Download Chapter 16 Instructor Manual

CHAPTER 16: CONTROL OF GENE EXPRESSION
WHERE DOES IT ALL FIT IN?
Chapter 16 builds upon the coverage of protein synthesis in Chapter 15 and provides detailed
information about gene regulation. As in Chapter 15, it is important to stress the differences between
prokaryotes and eukaryotes. This information in Chapter 16 is needed to fully understanding the
principles of biotechnology covered in Chapter 17 and genomics discussed in Chapter 18.
SYNOPSIS
Prokaryotes and multicellular eukaryotes both control gene expression, but for quite different
reasons. Bacteria must exploit the resources of a changing environment. If they do not adapt, they
die, but maintaining numerous unused enzymes is metabolically expensive. Multicellular eukaryotes
must be protected from those changes. The hallmark of multicellular organisms is homeostasis:
maintaining a constant internal environment. To ensure this, genes must be transcribed in a specific
order over a specific time frame. Transcriptional control and posttranscriptional control are two
primary levels of gene regulation. The former is the more common method. Transcriptional gene
control is mediated by influencing the binding of RNA polymerase to the DNA helix. An mRNA
transcript cannot be produced if RNA polymerase cannot bind to the promoter. Control to stimulate
transcription can also be effected, thus facilitating the binding of polymerase and promoter.
The entire DNA helix does not need to unwind for transcription to ensue. Only a small section needs
to unwind, just enough to expose the major groove to the structural motif of the correct protein.
Nearly all proteins use one of four motifs to bind with their respective DNA region. The most
common is the helix-turn-helix motif, two alphahelical regions linked by a short nonhelical region.
One of the helices aligns next to the DNA. The other, the recognition helix, physically fits into the
DNA major groove. The homeodomain motif is a specialized class of helix-turn-helix that was
discovered in homeotic mutants Drosophila. The zinc finger motif uses atoms of zinc to help the
protein bind to its DNA. In the leucine zipper motif, two protein subunits create a single Y-shaped
DNA-binding site that resembles a partially opened zipper.
Prokaryotes alter expression of genes when their environment changes. A common pattern in
prokaryotes is that gene products necessary for certain catabolic reactions are only expressed when
the substrate is present. Such systems are said to be inducible. Other gene products necessary for
anabolic pathways are only expressed when the cell needs to build that particular molecule. These
are referred to as repressible systems. Each system involves regulatory proteins that will bind to the
DNA and alter genetic expression, either by initiating expression (positive) or suppressing expression
(negative). Repressors, regulatory proteins that exhibit negative control, act as OFF switches. These
can be seen in both inducible and repressible systems. In the inducible E. coli lac operon, lactose
binds to the regulatory protein and prevents it from halting transcription necessary for lactose
metabolism. In the repressible trp operon, tryptophan binds to the regulatory protein allowing for the
suppression of expression genes necessary for tryptophan synthesis. Activators, regulatory proteins
that exhibit positive control, are ON switches to ensure that transcription does not occur unless a
specific activating chemical is present. The E. coli catabolite activator protein (CAP) is a good
representation of this system. The lac operon of E. coli combines ON and OFF switches to ensure
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that (1) the lactose degrading enzymes are not produced when glucose is present – there’s no need for
it since glucose is a better food source, and (2) they are only produced when lactose is present –
there’s no need to make enzymes if their substrate isn’t present.
Genetic regulation in eukaryotes is much more complicated than what is seen in prokaryotes. In
comparing transcriptional control between eukaryotes and prokaryotes, similarities due exist.
Regulatory proteins, called transcription factors, must bind to DNA to regulate transcription.
Transcription factors can either be basal transcription factors, proteins necessary for recruitment and
proper binding of RNA pol II, or specific transcription factors, proteins that alter expression levels
depending on specific signals.
Eukaryote gene control greatly depends on the structure of the eukaryotic chromosome. Histones
affect gene transcription by physically blocking the promoter with the nucleosome they create.
Methylation, once thought to be a primary regulator in vertebrates, helps ensure that once a gene is
turned off, it stays off. Posttranscriptional control is common in eukaryotes. Researchers have found
that small RNA molecules seem to interfere with translation directly or the breakdown of the mRNA
before translation. The eukaryote primary mRNA transcript is a linear patchwork of coding exons
and noncoding introns. The entire sequence is made during transcription, the introns are cut out later.
In many cases, the various ways the exons can be spliced back together allows for production of
different polypeptides from just one gene. Aside from the importance of gene control, this kind of
transcription seems quite wasteful. Only ten percent of all transcribed genes are exons and only half
of that ever gets out of the nucleus. It is yet unknown as to whether this is under any kind of selective
control. Proteins called translation factors regulate production of polypeptides from the mRNA
transcript. Translation repressor proteins can also shut down translation by preventing the attachment
of the transcript to a ribosome. Although most mRNA transcripts are very stable, some, like those
associated with regulatory proteins and growth factors, are less stable. They possess certain 3’
sequences that make them attractive to mRNA degrading enzymes. This ensures that control by these
proteins remains as transitory as it should be.
LEARNING OUTCOMES
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Understand how regulatory proteins work and why gene control is necessary for a cell’s survival.
Differentiate between transcriptional and post-transcriptional control of gene regulation.
Know how RNA polymerase is linked to control of transcription.
List the four primary kinds of structural motifs and delineate their modes of action.
Differentiate between repressors and activators, using the lac operon as an example.
Describe the two primary kinds of transcription factors in eukaryotes.
Understand how eukaryotic chromosome structure is associated with gene regulation.
Know how a primary transcript is processed to effect post-transcriptional gene control.
Differentiate between introns and exons.
COMMON STUDENT MISCONCEPTIONS
There is ample evidence in the educational literature that student misconceptions of information
will inhibit the learning of concepts related to the misinformation. The following concepts
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covered in Chapter 16 are commonly the subject of student misconceptions. This information on
“bioliteracy” was collected from faculty and the science education literature.
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Students have trouble distinguishing chromatin from chromosomes
Students do not fully understand the role of genetics and environment on determining
observable variation in organisms
Students think that prokaryotes and eukaryotes have the same DNA structure
Students do not make the connection between environmental or cell signals with gene
regulation
Students believe that all genes program for proteins
Students believe the eukaryotes have operons
Students believe that all transcription factors are general
Students are unaware of the enzymatic nature of RNA
Students believe that mRNA splicing occurs without variation
Student believe that all gene regulation occurs before or during transcription
INSTRUCTIONAL STRATEGY PRESENTATION ASSISTANCE
Not only did the cell beat us to the punch as far as the assembly line, it also did module building
first. Alternative splicing is like building a modular home. The company makes a selection of
room modules; the buyer decides which ones to use and where to put them. Do you want two
bedrooms or three? Should the dining room or the family room be to the left of the kitchen? It
ends up looking like an entirely different house than the one next door.
Students must know what each part of the operon does to clearly understand gene regulation and
the lac operon. A regulator wouldn’t function properly if it were at the end of the operon any
more than a spillway would regulate the flow of water into a mill if it were on the downstream
side of the wheel.
Don’t let the students confuse exons and introns. The immediate tendency is to associate exon
with other words starting with “ex,” where “ex” means out, and assume that an exon is cut out.
WRONG! The “ex” in exon derives from expressed, as in expressed sequence. The “in” in intron
comes from intervening sequence, that is, the section that is later cut out. (This may be one time
that it is beneficial that most students merely memorize words rather than try to understand
where they come from.)
HIGHER LEVEL ASSESSMENT
Higher level assessment measures a student’s ability to use terms and concepts learned from the
lecture and the textbook. A complete understanding of biology content provides students with the
tools to synthesize new hypotheses and knowledge using the facts they have learned. The
following table provides examples of assessing a student’s ability to apply, analyze, synthesize,
and evaluate information from Chapter 16.
Application
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Have students predict the type of gene regulation carried out by
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chloroplasts and mitochondria.
Analysis
Synthesis
Evaluation
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Have students design an experiment to see if a gene associated with the
breakdown of starch is inducible.
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Ask students to predict the outcomes of a mutation that prevents the
removal exons.
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Have students explain the differences and similarities between
prokaryotic and eukaryotic gene regulation.
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Ask students to determine the effects of genetic disease that prematurely
labels proteins with ubiquitin.
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Ask students to predict the possible outcomes if the promoter of a gene
develops a frameshift mutation.
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Ask students to come up with a way to get prokaryotes to regulate
eukaryotic enzymes after inserting a gene for that enzyme.
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Have students develop a medical use for ubiquitin.
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Ask students come up a reason for permanently activating certain
inducible genes in agricultural plants.
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Ask students to evaluate the possible medicinal value of chemicals that
inhibit certain transcription factors.
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Ask students to determine the safety of drugs that prevent the formation
of polyubiquitinated proteins involved in depression.
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Ask to evaluate the safety concerns of introducing eukaryotic genes into
prokaryotes.
VISUAL RESOURCES
Palindromes are words that exhibit two-fold rotational symmetry (bob, kook, deed). The phrase
“a toyota” is a palindrome as is “a man, a plan, a canal, panama.” Instruct students to search for
other examples of palindromes.
The scifi film “Gattaca” touches on future (or maybe not so future!) gene technology and the
ethical implications of genetic control. Substantial information is available at the movie website
http://www.sciflicks.com/gattaca/.
IN-CLASS CONCEPTUAL DEMONSTRATIONS
A. Stringing Along Gene Regulation
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Introduction
This demonstration provides a tangible model for showing students RNA splicing,
methylation, and histone modification.
Materials
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Thick permanent markers
White Clothesline or thick rope
Yellow twine
Colored modeling clay
Toy car
1 inch thick slivers of duct tape
Scissors
Procedure & Inquiry
1. Review the concepts of eukaryotic gene regulation.
2. Tell the students you will be using rope to represent a the double helix of DNA,
a. Use clay to represent the histones and show how DNA can be wrapped tightly
around histones to prevent expression.
b. Then take the DNA and say you will be adding methyl groups to the DNA strand.
Place small chunks of clay on the string to represent methylation. Then say that
the car is RNA polymerase and “run” it down the strand. Explain that the “road
bumps” inhibit the function of RNA polymerase.
3. Now, tell the students you will be using rope to represent a pre-mRNA molecule.
a. Mark introns with the colored markers
b. Ask the students to tell you what happens next and why
c. Proceed to cut out the introns while explaining pre-mRNA splicing
d. Ask the students to tell you what happens next and why
e. Tape the pieces together using the duct tape
f. Then explain the addition of the poly A tail by taping the yellow twine to the rope
g. Ask the students to explain the function of the poly A tail
h. Discuss the mRNA capping process and add a large nub of clay to the end of rope
opposite the poly A tail
i. Ask the students to explain the function of the capping process
j. Explain that the mRNA can now be transported to ribosomes
4. Now use the scissors to chop up the mRNA explaining that mRNA is destroyed in the
cytoplasm as a way of regulating gene expression
USEFUL INTERNET RESOURCES
1. Animations are a valuable classroom resource for reinforcing a lecture on gene
regulation. The National Cancer Institute provides a wonderful animation about current
topics on gene regulation. Included is methylation and other regulatory mechanisms. This
website can be found at
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http://www.nci.nih.gov/newscenter/benchmarks-vol5-issue1/Video
2. Presenting students with research applications of metabolic engineering is good way to
reinforce the learning of gene regulation concepts. Metabolic engineering is a new
approach to understanding and using metabolic processes. It relies on a knowledge of
gene regulation. An intergovernmental website on metabolic engineering can be found at
http://www.metabolicengineering.gov/
3. Microarrays are new tools for investigating gene regulation. The National Institutes of
Health has an informative website about the use of microarrays in studying genetics. This
website can be found at http://www.ncbi.nlm.nih.gov/About/primer/microarrays.html
4. Case studies are a highly effective way to reinforce the learning of complex topics in
genetics. A case study called “In the Genes or in the Jeans? A Case Study on Sexual
Differentiation” has students challenging their views on gender. The case students
investigate the role of gene regulation in determining human gender. The website can be
found at http://www.sciencecases.org/gender/gender.asp.
LABORATORY IDEAS
Lego® My Genes Activity
a. Tell students that you would like them to design a model of depicting gene regulation in
prokaryotes and eukaryotes. Explain that scientists commonly make tangible models of
biological molecules to better understand cellular functions.
b. The following materials should be provided to a small group of students:
a. Lego® blocks of various colors
b. Colored markers
c. Scissors
d. A roll of cellophane tape
e. A roll of Velcro®-type adhesive tape
f. Yarn or thick string
g. Pop beads of various colors
c. Explain to students that the models should show the differences between prokaryotic and
eukaryotic gene regulation. The models should also take into account all of the factors
involved in controlling genes.
d. Have the students explain their models to the class. The students should use their models
to compare and contrast the genomic regulation of different cells.
e. Then have the class briefly evaluate the various group models for accuracy/
LEARNING THROUGH SERVICE
Service learning is a strategy of teaching, learning and reflective assessment that merges the
academic curriculum with meaningful community service. As a teaching methodology, it falls
under the category of experiential education. It is a way students can carry out volunteer projects
in the community for public agencies, nonprofit agencies, civic groups, charitable organizations,
and governmental organizations. It encourages critical thinking and reinforces many of the
concepts learned in a course.
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1. Have students do a presentation on the link between gene regulation and cancer at a
college or school health fair.
2. Have students design an educational PowerPoint presentation on gene regulation for high
school teachers.
3. Have students tutor middle school or high school biology students studying genetics.
4. Have students design and build an accurate model of operons for a school library or
science department.
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