Tips for Teachers Gene Expression Essentials
Expression Screen
Explore the main sequence of events that occur within a cell that leads to protein synthesis. Generate
and collect three types of protein.
EXPERIMENT COLLECT
with biomolecules proteins
OBSERVE
translation
EXPLORE three
ATTACH
different genes
transcription
factors
mRNA Screen
Explore the factors that affect transcription, including positive and negative transcription factor
concentration and af nity, and RNA polymerase af nity.
ADJUST the
concentration OBSERVE
and af nity transcription
SHOW/HIDE
negative
transcription
factor
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Multiple Cells Screen
Explore the factors that affect protein synthesis in a cell, and relate protein production in a single cell to
the quantity produced by a collection of cells.
SEE real protein
cells (GFP) CONTROL
concentration,
af nities, and
degradation
OBSERVE the
average protein PAUSE and
level in real-time advance frame-
by-frame
ADJUST the
number of cells
Insights into Student Use
• One of the learning goals of the Multiple Cells screen tries to lead students to see the difference
between the average protein level expressed by a single cell and multiple cells. Students will likely need
to pay attention to the level of uctuations on the dynamic protein level graph to make sense of this
connection.
• On the mRNA screen, consider asking students to describe the factors that affect mRNA production,
or rst challenge them to produce mRNA as quickly as possible.
Model Simpli cations
• The process being portrayed does not show the mRNA moving out of the nucleus, and is thus
essentially showing a prokaryotic cell, rather than a eukaryotic cell.
• The RNA polymerase and transcription factors have pseudo-random movement which tends to drive
towards the gene region.
• Ribosomes are available to the user in "pre-assembled" form, meaning that the large and small
subunits are already together, rather than having the subunits come together as mRNA transcription
begins.
• The genes being transcribed are signi cantly shorter (in terms of the number of base pairs) than real-life
genes. On average, a real gene in a prokaryotic organism is 1000 base pairs, whereas the genes in this
simulation contain less than 100 base pairs.
• For simpli cation, some facets of gene expression/protein synthesis are not depicted — including
individual amino acids, protein folding, and tRNA.
• On the Multiple Cells screen, the protein production being modeled is green uorescent protein (GFP).
• The sizes and shapes of the biomolecules were inspired by the illustrations in "The Machinery of Life"
by David S. Goodsell.
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Suggestions for Use
Sample Challenge Prompts
• Synthesize and collect all three types of protein.
• Compare and contrast the three genes.
• Explain what happens when a negative transcription factor binds to a gene.
• Predict how changing the concentrations and af nities of biomolecules affects protein production.
• Determine a way to (a) synthesize lots of mRNA, (b) synthesize a little mRNA, and (c) completely block
mRNA synthesis.
• Maximize the average protein level in a group of cells.
Customization Options
Query parameters allow for customization of the simulation, and can be added by appending a '?' to the
sim URL, and separating each query parameter with a ‘&’. The general URL pattern is:
…html?queryParameter1&queryParameter2&queryParameter3
For example, in Gene Expression Essentials, if you only want to include the 1st and 2nd screens
(screens=1,2), with the 2nd screen open by default (initialScreen=2) use:
[Link]
To run this in Spanish (locale=es), the URL would become:
[Link]
Query Parameter and Description Example Links
screens - speci es which screens are included in screens=1
the sim and their order. Each screen should be
separated by a comma. For more information, visit screens=2,1
the Help Center.
initialScreen - opens the sim directly to the initialScreen=1
speci ed screen, bypassing the home screen. initialScreen=3
locale - specify the language of the simulation locale=es (Spanish)
using ISO 639-1 codes. Available locales can be locale=fr (French)
found on the simulation page on the Translations
tab. Note: this only works if the simulation URL
ends in “_all.html”.
allowLinks - when false, disables links that allowLinks=false
take students to an external URL. Default is true.
See all published activities for Gene Expression Essentials here.
For more tips on using PhET sims with your students, see Tips for Using PhET.
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