Download Biology 309 – Cellular Physiology SUNY Oswego – Fall 2012 FINAL

Biology 309 – Cellular Physiology
SUNY Oswego – Fall 2012
FINAL Exam
1.
(25 Points) Throughout the second half of the semester, we have discussed EIGHT papers
based on topics essential to the study of cell biology. The purpose of the student presentation of
these papers was to reduce each document down to its key elements. Please review that paper
again and answer the following questions:
Cell mechanics and the cytoskeleton.
a. What is the focus of this paper? What question is it asking?
b. How does this paper relate to the study of cellular biology?
c. What physiological process(es) does the paper focus on?
d. What Cell Biology techniques do the authors of the paper employ? Give a brief
description of the technique.
e. In 1-3 sentences, explain the take-home message of each figure in the paper.
f. In a paragraph, sum up the take-home message of the entire paper. Take time to
reiterate the role each figure plays in composing this message.
g. Offer up one or more possible ideas for the next step in this research project.
Early biologists encourage the scientific community to think of the cell as an ordered
system rather than a collection of cellular components. As a system, the components work
together, and life depends on the interactions between them. Observing the exact inner workings
of a cellular network have proven hard due to the fact that a cellular network growing in a culture
behaves much differently than one in living tissues. The study of the cytoskeleton has offered the
best insight into the cell. This paper focuses on three main questions. The first is of the spatial
cues and physical restraints that allow the self-assembly of cellular components. Secondly this
paper aims to study the architecture of the cytoskeleton beyond the basic components and
composition. Lastly, the authors attempt to define the interactions that the cytoskeleton has with
its microenvironment in an attempt to determine the influences on cellular behavior. Another
component of cellular behavior is the question of a possible cellular memory function as an
influence on future cellular behavior (Fletcher et al., 2012).
The cytoskeleton has three main functions. It is involved in the spatial organization of the
cellular components, it connects the cell to its external environment, and it also generates forces
that allow the cell to move and change shape. To accomplish these tasks the cytoskeletal
components must also interact with cytoplasmic proteins and organelles (Fletcher et al., 2012).
Due to these functions and the importance of the tasks, the study of the cytoskeleton is essential
and to understanding the cellular biology. Many diseases are caused by a dysfunction in any
number of cytoskeletal components or processes (Ramaekers et al., 2004).
The authors of this paper employ a multitude of different cell biology techniques in order
to visualize their goals. A fluorescence microscope along with fluorescence markers bound to the
cytoskeleton was used to visualize growth and spatial organization as well as to determine the
form of the cytoskeleton. One experiment that was used to visualize the growth of the
cytoskeleton was injecting purified proteins into a vesicle and observing the growth. To
determine the effect that force and pressure has on the shape held by the cytoskeleton a cell was
attached to the cantilever of an atomic force microscope and the change in shape in correlation
with force applied was visualized with a fluorescence microscope.
Figure 1: This figure is depicting the three elements of the cytoskeleton and their relative
placement within a neural cell. It is meaning to show that actin filaments are located at the
axonal end of a neuron and the microtubules and intermediate filaments are located in the axon
arm.
Figure 2: This figure is visualizing the motility or the outer edge of cells, the process by which
the cytoskeleton is formed and the concept that there is not just one path for the cytoskeleton to
grow.
Figure 3: This figure is depicting that based on the architecture of the cytoskeletal elements, the
cellular force varies.
Figure 4: This figure is visualizing how the shape of the cell changes as the cytoskeleton
migrates to accommodate additional force being applied to the cell.
Figure 5: This figure is showing the method used to visualize the growth of the cytoskeleton. In
this method purified proteins were injected into a vesicle and the growth from single protein
monomers into a cytoskeleton was observed.
The take-home message of this paper is that the cytoskeleton is an essential element of
the cellular community that allows life. This component plays such an essential role because it is
abundant and has many functions (Alberts et al., 2008). It is also very complex and any mistakes
in the architecture can result in many diseases. In depth study of the cytoskeleton prove to be
important to understand the diseases that result from mistakes and to develop techniques to better
understand cellular behavior.
I feel like the necessary next step in research of the cytoskeleton would be to focus on
the genetic mutations that can cause cytoskeletal mutations that in turn lead to very devastating
disease. If we could understand this better it may be possible to develop screen for these genetic
mutations, or drugs that can replace the mutated cytoskeletal elements. If we could find a way to
replace mutated elements with functioning elements, it would eliminate all disease symptoms.
References
Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., Walter, P. (Eds). (2008) Molecular
biology of a cell (5th ed.). New York: Garland Science, Taylor & Francis Group, LLC.
Fletcher, D., Mullins, M. (2010). Cell mechanics and the cytoskeleton. Nature, 463, 485-492.
Ramaekers, F., Bosman, F. (2004). The cytoskeleton and disease. Journal of Pathology, 204,
351-354.
2. (25 Points) We spoke about cancer for a few class sessions. The disease is commonly caused
by combined defects in cell division & growth, and decreased induction of cell death in damaged
cells. We touched upon a few possible avenues for cures and treatments of this disease. Many of
you offered clever and interesting possibilities. For this question, I would like you to clarify
those ideas. Please give me a possible cancer treatment/ cure, based on the either current research
or on a new idea stemming from research into the systems involved in tumor formation. Do not
choose a current, common treatment. However, an experimental treatment, still in testing, would
be appropriate. Please include at least three references from the literature. They need not be
recent, but please clarify your decision to include any old papers. Your response should answer
the following questions
a. What is the target of your cure? Which system/ gene/ protein/ signal/ molecule?
b. What physiological process(es) would the cure affect? What are the potential sideeffects?
c. How will this cure be delivered? How long will treatment take? Up to which stage of
cancer will it remain effective?
d. What research would need to be done to begin testing of your cure? How long do
you think it would take to go from bench to patient?
e. Explain why you chose each paper in your bibliography. What about it attracted your
attention?
Many recent studies have implicated an abnormal mitochondrial function in tumor cells.
It has been shown that tumor cells have a defect in their mitochondrial function leading to
abnormally high glycolysis and lactate production; this has been termed aerobic glycolysis
(Frezza et al., 2009). The cure that I will propose will specifically target the mitochondria. More
specifically it will target the glycolysis pathway that takes place within the mitochondria.
Typically glycolysis is the form of energy production when cells are not in the presence of
oxygen; normal cells with oxygen access produce energy through oxidative phosphorylation
(Alberts et al., 2008). However, it has been shown that tumor cells, even in the presence of
oxygen are producing energy through glycolysis. This does two things, first it increases the
amount of glucose uptake in the cell dramatically, and secondly, the amount of the lactate
produced as a side product of glycolysis increases as well (Frezza et al., 2009). It is though that
this alternative way for producing energy that is present in tumor cells is the driving force behind
their uncontrolled and rapid growth. The mitochondria is effectively changed to convert its
products into usable anabolic pathway substrates and to increase its uptake of extracellular
nutrients (Barbosa et al., 2012).
As stated above the cure that is proposed will affect the glycolytic pathway of the
mitochondria. The most efficient way to accomplish this would be to create glycolytic inhibitors,
analogs for both the substrate and the product, or secondary substrate. The research for this cure
is already underway. The first analog would be for glucose, more precisely 2-deoxyglucose, a
compound that is metabolically inactive. This first analog is presently in its third phase of
clinical trials. Secondly, 3-bromopyruvate, a lactic acid analog currently only in pre-clinical
trials. 3-Bromopyruvate will result in a decreased ATP production, and 2-deoxyglucose will still
cause the mitochondria to use up ATP to attempt to convert it into lactate; however it is
unsuccessful due to its metabolic inactivity. Therefore after introduction these two analogs will
efficiently deplete the ATP store which will lead to the activation of apoptotic pathway
activation and cell death. This process offers few side effects; the analogs function in a way that
the cell tells itself to trigger apoptosis therefore there is minimal toxicity in the process. However
the patients, if the analogs are successful will be suffering from a significant amount of rapid cell
death, this process may come with some pain and discomfort. Some mild nausea was reported
along with slightly low blood sugar levels. However all side effects are easily treatable. This cure
will be delivered via an oral solution taken twice daily. The patients taking this cure will be
monitored closely with PET scans every three weeks, and CT scans every nine weeks and the
treatment will continue until those scans show a significant decrease in the tumor size (Pathania
et al., 2009). Perhaps once the size is reduced the tumor may become operable. This cure could
potentially be taken until the tumor is essentially void. This line of treatment is effective on all
stages of cancer however; it would be most effective in stage three cancers where the tumors
have become very solid. Solid tumors have shown the highest increase in glycolysis (Barbosa et
al., 2012).
I believe that studies will need to be done to ensure that the presence of a molecule that
mimics glucose will not significantly alter any other tissues or organs. The effect of these
inhibitors should also be studied with tumors that have metastasized should be studied to ensure
that unnecessary damage is not done to other areas of the body. I also believe that this cure needs
to be tested on a large array of tumor types and stages to ensure safety. Due to all of the steps in
drug trials and the long term studies that are needed I would believe that this cure would not be
available for at least two years after trials begin.
The first paper that I chose for the conception of a cure for cancer was a paper titled
Mitochondria in cancer: Not just innocent bystanders. This article peaked my interest because it
is hard to grasp that an organelle that is so abundant throughout our entire body and which has
such an essential function could be turns against us. This inspired my search into drugs that
could potentially mask the ill effects of these traitor organelles where I found Mitochondrial
remodeling in cancer metabolism and survival: Potential for new therapies. The biggest eye
catcher for this article was an enormous table filled with anticancer drugs targeting various
cellular molecules. Finally I found an article entitled Opportunities in discovery and delivery of
anticancer drugs targeting mitochondria and cancer cell metabolism. This article did provide me
with intriguing and helpful information but the sole reason that I even took a second glance at the
article is because it was a review article with over 300 references.
References
Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., Walter, P. (Eds). (2008) Molecular
biology of a cell (5th ed.). New York: Garland Science, Taylor & Francis Group, LLC.
Barbosa, I., Machado, N., Skildum, A., Scott, P., Oliveira, P. (2012). Mitochondrial remodeling
in cancer metabolism and survival: Potential for new therapies. Biochimica et Biophysica Acta,
1826, 238-254.
Frezza, C., Gottlieb, E. (2009). Mitochondria in cancer: Not just innocent bystanders. Seminars
in Cancer Biology, 19, 4-11.
Pathania, D., Millard, M., Neamati, N. (2009). Opportunities in discovery and delivery of
anticancer drugs targeting mitochondria and cancer cell metabolism. Advance Drug Delivery
Reviews, 61, 1250-1275.
3. (25 Points) During the second half of this class, we reviewed several processes common to the
study of cell physiology in robust detail. Some of these processes are well understood, while
others are currently being researched still. Choose one of the processes in the following list and
answer the questions below:
Membranes and Transport
Cellular Determination and Differentiation
Cellular Metabolism (using iPath as an example)
Signal Transduction
The Cytoskeleton
Cell Death
Cancer
The Extracellular Matrix
a.
b.
c.
d.
e.
Give a basic description of the process/ concept. Feel free to include figures/
diagrams/flowcharts.
What is the purpose of the process/ concept in the cell? What function/ benefit can it
provide?
Describe one disease specifically associated with this process.
Are there any key individuals identified in the original research that led to the current
accepted theories/ model describing this process?
Choose three research articles (from after 2008) that discuss the process. Explain the
importance of results/ analysis in each paper that led to a greater understanding of the
process. What important fact(s)/ idea(s) did the paper/ research reveal?
The cytoskeleton is a system of three different types of protein filaments, actin filaments,
intermediate filaments, and microtubules. Together these three types of protein establish cell
shape, provide mechanical strength, assist in locomotion and chromosome separation during
mitosis and meiosis, and function in the intracellular transport of organelles (Fletcher et al,
2010). One particular function that is interesting is the surface expression of certain
transmembrane proteins. One of which is the sodium potassium channel in the heart which uses
up 50% of the bodies energy to constantly keep the sodium and potassium levels accurate
(Loewen et al., 2008). This channel is essential to life and without its continuous normal function
we would die in a matter of minutes.
Actin filaments form a band just beneath the plasma membrane that provides mechanical
strength to the cell, links transmembrane proteins to cytoplasmic proteins pinches dividing
animal cells apart during cytokinesis. They can also generate cytoplasmic streaming in some
cells, generate locomotion in cells such as white blood cells and the amoeba, and interact with
myosin filaments in skeletal muscle fibers to provide the force of muscular contraction (Alberts
et al., 2008). Intermediate filaments have more than one variety based on the protein monomers
that make up the specific filament. Some of these proteins monomers are keratins which are
found in epithelial cells and also form hair and nails; nuclear lamins that form a meshwork that
stabilizes the inner membrane of the nuclear envelope; neurofilaments function to strengthen the
long axons of neurons; and vimentins which provide mechanical strength to muscle (and other)
cells (Alberts et al., 2008). Microtubules perhaps have the most diverse functions they participate
in a wide variety of cell activities; most involve motion. The motion is provided by protein
motors that use the energy of ATP to move along the microtubule (Albert et al., 2008). As you
can see the cytoskeleton encompasses a large amount of cellular process and is widely
distributed amongst individual cells and within the body. This allows a large amount of room for
error, and due to its significance these errors typically convert into diseases.
One disease that is caused by a cytoskeletal mutation is amyotrophic lateral sclerosis
(ALS), a neurodegenerative disease characterized by progressive muscular paralysis reflecting
degeneration of motor neurons in the primary motor cortex, corticospinal tracts, brainstem and
spinal cord. Limb onset ALS presents itself with symptoms related to focal muscle weakness and
wasting, where the symptoms may start either distally or proximally in the upper and lower
limbs. Bulbar onset ALS usually present with dysarthria and dysphagia for solid or liquids, and
limbs symptoms can develop almost simultaneously. Paralysis is progressive and leads to death
due to respiratory failure within 2–3 years for bulbar onset cases and 3–5 years for limb onset
ALS cases (Wijesekera et al., 2009). Abnormal assembly with accumulation of neurofilaments
together with Peripherin, an intermediate filament protein, are found in the majority of axonal
inclusions and motor neurons of ALS patients. A toxic isoform of Peripherin (Peripherin 61), has
been found to be toxic to motor neurons even when expressed at modest levels and is detectable
in spinal cords of ALS patients but not controls (Wijesekera et al., 2009)
I would say that there is not one specific individual that has been identified as a key
individual in the current theory on the cytoskeletal system. There are many individuals that are
working on different areas of the cytoskeleton and I believe that they all deserve credit for their
respective cytoskeletal niche. I also believe that the individuals who take the time to comb
through the extensive amount of research being done and collects it into one cohesive review is
also a key player. Daniel Fletcher, the primary author of Cell mechanics and the cytoskeleton
would be one of those individuals.
The first of my three articles offers research on the cytoskeleton and how it affects
cellular behavior. There was also research done on how the cytoskeletal networks generate and
how they transmit and respond to mechanical signals. It was found that the cytoskeleton is not
stationary and can shift in response to external force which is an important concept in living
beings. Based on the form of the cytoskeleton, there is four different types and each has a
different function, and that the three filament types are made up of different subunits that are
continuously recycled. The second article was into the symptoms and causes of amyotrophic
lateral sclerosis. It was found that among many other causes a defect in an intermediate filament
protein is proven to be toxic to neurons, these findings are essential because any research into a
disease is one step closer to a cure. The final article did research to find the effect that the
cytoskeleton had on surface expression of the sodium potassium channel that is essential in the
heart. I have done other research on this topic so I am aware just how important the sodium
potassium channel in to life therefore this research was significant because it demonstrated that
simple mutations in a somewhat simple system can have a devastating effect. This research all
pulls together into a recurring theme. The cytoskeleton is abundant, it encompasses every region
of the living body and small mutations can have devastating outcomes.
References
Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., Walter, P. (Eds). (2008) Molecular
biology of a cell (5th ed.). New York: Garland Science, Taylor & Francis Group, LLC.
Fletcher, D., Mullins, M. (2010). Cell mechanics and the cytoskeleton. Nature, 463, 485-492.
Loewen, M., Wang, Z., Eldstrom, J., Zadeh, A., Khurana, A., Steele, D. et al. (2008). Shared
requirement for dynein function and intact microtubule cytoskeleton for normal surface
expression of cardiac potassium channels. Heart and Circulatory Physiology, 296, 71-83.
Wijesekera, L., Leigh, P. (2009). Amyotrophic lateral sclerosis. Orphanet Journal of Rare
Diseases, 4 (3), 137-145.
4. (25 Points) In class, we discussed the cellular physiology of disease. Choose one specific
disease and, in robust detail please create a flowchart/ diagram that describes all of the cellular
factors involved in the onset/ causes of this disease. Please do not choose a disease that has
already been discussed on the wiki. Please label any molecular components involved in each
step. Be sure to point out any steps in the process where regulation may occur, or may be
defective. Then create a fact sheet that utilizes the categories listed below. When you are
finished, please post your disease flowchart and factsheet on the Class’s Wiki page.
A. Name of disease:
B.
Root cause of disease:
C.
Affected cell types/ tissues/
organs/ systems:
D. Historical background:
(Include discoverer(s),
famous victims, and any
historical events linked to the
disease).
Rheumatoid Arthritus (RA)
The root cause of this disease is unknown, it is an
autoimmune disease, meaning that the body’s immune
system mistakenly attacks healthy tissue. Thought to be a
combination of genetic, environmental, and hormonal
factors.
RA typically affects joints, such as wrists, fingers, knees,
feet, and ankles. However it can also affect, blood vessels,
heart tissue and lung tissue.
The first recognized description of rheumatoid arthritis was
in 1800 by the French physician Dr Augustin Jacob
Landré-Beauvais. The name "rheumatoid arthritis" itself
was coined in 1859 by British rheumatologist Dr Alfred
Baring Garrod (News Medical 2012). Christiaan Barnard,
the first surgeon to perform a human-to-human heart
transplant, Dorothy Hodgkin, a Nobel prize winning
scientist, and Jamie Farr, an American actor have all had
rheumatoid arthritis.
E.
Common symptoms:
F.
Standard treatments:
G. Current research: (Please
include reference citations
here).
H. References:
Morning stiffness lasting longer than 1 hour, warm tender,
or stiff joints when not being used, joint pain, decreased
range of motion, and deformation of joints are the most
common symptoms. Numbness, tingling or burning may be
felt in the hands and feet and in more severe cases, nodules
can be felt under the skin and sleep difficulties are present.
Disease modifying antirheumatic drugs are most
commonly used in association with physical therapy,
exercise, education and in some cases surgery. Antiinflammatory medications are also common to reduce
swelling. Corticosteroids are another common medication
but can only be used in low doses for short periods of time.
Current research is being done to make biologic agents as
treatment sources more useful and increase their safety,
white blood cell modulators, tumor necrosis factors, and
interleukin-6 inhibitors have been shown effective. These
treatments are given subcutaneously or intravenously
(Teitel, 2012). Research is also being done to measure the
effectiveness of deep heat or electrical impulses (Teitel,
2012). The newest compound to be tested with RA is a
compound named PS372424, this compound effectively
“blindfolds” white blood cells and keeps them from
reaching the joints where they cause damage to the healthy
tissues (O’Boyle et al., 2012).
O’ Boyle, G., Fox, C., Walden, H., Willet, J., Mavin, E.,
Hine, D., et al. (2012) Chemokine receptor CXCR3 agonist
prevents human T-cell migration in a humanized model of
arthritic inflammation. Proc. Of the Natl. Acad. of Sci., 109
(12), 4598-4603.
Ruderman, E., Tambar, S. (2012). Rheumatoid arthritis.
American College of Rheumatology.
Teitel, A. (2012) Rheumatoid arthritis. A.D.A.M. Medical
Encylcopedia.
Rheumatoid arthritis history. (2012). New Medical.