arrows not shown yet in this concept map.
Put a star on these arrows to identify them.
/4
2e) Include a new term on this map that has links to Transposon and Promoter.
You do not need to write anything on the arrows to/from this term.
Total: _____
Page 3 of 6
Exam 3
[20 points] Fertilization and Organogenesis
Name:_____________________________
A species of underwater insect uses similar fertilization mechanisms to those found in sea urchins, but has developed
under the same kind of genetic cascade as do common fruit flies.
/5
3a) Most of the genes that control the development of the ovary in female insects:
Mark all correct answers:
_____ Encode transcription factors
_____ Are Hox genes
_____ Do not have promoters
_____ Encode structural genes
_____ Are controlled by transcription factors
_____ All have the same promoter sequence
/5 3b) You isolate a mutant strain of insect in which fertilization is efficient. However, this mutant
strain is less fit than the wild-type strain because it wastes gametes in cross-species fertilization
attempts. Where is the mutation? Mark the single best answer and explain your answer in 1-2 sentences, max.
_____ A mutation in a gene encoding a receptor protein on the oocyte
_____ A mutation in a gene encoding a receptor protein on the sperm
_____ A mutation in a gene encoding a receptor protein within the oocyte
_____ A mutation in a gene encoding a receptor protein within the sperm
/5 3c) Typically, axis formation in these insects is controlled by a maternal determinant. A single
mother insect has a mutation in the nurse cells such that they cannot donate the determinant RNA.
Mark the single best answer and explain your answer in 1-2 sentences, max.
_____ This may cause immediate problems for a single oocyte
_____ This may cause immediate problems for many oocytes
_____ This may cause immediate problems for at least one sperm
_____ This is unlikely to cause any problems for fertilization
/5 3d) A environmental pollutant catalyzes a strong chemical linkage in the sperm of these insects.
Some ‘N-sperm’ have a new link (
) between nucleus and tail membrane proteins, and some ‘Bsperm’ have a new link between bindin molecules.
Centriole
Acrosome
Tail membrane
protein
N-sperm
B-sperm
Bindin
Nucleus
Mark all correct answers:
_____ N sperm will not be able to fertilize well
_____ B sperm will not be able to fertilize well
Total: _____
_____ N sperm will fertilize oocytes as normal
_____ B sperm will fertilize oocytes as normal
Page 4 of 6
Exam 3
[20 points] Case Study of Immune Response
Name:_____________________________
Case Study: A visitor to the Amazon Basin was unfortunately injured by a pirarucu.
This injury caused the introduction of both river water and pirarucu saliva to the patient’s bloodstream. The river water
contains several kinds of common bacteria, including those found primarily in primate fecal remains dropped into the
river. The saliva contains two different viruses known to parasitize pirarucu. The pirarucu itself escaped unharmed and
cannot be tested.
Within the next hour, mast cells and macrophages become active in the patient. Other cells may be active as well,
but the field hospital is only able to test the activity of these two cell types. However, it is discovered that this patient has a
very specific mutation in which platelets are able to congregate as normal, but platelet cells absorb the signaling molecules
released by mast cells and macrophages so that these signals cannot be transmitted efficiently to any other cells.
The injured visitor does have 5 different B-cells that recognize the first virus, but it has no B-cells that recognize the
second virus. A protein-level examination of dendritic cells indicates that dendritic cells have successfully taken up
several proteins with epitopes found in the second virus but not the first.
The injured visitor is treated for their wounds in the short term, develops a fever and signs of infection that last 4-5
days and then dissipate. Recovery is rapid, uneventful and complete over the next several months.
/5 4a) Which of these is true? Mark all correct answers:
_____ B-cells are unlikely to help with the innate immune response in this patient
_____ The innate immune response is negatively influenced by this mutation
_____ Some engulfing of bacterial cells is done by macrophages
_____ Fever is part of the immune response in this patient
_____ Most of the potential bacterial invaders were fended off by passive barriers
/5 4b) Adaptive immune cells respond to fight off the second virus. Which cells? How?
Explain your answer in 1-3 sentences, max.
/5 4c) Eventually, the adaptive response to the first virus is successful. The five specific B-cells:
Mark all correct answers:
_____ Have receptors that bind to the viral genome
_____ Are triggered to go through rapid mitosis
_____ Change their DNA in response to the virus
_____ Keep all antibodies within their cells
/5 4c) When reviewing this case, your colleague notes that the bacteria were the much scarier threat
to the health of the patient (and that the viruses were unlikely to cause any illness). You agree: why?
What about the molecules involved makes you sure? Explain your answer in 1-3 sentences, max.
Total: _____
Page 5 of 6
Exam 3
Name:_____________________________
[19 points] This take home portion should be completed before the exam and turned in at the start of the exam. Neatness
and clarity are important. Course staff (TAs, Liz, or Ben) will politely refuse to answer questions that directly relate to
this take-home portion. This Take Home portion must be completed using a computer program (PowerPoint, Word, etc.).
There are many possible ways to go about good answers for this problem.
5) Development of a new species.
A probe returning from the Challenger Deep has discovered a new carbon-based diploid
sexually-reproducing organism. Because the organism lives under tremendous pressure, only the
adults can be recovered. You are left to hypothesize about the development of this species from
zygote to mature adult.
We know very little about this unusual species:
 The adult stage has a total of 29 cells
 It has a toroidal shape with three appendages
o Two of the appendages are equivalent manipulating ‘arms’, and
o The other appendage is a sensory organ
 Traces of developmental proteins indicate that development of this organism requires
significant differentiation, signaling, at least one maternal determinant, and may require
proliferation, apoptosis and/or cell migration.
Your task is to diagram a possible developmental scheme for this new species. For this
developmental scheme, create a single computer-built diagram that shows:
 An example showing your understanding of how differentiation works in this species
 An example showing your understanding of how signaling works in this species
 An example showing your understanding of how a maternal determinant works in this species
 Indications of apoptosis, proliferation and migration in this species
 Indications of your understanding of the relative sizes of the following:
 organisms, enzymes, cells, organelles, water molecules, phospholipids, and ions
You have very little information, so you can be creative in describing the development of this
organism. When in doubt, try to keep your pathways simple, clear, and specific. Use the given colorcode to ensure that other scientists can decipher your work. Text should be limited to brief notes; the
diagram should do the explaining, not a written description.
The average grade on this part of the assignment will be ~13-15 points, with few 19/19 grades given. You can
work with other students in developing your diagram, but your final work must be obviously your own.
Special note: Doing a good job on the formatting (using a computer program and keeping a good color scheme) is not intended to help you learn how
immunity or development works. They ARE, however, great practice for the kinds of data presentation tasks that you’ll do in future jobs, both in
molecular science and in the greater world of all kinds of complex work. Take your presentation seriously. When you are giving a job talk or a grant
proposal or a team-designed blueprint or a sales pitch it is this kind of information organization that will matter (sometimes even more than what
you actually know). Because people have reported that the organizational tasks have been confusing, this task is intentionally designed as a way to
practice this.
Even very simple programs can be extremely useful in designing and redesigning good displays of your understanding (in other words, you don't
need to learn Illustrator or Photoshop to do a good job with this).
Total: _____
Page 6 of 6
Exam 3
Total: _____
Name:_____________________________
Page 7 of 6