Last updated 9/6/23

Week 4 Pre-Class Study Guide

Gene Regulation

General Format:
These study guides (SGs) will have several parts; only parts 1 and 2 will be turned in
for class credit. All the SGs that are turned in are individual work (you are to express
everything here in your own words). Any instances of copying from other students or
resources will be considered academic misconduct.

Part 1: Reflection/Metacognition: Part of studying is reflecting on what you have learned

and reflecting on the process of your learning, how it may have changed your thinking,
what concerns you have or how you reacted to the material. This is called
metacognition.
Part 2: Learning objectives: We want you to learn how to use a textbook in a way that is
helpful to your learning and is efficient for this class. Texts often have a lot of
information that can be overwhelming when you first read. Not everything in the text will
be covered in detail in the class.
Part 3: Terms (not graded, but feel free to define)
Part 4: Exploration questions, study question, study tips (not graded)

Part 1: Reflection/Metacognition
Length guidelines for weekly metacognitions: We are looking for 1-2 decent paragraphs
or about 200 words. These will be graded on the basis of whether or not your writing
shows evidence of thoughtful reflection on your learning.
Answer 1-2 of the following questions, or add your own.
1. What role does chromatin remodeling play in gene regulation?

Chromatins are the building blocks of chromosomes and also play a big part in
controlling how available and accessible the DNA is during transcription. Chromatin is
made up of RNA, DNA, and protein. The most basic unit of chromatin is made up of
DNA that surrounds a protein in a specific structure. Chromatin remodeling is when
there are changes within the chromatins structure that regulate access to certain areas
in the DNA, and this restriction changes gene expression.
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2. How do mutations in regulatory regions impact gene regulation and contribute to

disease?
3. How do environmental factors affect gene regulation?
One way that environmental factors could affect gene regulation is through epigenetic
changes, like changing the functioning of genes without actually altering the DNA at all.
Environmental factors that could cause this change are stress, toxins, diet, etc. these
may seem like insignificant factors but can actually change how non-coded RNA is
expressed, and the process of DNA methylation.
4. How does epigenetics impact gene regulation?
5. How does a cell "decide" which genes to express and when?
6. What are the key players in gene regulation, and how do they interact?
7. What do you think is the most important anthropogenic pollutant and why?

Part 2: Learning Objectives

Instructions: Prior to class on Monday you should fill out the learning objectives as you
read the assigned reading. This work should indicate a good effort to understand the
upcoming week’s material. You may not be able to completely fill out each learning
objective, and that is ok. We are expecting 80-90% of these objectives filled out. This
document will serve as a good study guide. As you learn more about the topics during
class, fill out this document more fully.

Week 3 Gene Structure and Expression Learning Objectives

Students will be able to:
● Understand how the control of gene expression is different in eukaryotes and
prokaryotes.

Prokaryotic gene expression is primarily controlled at the level of transcription.

Eukaryotic gene expression is controlled at the levels of epigenetics, transcription, post-
transcription, translation, and post-translation. Prokaryotic gene expression (both
transcription and translation) occurs within the cytoplasm of a cell due to the lack of a
defined nucleus; thus, the DNA is freely located within the cytoplasm. Eukaryotic gene
expression occurs in both the nucleus (transcription) and cytoplasm (translation)

● Draw the organization of the elements of the lac operon of E. coli. Label all
features relevant to the control of transcription at the lac operon under different
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nutrient conditions (high glucose, low lactose; high glucose, high lactose; low
glucose, low lactose; low glucose, high lactose).
● Distinguish between positive and negative control of transcription.
Positive regulation is that regulation in which the presence of specific regulatory
element increases the expression of genetic information quantitatively. Negative
regulation is regulation in which the presence of specific regulatory elements diminishes
the expression of genetic information.
● Explain how you would go about choosing and arranging the elements of a
transgene (a recombinant [promoter + gene] that can be/has been added to
another organism) to get a human growth hormone gene to be expressed in the
same tissues in a mouse as mouse growth hormone normally is.
To achieve the expression of a human growth hormone gene in a mouse's tissues
where the mouse growth hormone is typically expressed, several steps can be taken.
First, it's crucial to select a suitable promoter region, ideally one that is active in the
same tissues as mouse growth hormone. The promoter region controls when and where
the gene is expressed. In this case, the mouse growth hormone promoter would be an
excellent choice. Second, the human growth hormone gene should be inserted
downstream of the mouse growth hormone promoter. This ensures that the regulatory
elements that govern the expression of mouse growth hormone are controlling the
expression of the human gene. Additionally, including appropriate enhancer sequences,
which are often found in the vicinity of the mouse growth hormone gene, can further
enhance the specificity and strength of the expression in the desired tissues. Finally, the
transgene construct should be inserted into the mouse genome using techniques like
pronuclear injection or CRISPR-Cas9 genome editing to achieve stable integration. By
combining these elements – the mouse growth hormone promoter, human growth
hormone gene, enhancer sequences, and proper integration – you can direct the
expression of the human growth hormone gene to mimic the pattern of mouse growth
hormone expression in the mouse's tissues.

● Define and explain the difference between genome, transcriptome and proteome.
The genome refers to an organism's complete set of genetic material, encompassing all
its DNA, both coding and non-coding. It provides the blueprint for all the genes an
organism can potentially express. The transcriptome represents the specific subset of
genes in the genome that are actively transcribed into RNA molecules (e.g., mRNA,
tRNA, rRNA) in a given cell or tissue at a particular moment, reflecting the dynamic
gene expression patterns. In contrast, the proteome comprises the complete set of
proteins synthesized from these RNA molecules, embodying the functional molecules
that carry out various cellular processes. While the genome is relatively stable and
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constant, the transcriptome and proteome are highly dynamic and can change in
response to environmental cues, developmental stages, or diseases, providing insights
into the regulation and functional diversity of an organism's genetic information.
● Explain how RNAseq (i.e. transcriptomics) and proteomics can be used to
assess gene expression.
Prokaryotic Gene Regulation
● Define operon, label an operon.
A unit made up of linked genes which is thought to regulate other genes responsible for
protein synthesis.

● Distinguish between promoter, operator and between repressors and activators.

Eukaryotic Gene Regulation
● Identify, describe, and provide an example of different levels of gene regulation in
eukaryotes including at the level of the chromosome, the level of gene
transcription, transcriptional processing, transportation from the nucleus,
translation, and posttranslational modifications.
● Define alternative splicing and explain how it may provide for increased
complexity in organisms.
Alternative splicing is a molecular process in gene expression where a single pre-
messenger RNA (pre-mRNA) molecule can be spliced in different ways to produce
multiple mRNA transcripts, resulting in the generation of distinct protein isoforms from a
single gene. This phenomenon increases complexity in organisms by expanding the
functional diversity of the proteome. It allows for the production of multiple protein
variants with distinct functions, tissue-specific expression patterns, and regulatory
properties from a single gene, thereby enabling organisms to perform a wide range of
specialized functions, adapt to changing environments, and efficiently utilize their
genetic information. Alternative splicing plays a crucial role in enhancing biological
complexity and is a fundamental mechanism underlying the diversity of multicellular
organisms.

● Distinguish between promoters, enhancers and silencers.

● Distinguish between basal level of transcription and regulated transcription and
between general transcription factors and regulatory transcription factors.
The basal level of transcription represents the constant, minimal level of gene
expression that occurs in the absence of specific regulatory signals. It involves the core
transcriptional machinery, including general transcription factors (GTFs), and ensures
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essential cellular functions are maintained continuously. In contrast, regulated

transcription is a dynamic process in which gene expression is modulated in response
to various signals or stimuli. It requires the involvement of regulatory transcription
factors (TFs) that bind to enhancers or promoters, interacting with GTFs and the RNA
polymerase to either enhance or suppress gene expression. While GTFs are essential
for the initiation of transcription at all genes and constitute the basal transcriptional
machinery, regulatory TFs play a specific role in modulating gene expression in a
context-dependent manner, allowing cells to respond to environmental cues,
developmental signals, or other cellular requirements.

● Explain how regulation of gene expression is essential for development of

multicellular organisms.
The regulation of gene expression is essential for the development of multicellular
organisms as it governs the highly coordinated processes that lead to cell
differentiation, tissue formation, and the overall organization of complex body structures.
Through precise control of which genes are turned on or off in specific cells at distinct
developmental stages, gene regulation guides the specialization of cell types, ensuring
that cells perform their intended functions. This orchestration is crucial for creating
diverse tissues and organs and for maintaining the overall integrity of the organism. It
allows multicellular organisms to generate the cellular diversity necessary for functions
like digestion, respiration, and reproduction, ultimately enabling them to adapt to their
environments and thrive in diverse ecological niches.

Part 3: Terms (be able to understand & use correctly):

We will expect that you will understand and be able to correctly use these terms. We
will not necessarily be defining them during class. You may find it helpful to look these
terms up to check your understanding, however you do not need to fill the terms out for
the LRR you turn in (though you may choose to for your own studying).

Terms from Week 2

Promoter Poly-cistronic RNA
Operator Expression
Enhancer Basal transcription
Silencer Transcription start site
Transcription unit Transcription factor
Operon Sigma factor
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RNA polymerase Regulated gene

Repressor Negative control
Activator Positive control
Small effector molecule Inducible operon
Lactose / allolactose Repressible operon
CAP Regulatory gene
Pre-initiation complex Combinatorial control
Transgene Gene silencing
Proteomics RNAseq
Constitutive genes

Exploration Questions, Study Questions & Tips (Not-graded)

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Additional Resources
If you are finding Chapter 14 a little difficult to process, I have posted some additional
links that may help below.
Prokaryotic Gene Regulation
Lac Operon: https://www.viddler.com/embed/998932a2/?
f=1&autoplay=0&player=simple&secret=90576092&loop=0&nologo=0&hd=0
Trp Operon:
https://www.viddler.com/embed/59ca406e/?
f=1&autoplay=0&player=simple&secret=90576092&loop=0&nologo=0&hd=0
Eukaryotic Gene Regulation
Transcription complex and enhancers:
https://www.viddler.com/embed/2655249/?
f=1&autoplay=0&player=simple&secret=90576092&loop=0&nologo=0&hd=0
Different levels of control of gene expression:
https://www.viddler.com/embed/9dda78fd/?
f=1&autoplay=0&player=simple&secret=90576092&loop=0&nologo=0&hd=0

Common Misconceptions to Avoid

• It is easy to think that just because a gene is present in the genome, that it will be
expressed. Actually, any gene without a promoter will be silently carried, not
transcribed, not directing production of protein, and not contributing to the phenotype of
the individual.
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• Some people think that a gene is either on or off. In reality a promoter can direct just a
few transcripts to be made, or thousands. It can be on at one stage of life, or at many.
It can be on in all cells or in just some. Genes are regulated with tremendous nuance.
• Also, it is easy to think that a promoter of one organism would work well in another
organism. This isn’t always the case. A human (eukaryotic) promoter might not, for
example, drive the transcription of a gene – either human or bacterial – in an E. coli
bacterium (prokaryote).

Study Questions (be able to answer these by the end of the week)
1) What is an operon? Define and draw an example below and label the elements
that make up the operon.

a. Complete the following table.

Operon Stimulus Effect on regulation Effect on transcription
Lac Glucose
present
Lac Lactose
present
Trp Tryptophan binds
trp repressor

b. Evolutionarily why might it be advantageous for the Lac and Trp operons
to function as they do?

2) In reproduction, egg and sperm join to form a zygote, a single cell. This cell
divides through mitosis and forms a multicellular organism with cells of different
functions.
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What can you say about the genome in each of the cells of the multicellular organism?
Define genome in your answer.

What can you say about the proteome in each of the cells of the multicellular organism?
Define proteome in your answer.

Explain the role that gene regulation plays in the formation of a multicellular organism
with cells of different functions from a single cell.

3) Describe and provide an example of gene regulation in eukaryotic organisms at

the level of
a. Chromosome

b. Gene transcription
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c. Posttranscriptional processing

d. Translation

e. Posttranslational processing

4) Define alternative splicing. Draw an example. Explain how alternative splicing

may increase complexity without increasing number of genes.