Download Eukaryotic Gene Regulation

Name
Controlling Eukaryotic Gene Expression
3.2
Regulation of gene expression is important for two reasons:
•
Responding to _________________ from external and internal environments
•
Essential for _________________ cells in multicellular organisms
Consider humans…
•
•
_______% of our DNA codes for proteins
–
The rest codes for _______ products (like tRNA)
–
Some not transcribed at all
–
Some genes are transcribed constantly, like the ones that make ribosomes
All of our cells have identical genomes. Differences in cell types due to _________________________
Gene expression can be turned on or off, accelerated or slowed
down. There are various levels of eukaryotic gene regulation.
Level 1: Modifications of chromatin structure
•
Tightly wound DNA less accessible for transcription
•
: methyl groups added
to DNA or histones; makes it condense (wind up tighter); 
transcription
•
: acetyl groups added
to histones; loosened;  transcription
•
Epigenetic inheritance results from this.
•
These DNA modifications can be passed to future
generations, but unlike mutations, these can be
reversed. This explains difference between identical
twins!
Level 2: Modifications of transcription
•
Control elements, such as ________________________
and enhancers, affect how often transcription happens
–
•
These can be ______________ or ____________
The combination of transcription factors determines how
much, if any, product is made
Side note about control elements and how they work
•
DNA still has a _____________________ region for RNA
polymerase to bind…but there are other elements too
•
•
__________________ region: located near or in the promoter
When the enhancer is bound to the __________________,
transcription happens
– Controlled by activators, repressors, and transcription
factors
•
When an ________________________ binds an enhancer…
– DNA bends, other regulatory proteins bind and connect the
two areas of DNA, transcriptoin occurs
•
______________________ proteins can work by….
– Binding to a control element
– Blocking activators
– Turning off transcription, even if activators bind
•
Soon we will come back to how this allows differential gene expression
Level 3: Post-Transcriptional Control
Before the mRNA is transcribed:

_______________________________________ (“cut and paste” differently)

mRNA degradation by ____________________ (remove 5’ cap)

__________________ (small, single-stranded mRNA) might bind to the newly-created mRNA

The miRNA complex then degrades the mRNA or blocks translation

This is called _____________________________ (or RNAi).
At the start of translation:

Regulatory proteins or molecules (like miRNA) bind to the 5’ end so a ribosome can’t attach
A protein is made, and then the following might happen…

The protein is processed (cleavage, chemical modification)

It gets tagged with _______________ and then a ______________________ finds the tag and
destroys the protein
REMEMBER!
Signal transduction pathways often cause transcription factors to
bind to DNA—this is one way that a ligand can influence gene regulation!!!
This information comes from Expression in Eukaryotic Cells (pages 356-372)
I.
Combinational control of gene activation
a. In eukaryotes, which genes are transcribed depends mainly on the binding of activators to DNA
control elements.
i. Go back to page 359. What is a control element?
b. Read the rest of this section, but don’t get too lost in the details. The main idea is found in figure
18.10. Study the figure first, and then come back to the notes to walk through what is going on.
i. Remember that ALL cells in your body have
the SAME DNA. What makes a liver cell
different from a lens cell (in your eye) is
WHICH genes are turned on. All the genes
are there, but not all are being expressed.
In the picture, two genes are being
considered in both cells.
1.
What are the two genes?
2. Which one of the two genes does a
liver cell express?
3. Which one of the two genes does a
lens cell express?
ii. You can see that the enhancer region (the series of 3 colors) is different for both cells.
iii. I find it easier to cover up part of each picture to understand what’s going on. Let’s walk
through it. Follow along on the next page.
Understanding how different cells, despite having identical DNA,
turn “on” different genes using Fig. 18.10:
Look at the liver cell 1st. Using your hand, cover up the crystallin gene (it’s not expressed in the liver).
The gene is STILL THERE, though, because all cells have the same DNA!

What are the three pieces of the enhancer in
the liver cell? (list the 3 colors you see).

A cell makes its own transcription factors.
Transcription factors are proteins that help a
cell “decide” which genes will be expressed.
What three transcription factors does the liver
cell make? (what are the colors of the “available
factors” at the top?)

Now take your hand off the bottom part of the
picture. The crystallin gene enhancer consists of
orange, gray, and pink pieces. You can see that
the liver cell’s transcription factors will not activate this gene because the colors do not match the
enhancer colors of the crystallin gene (except one- the gray one).

Thus, we can say that the two genes share one control element [the gray one], but ALL of the
activators are needed to express the particular gene.

So only albumin, but not crystallin, is expressed in the liver.

Using the same logic, please explain how the lens cell expresses crystallin, but not albumin.
18.4 A program of differential gene expression leads to the different cell types in a
multicellular organism
I.
A genetic program for embryonic development
a. Define cell differentiation
b. Define morphogenesis
c.
These processes have their basis in cellular behavior. Materials placed in the ________ by the
mother set up a sequential program of gene regulation that is carried out as cells divide (see
figure 18.15a).
d. Cytoplasmic determinants and inductive signals:
The specific genes expressed in any particular cell of a developing cell
of a developing organism determine the cell’s path.
e.
One source of info that tells a cell which genes to express is in the egg’s cytoplasm.
i. The cytoplasm contains mRNA, proteins, other substances, and organelles distributed
unevenly in the egg. What are these substances in the egg that influence the course of
development called?
ii. When fertilization occurs, a sperm joins with the egg and contributes its genetic
information.
iii. After fertilization occurs, which cellular process distributes the zygote’s cytoplasm into
separate cells?
iv. As a result of the heterogeneous (uneven) mixture of “things “ in the egg, and the way the
cells divide, each resulting cell is exposed to different cytoplasmic determinants. This
helps regulate what the cell becomes over the course of differentiation. How amazing is
that?!?!
f.
Another source of info that tells a cell which genes to express is the environment around the
cells. This becomes more important as more and more cells arise via mitosis.
i. Which signals are the most influential?
ii. What is induction?
II.
Sequential regulation of gene expression during cellular differentiation
a.
As tissues and organs of an embryo develop and their cells differentiate, the cells become
noticeably different in structure and function. Once a cell undergoes ________________, it is
irreversibly committed to its final fate (whatever kind of cell it’s programmed to become).
b. Determination of a cell occurs due to molecular changes. Once a cell differentiates, it expresses
genes based on what kind of cell it is/what kind of tissue it makes up. Thus, they only express
genes for _____________________________.
i. These proteins are found only in a specific cell type.
ii. They give the cell its characteristic _______________ and function.
iii. Many of these proteins are transcription factors, which bind to specific control elements
in the enhancers of various target genes. This binding stimulates their expression.
1.
Read through the information about myoD and view figure 18.16 to see a specific
example of how this occurs in muscle cells.
III.
Pattern formation: setting up the body plan
a. Introduction
i. This section is going to go through how the fruit fly, Drosophila, develops.
ii. What is pattern formation?
1.
This begins in the early embryo, when the major axes of the body are established.
The molecular cues that control pattern formation are called positional
information and are provided by what?
iii. Studying the development of Drosophlia embryos provides hints about developmental
principles common to many other species, including humans.
b. The life cycle of Drosophila
i. What are the 3 major body parts of fruit flies and other arthropods?
ii. What axes are present in fruit flies and other bilaterally symmetrical animals? Also draw
these out (see fig. 18.17a).
iii. Describe or draw a simple flowchart for life cycle of a fruit fly, from egg to adult fly.
c.
Genetic analysis of early development
i. What are homeotic genes?
ii. What are embryonic lethals?
d. Axis establishment
i. Cytoplasmic determinants in the egg are the substances that initially establish the axes
of the Drosophila body. These substances are encoded by genes of the mother, called
what?
1.
This gene is a gene that, when mutant in the mother, results in what?
2. Since these proteins (encoded by the maternal effect genes) control the
orientation of the egg and therefore the fly, these genes are also called eggpolarity genes. Mutations in these genes are usually what?
e.
Bicoid: A morphogen determining head structure
i. A mother fly has a mutant bicoid gene. What happens to the embryo as a result?
ii. This mutation led the scientists to decide that in normal development, the product of the
mother’s bicoid gene helps set up the anterior (front) end of the fly and might be more
concentrated in that area.
1.
This led to the morphogen gradient hypothesis- the idea that gradients of
substances called morphogens help establish what?
2. View and read figure 18.19.
a. What question were Nüsslein-Volhard and her colleagues trying to answer?
b. What was their hypothesis?
c.
What were their results?
d. What was their conclusion?
3. When the researchers injected pure Bicoid mRNA into various regions of early
fruit fly embryos, what resulted?
Bozeman WAL: Regulation of Timing and Coordination of Development (13:41)

Differentiation: expressing specific

_________________________ is just as important as cell growth.

__________________ genes, or body genes, place different body parts where they should go.
that determine what kind of cell a cell is going to be.
Plant Germination

In order to grow a sunflower seed, you need to increase _____________________ and also add
___________ to activate it. As it grows, the cells of the root are different from the shoot, etc.

Cell differentiation is how cells become the cells they're going to be. Once a cell becomes one type, can
it ever go back? ________!
When DNA isn't needed for a certain cell type (for example, red blood cells vs neurons), the unneeded genes get
"wadded up" and those genes are not expressed.
Stem Cells and Differentiation

_______________ cells are cells that can become any type of cell that they "want to" (but please note,
they don't really get to choose like you have the opportunity to choose the outfit you wore today. These
cells don't "think" like you do….they are genetically programmed).

How cells determine what they will be- ________________________________ are proteins that
determine what type of cell they will become.

Transcription factors affect adjacent cells- causes a cascade. For example, in males, the _________
gene triggers a response that affects other cells to eventually make the organism a boy.
Embryonic Induction: a cell can induce cells/tissues adjacent to it. Explain the example of the Mexican cave fish:
Cell Death

___________________, or cell death, is important for forming new organisms too.

In Drosophila, three genes cause cells to die. What are the names of these 3 genes? __________,
___________, and _____________.

MicroRNA (miRNA) is important because it disrupts mRNA so it can't make protein. When scientists
removed the miRNAs in Drosophila, what happened to the three genes you mentioned above?
________________________________________________

So, development includes both the ______________ and ______________ of cells. miRNA's are very
important to this process as well.
Homeotic Genes

Homeotic genes are genes that tell an organism where to put __________________________

We learn about them by studying mutants
o
The _________________________________________ gene causes the development of an
extra thorax in fruit flies (when the Dbx gene has a mutation).

This tells us that a series of genes tell things where to go.
Review questions about eukaryotic gene expression- from The Biology Project (Arizona).
____1. What is added to the 3’ end of many eukaryotic mRNAs after transcription?
a. Introns
c. A cap structure, consisting of a modified G nucleotide
b. Poly-A tail
d. The trinucleotide 5’-CCA
____2. The primary RNA transcript of the chicken ovalbumin gene is 7700 nucleotides long, but the mature
mRNA that is translated on the ribosome is 1872 nucleotides long. This size difference occurs primarily as a
result of:
a. Capping
c. Removal of poly A tails
b. Reverse transcription
d. Splicing
Review questions, continued
____3. RNAs that catalyze biological reactions, such as self-splicing introns, are known as
a. Enzymes
d. lariats
b. Spliceosomes
e. Mature RNAs
c. Ribozymes
____4. Which
a.
b.
c.
d.
is NOT true about nucleic acid hybridization?
It depends on complimentary base pairing
A polysaccharide can hybridize with a DNA strand
A DNA strand can hybridize with another DNA strand
An RNA strand can hybridize with a DNA strand
____5. In the picture to the right, A and C are…
a. Introns
b. snRNPs
c. Spliceosomes
d. Exons
____6. Promoters for eukaryotic mRNA synthesis:
a. Are more complex than prokaryotic promoters
b. Can require binding of multiple transcription factors to form a transcription complex
c. Have specific DNA sequences such as the TATA box that are recognized by proteins
d. Are the stretches of DNA to which RNA polymerase binds to initiate transcirption
e. All of the above