Teacher Resource for:
Full title of research paper
Cover image will go here
Table of Contents:
I.
GENERAL USE OF Science in the Classroom
a. Student Learning Goals (general)
b. Using this Resource
i. Learning Lens
ii. Learning Notes
iii. References
iv. Thought Questions
c. Suggestions for Classroom Use
II.
ARTICLE-SPECIFIC MATERIALS
a. Article Specific Materials
b. Connect to Learning Standards
c. Summary of the Article for the Teacher
d. Discussion Questions
GENERAL USE OF Science in the Classroom
Student Learning Goals:
“One fundamental goal for K-12 science education is a scientifically literate person who
can understand the nature of scientific knowledge.”1
The U.S. National Academy of Sciences defines science as: “Any new finding requires
independent testing before it is accepted as scientific knowledge; a scientist is therefore
required to honestly and openly report results so that they can readily be repeated,
challenged, and built upon by other scientists. Proceeding in this way over centuries,
the community effort that we call science has developed an increasingly accurate
understanding of how the world works. To do so, it has had to reject all dogmatic claims
based on authority, insisting instead that there be reproducible evidence for any
scientific claim.”
An important student learning goal, central to any understanding of “the nature of
scientific knowledge,” is to give each student an appreciation of how science is done.
This includes knowing why:
 Scientists must be independent thinkers, who are free to dissent from what the
majority believes.

Science can deal only with issues for which testable evidence can be obtained.

All scientific understandings are built on previous work

It is to be expected that one scientist’s conclusions will sometimes contradict the
conclusions of other scientists.

Science is a never-ending venture, as the results from one study always lead to
more questions to investigate.
1
A Framework for K-12 Science Education, National Research Council, 2012
Using This Resource
Learning Lens:
The Learning Lens tool can be found on the right sidebar of each resource and is the
source of annotations. Click on the headings to highlight portions of the text of the
corresponding research article. A subsequent click on the highlighted text will produce
a text box containing more information about that particular piece of text. Below is an
example of the Glossary function of the Learning Lens.
An example of the resource with the Glossary, Previous Work, Author’s Experiments,
News and Policy Links, and References and Notes tools turned on. The Glossary tool
is in use.
Learning Notes:
Learning Notes accompany each figure and are designed to help students deconstruct
the methods and data analysis contained within each figure.
References:
The Reference section of each resource is annotated with a short statement about how
or why each reference relates to the current research study.
Thought Questions
Thought Questions are located above the Learning Lens in the right sidebar of each resource.
These questions were written to be universal and applicable to any primary research paper.
Thought questions do not have a single answer, or a correct answer for that matter, and can be
used to stimulate discussion among students.
Suggestions for Classroom Use:
In addition to the thought questions discussed above, other resources are provided for
use in the classroom. These can be found toward the end of the teacher guides
associated with each specific article and include:
1. Discussion questions specific to the article, related to the standards, and/or
associated with the figures.
2. Activities tied to the articles.
Some ways to use the Science in the Classroom articles:
1. Assign to student groups to read and discuss during class.
2. Assign small sections of the article to student groups to read and discuss during
class, with the expectation that they will present or use jigsaw to teach the entire
class what is in their part of the article.
3. Assign to individual students to complete during class or as homework.
4. Assign reading as an extra credit project.
Some ideas for interactive student engagement after reading the article:
1. Students write answers to discussion questions (for example, those linked to the
standards or those linked to the diagrams).
2. Go over the abstract, as well as information about the purpose and structure of
an abstract, and have students write their own abstracts for the articles in
language that could be understood by their peers.
3. Have students edit the article, or parts of the article, to a simpler reading level.
4. Have students, alone or in small groups, use the annotated list of references to
explain how the scientists who wrote this article built on the published work of at
least one independent group of scientists in making their discoveries. In the
process, did they produce data that supports the findings of the earlier
publication that they have cited in the text? In what way does this article support
the statement that scientific knowledge is built up as a “community effort”?
5. Use the article and discussion questions linked to the standards and the
diagrams for a teacher-led classroom discussion. The discussion can focus on
the nature of science and scientific research, as well as on the science in the
article itself.
6. Have students give a classroom presentation about the article, parts of the
article, or their answers to discussion questions.
ARTICLE-SPECIFIC MATERIALS
Connections to the nature of science from the article


Why do scientists want to look at synaptic boutons in such detail?
How can this be achieved?
The importance of this scientific research

Further understanding of the architecture of the synaptic bouton; in particular, the
organization of trafficking proteins
The actual science involved
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Neurobiology
Proteomics
3D Modeling
Connect to Learning Standards
The AP Bio Standards
http://media.collegeboard.com/digitalServices/pdf/ap/10b_2727_AP_Biology_CF_WEB_
110128.pdf



Essential knowledge 2.E.2: Timing and coordination of physiological events are
regulated by multiple mechanisms.
Essential knowledge 3.D.2: Cells communicate with each other through direct
contact with other cells or from a distance through chemical signaling.
Essential knowledge 4.A.2: The structure and function of subcellular components,
and their interactions, provide essential cellular processes.
The Science and Engineering Practices contained in the Next Generation Science
Standards
http://www.nextgenscience.org/sites/ngss/files/Appendix%20F%20%20Science%20and
%20Engineering%20Practices%20in%20the%20NGSS%20-%20FINAL%20060513.pdf


Practice 2: Developing and Using Models
Practice 6: Constructing explanations (for science) and designing solutions (for
engineering)
The Common Core English and Language Arts Standards
http://www.corestandards.org/ELA-Literacy/RST/11-12/

Integration of Knowledge and Ideas: CCSS.ELA-Literacy.RST.11.12.8: Evaluate the
hypotheses, data, analysis, and conclusions in a science or technical test, verifying
the data when possible and corroborating or challenging conclusions with other
sources of information.
Summary of the Article for the Teacher:
It is recommended that this not be used by students in place of reading the article.
General Overview:
Sometimes we think of the brain as a large biocomputer, taking in information from our
senses and sending commands to our body in return. But how does information get
from one part of the brain to the other? Neurons pass electrical signals throughout the
brain through synapses, but what are the gears making that happen? The brain, and in
particular the synaptic terminal, uses a complex set of specialized proteins to create a
system of chemical reception and release. Moving beyond the mere identification of the
proteins involved, scientists are now using advances in analytics and 3D modeling to
create some of the most detailed models of the neuronal synapses to date.
Topics Covered:




Synapses and synaptic boutons
Cellular trafficking
Protein localization
Imaging and protein quantification techniques
Why this Research is Important:
Characterizing the architecture and mechanisms of the synapse is crucial to our
understanding of the way the brain works. Synapses form the basis of all chemical
communication and thus the basis of all functionality in the nervous system. While many
advances have been made as to the nature of large neural networks and the small
scale nature of particular proteins, not enough has been done to characterize the
system of synaptic proteins involved in a given synaptosome. Copy numbers and
localization of proteins informs their functionality and the larger functionality of the cell.
For example, low copy numbers of endocytotic proteins raise interesting efficiency
concerns and the “crowded” nature of the cell suggests potential problems for
intracellular diffusion.
Methods used in the Research:
 Ficoll density gradient
 Immunoblotting
 Immunostaining
 Electron microscopy
 Fluorescence microscopy (here, STED)
 Mass spectrometry
Conclusions:


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By mass, proteins take up ~7% of the synaptic volume; ~6% of the volume is
synaptic vesicles.
3D model shows that the synaptic terminal is highly crowded despite proteins
representing “only 7%” of the volume.
Proteins involved in exocytosis have high copy numbers.
Proteins that act in the same steps of synaptic vesicle recycling have strongly
correlated copy numbers.
Although some proteins maintain a linear relation between copy number and
synaptic size, many are related exponentially (particularly exponential proteins) -this suggests that some synaptic proteins are relatively more abundant in small
synapses than in large synapses.
Areas of further study:


How does the crowded nature of the synaptic terminal impact intra (and extra)
cellular diffusion?
How does the cell maintain similar copy numbers of functionally related proteins
despite drastic differences in the half-life and synthesis mechanisms of those
proteins?
Discussion Questions
Discussion questions associated with the learning standards
Essential knowledge 2.E.2: Timing and coordination of physiological events are
regulated by multiple mechanisms.

The researchers suggest that copy numbers of functionally related proteins are
correlated but are unsure of the mechanism keeping these numbers homeostatic.
What are some potential mechanisms? What are some common mechanisms
used to create homeostasis in other cellular systems?
Essential knowledge 3.D.2: Cells communicate with each other through direct contact
with other cells or from a distance through chemical signaling.

Why might cells use both direct and indirect signaling? Can you think of an
evolutionary rationale for using either/both forms? When might one type of
signaling be preferable?
Essential knowledge 4.A.2: The structure and function of subcellular components, and
their interactions, provide essential cellular processes.

Why might it be useful for cells to use smaller molecules, ions, or proteins to
mediate and facilitate the processes of larger functional systems?
Practice 2: Developing and using models

Why is 3D modeling useful in the study of very small cellular systems? Why
might numerical data about the physical characteristics of subcellular
components be misleading?
Practice 6: Constructing explanations (for science) and designing solutions (for
engineering)

Why is it important for researchers to expand upon their data? How do they go
about creating explanations for questions raised by their findings?
Integration of knowledge and ideas: CCSS.ELA-Literacy.RST.11.12.8: Evaluate the
hypotheses, data, analysis, and conclusions in a science or technical test, verifying the
data when possible and corroborating or challenging conclusions with other sources of
information.

What were the researchers trying to measure? How and why did they use
comparative analysis between their findings and those of other researchers?
Discussion questions associated with the figures
Fig. 1:

Panel A: Explain the mechanism of the Ficoll density protocol. Why are the
mitochondria, synaptosomes, and myelin separated by this technique? What is
centrifugation?

Panel B: Does this model represent a particular synaptosome, or the synaptosome
in general? Why is it important to create?

Panels D and E: What is a standard curve? How to do it and what is its purpose?
Fig. 2:

Panels A, B, and C: Why did the authors look at three different type of
organelles/cells (synaptosomes, hippocampal cultures, and mouse neuromuscular
junction)?

Panels A, B, and C: Why might there be a higher number of proteins in the
neuromuscular junction sample?
Fig. 3:

How many SNAP 29s are there in the figure of panel A? (Hint: Do not confuse SNAP
29 with the actin monomer.)