Question Key
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Let’s work on thinking carefully about genes and the processes in which
they are involved.
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What is gene expression? How does gene expression differ from DNA
replication?
Gene expression is the
process by which the information encoded in DNA is used to create RNA
and proteins. Thus, gene expression is how cells perform actions, using
their library of information in DNA to produce outputs (proteins, RNA)
that can carry out specific activities. This is very different from DNA
replication, which merely makes a copy of the DNA but does not use the
DNA to do anything other than make more DNA.
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Gene expression produces RNA
and protein. DNA replication produces more DNA (a copy).
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DNA replication only* happens
in preparation for cell reproduction, once in the life of a cell. DNA
replication is happening all the time, as part of the regular life of a
cell maintaining its function.
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DNA replication occurs in the
nucleus in eukaryotes. In eukaryotes, gene expression begins in the
nucleus but part of it happens in the cytosol.
*Note: there are situations
in which a cell will make many copies of the DNA for other reasons,
sometimes unknown. In plants, this happens a lot in somatic tissues
(like leaves) and is known as endoreduplication.
Describe the basic structure of a eukaryotic gene. What do you think are
the “parts” of a gene? What important features that we should take note
of?
The “parts” of a gene
include:
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>Exons = the part of the
gene’s DNA sequence that encodes amino acids. Most genes have more than
one exon sequence. The exons are the “coding region” of the
gene.</text
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Introns = this part of the
gene’s DNA does NOT encode amino acids and is usually excised from the
RNA before protein is made. This is considered “non-coding” DNA even
though sometimes it contains sequences that act as signals of where to
splice the RNA. Most genes have more than one intron sequence.
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Promoter = this is a relatively
short sequence of DNA (100-1000 base pairs) that is located just before
the encoding sequence of the gene. Serves as a binding site for the RNA
polymerase, thus enabling the polymerase to begin transcription of the
gene.
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Terminator = sequence that
signals the end of the coding region of the gene, where transcription
stops. Reaching this sequence leads to the newly created RNA transcript
being released from the RNA polymerase.
Not strictly part of the
coding region of the gene but important to transcription of the
gene:
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Regulatory sequences = regions
of DNA sequence that serve as binding sites for proteins that can change
the probability or rate of transcription (for example, by interacting
with the transcription complex). These are usually outside of the gene
itself, often upstream (before) the gene sequence. They may be near or
far from the gene (up to 50,000 base pairs away).
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Enhancer = sequence that is
recognized and bound by an activator protein (a transcription factor)
that increases transcription of the gene.
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Silencer (operator) = sequence
recognized and bound by an active repressor protein (a transcription
factor) that reduces or prevents transcription of the gene.
Explain the slit-shaped eye phenotype found in female fruit flies
that have two copies of the Bar allele
(XBXB) for the BarH1 gene. Why do you think
the Bar allele (XB) leads to a misshapen adult
eye?
Resources to read about the BarH1 gene, if you don’t remember from
videos:
https://www.ndsu.edu/pubweb/~mcclean/plsc431/chromstruct/chrmo2.htm
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5105861/
https://www.sdbonline.org/sites/fly/gene/barh1-4.htm
Here we need to think about
how the Bar allele (XB) is different from the
wild-type allele (X+). The Bar allele has two copies
of gene right next to each other on the chromosome – it’s a duplication.
That means that while a wild-type individual
(X+X+) has 2 copies of the BarH1
gene, the homozygous Bar individual
(XBXB) has 4 copies of the gene.
When we think about gene expression, what could it mean to have 4 copies
instead of 2 copies of a gene? If all copies respond to the signal to
transcribe the gene, that might mean that the individual with 4 copies
make a lot more RNA for this gene and that might mean it makes a lot
more of the protein that is encoded (the BarH1 gene is over-expressed).
Because BarH1 encodes a transcription factor, making more of this
protein is likely to change (increase or decrease) how much RNA is
produced for the genes that BarH1 is regulating. Similarly, if we think
about the heterozygote (X+XB), we
note that the eye is less misshapen and this individual has 3 copies,
only one more than the wild-type. So, the heterozygote probably makes
less BarH1 protein product than the Bar homozygote and thus has less
several malformation of the eye.
Thus, we might conclude that
producing a different AMOUNT of the BarH1 protein product is why the Bar
allele causes a different eye shape. It’s not a difference in the shape
of the protein produced nor in the function it carries out. It’s a
change in how much protein is present that changes the eye
phenotype.
Describe the similarities and the differences in gene structure and gene
expression (or regulation thereof) between prokaryotes and eukaryotes.
Remember that eukaryotes includes plants, fungi, and animals so make
sure your response is general and not animal-specific.
Note: I am NOT asking you to
talk about specific proteins here. Notice the level of detail that I’m
aiming for. If we get too specific, we lose the ability to apply the
information to a broad array of organisms and situations.
Generally, gene structure is
pretty similar in prokaryotes and eukaryotes. Both have exons, introns,
promoters, and terminators as well as enhancer and silencer sequences.
Note: prokaryotic introns are self-splicing (auto-splicing), that is,
they cut themselves out of the RNA transcript.
While basic gene structure
is quite similar, gene expression differs substantially between these
two groups. In eukaryotes, transcription of RNA occurs in the nucleus
while RNA molecules must be moved to the cytosol for translation into
polypeptides (proteins). This process in eukaryotes also involves a
complicated sets of steps to “process” the RNA before it leaves the
nucleus: splicing out some introns and exons; adding a 5’ cap and poly-A
tail to the RNA molecule (these are signals important for export from
the nucleus and proper localization in the cytosol (cytoplasm). This
complicated process of gene expression may give eukaryotes a broader
range of proteins they can produce, giving more tailored responses to
stimuli (more combinations of things are possible).
Prokaryotes, in comparison,
have a more streamlined procedure. Both transcription and translation
take place in the cytosol (there’s no nucleus) and there is basically no
RNA processing (introns are self-splicing). In fact, ribosomes bind to
RNA and begin translation even before the RNA is fully transcribed! This
means that prokaryotic gene expression is much faster than in
eukaryotes, possibly giving them an advantage in responding to
environmental stimuli.
The human genome contains an estimated 25,000 genes and our bodies
include about 200 different types of cells. On average, a cell in the
human body typically expresses about 50% (∼12,500) of the genes in the
genome. However, about 8,000 of those genes are expressed in all cell or
tissue types (Ramsköld et
al. 2009). That means that about 2/3 of the genes expressed in a
cell are the same genes expressed in all types of cells, leaving
only 1/3 to distinguish different cell types from each other. Given this
information, consider the following.
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Given that we start out as a single cell, how do different cells come to
have different functions? Describe how you think cells regulate gene
expression to lead to cell differentiation. Think of describing what
makes a heart cell look and act differently from a skin cell even though
they have the same genome.
Here, like in an earlier
question, remember we want to think of the overall structure of the
system, not the details of specific proteins. Based on the information
provided, it seems like a cell’s identity as a heart cell depends on
around 4,000 genes that are being expressed differently by the heart
cell in comparison to the skin cell. The other about 8,000 genes being
expressed by both heart and skin cells might be encoding proteins (or
RNAs) that are important for functions that all cells need to carry out,
like making ribosomes. So, even though all the cells have the same DNA,
they use different subsets of the genome to make RNAs and proteins that
give the cells their identity.
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Once a cell has acquired a fate (such as “I’m a skin cell”), what
prevents the cell from changing its fate (say, to become a liver cell
instead)? How is cell identity maintained through regulation of gene
expression?
If which genes you express is
important to maintaining the identity of a cell, then there must be
something that prevents some genes from being expressed and makes sure
that others ARE expressed. Such a process is a method of gene
regulation. From the videos and reading in epigenetics, we might guess
that producing the appropriate repressors and activators would allow a
cell to control which genes are being expressed to make RNA or protein.
In addition, some proteins (like methylases or acetylases) can add
methyl groups or acetyl groups to DNA itself or to histones and these
molecules act like repressors and activators, reducing or increasing
transcription of a gene (but the methyl and acetyl groups are not
themselves proteins).
In chapter 3 of Richard Francis’ Epigenetics, he describes a
dramatic example of social interactions influencing the phenotype of
male African cichlids. Some animal species take this even further. For
example, in some fish species, such as the blue-headed wrasse
(Thalassoma bifasciatum), the biological sex an immature
individual develops will depend on the other fish it encounters. A
juvenile wrasse that finds a coral reef not defended by an adult male
will develop into a male, with sperm-producing gonads. But a juvenile
wrasse on a male-defended coral reef will develop into a female, with
egg-producing gonads. In some taxa, an individual may even change
biological sex (i.e., gamete production) multiple times in its lifetime.
Examples such as the wrasse abound among animals, as unfamiliar as they
may be to us. While we sometimes think of biological sex being
genetically pre-determined, these examples make clear that it is not so
simple or deterministic.
How could we alter our understanding of biological “sex determination”
in order to better represent what we see in the world around us? That
is, can you describe a possible mechanism or mechanisms by which sex
determination (i.e., type of gametes produced) occurs in eukaryotes?
(More on variation in sex determination next week!)
There are a wide variety of
reasonable responses here and we’re going to discuss how organisms do
this next week both in video lectures and via case study. What I’d
suggest here is to try to think clearly about what we mean (as
biologists) when we say “sex” and “sex determination”. It’s clear that
not all organisms use a genetic mechanism of sex determination. But at
the same time, gamete production and secondary sex characteristics are
clearly things an organism’s body produces based on information
available in its genome – there is a genetic basis. What’s important is
which gene pathways are activated or repressed in the organism’s genome.
If everyone has the ability to produce either male or female gametes (or
even both at once), then it’s gene regulation that determines which
thing a given individual does, in response to some signal, internal or
external. In organisms with sex chromosomes, it’s not so different.
Genes on the X and Y chromosomes are regulatory – they turn on or off
pathways of other genes (mostly on autosomes) that lead to the
development of gonads and secondary sex characteristics.