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CHAPTER XX: Genetic Control
A) Background Theory
1. Remember that in all organisms, the genetic code in EVERY cell is identical to all the others.
2. This means that chromosome #1 in one of your skin cells is the same as chromosome #1 in your
liver cells, and every other gazillion trillion cells in your body.
3. So what’s the deal? How come different types of cells are so different.
4. The answer lies in which genes are turned on or off, at any given time.
5. Stomach cells can make stomach acid and enzymes because those genes are triggered by
hormones and turned ON in stomach cells.
6. Other types of cells do not make receptors for those hormones and molecules, so those genes
are never turned on at all.
7. So basically, the pattern of which genes turn ‘on’ or ‘off’ determines the fate of individual cells.
8. This prevents you from growing an arm out of your face…you freak.
9. Genetic control is complex in pretty much all organisms.
10. Almost no traits are controlled by a single gene. Most traits and physiological responses are the
result of several (or hundreds) of genes working together and giving feedback.
11. There are several ways that genes (and the protein they make) are regulated.
12. Some genes are controlled by limiting the amount of mRNA available for transcription.
13. Other genes are controlled by regulating the rate of translation.
14. Still other genes make protein products that can be activated or de-activated.
15. Since it is hard to make too many other generalizations, particularly between prokaryotes and
eukaryotes (since they regulate genes differently), we’ll begin with how bacteria control genes.
B) Prokaryote Gene Control
1. Bacteria have relatively small genomes (usually only around 2000 genes) and are simple in
comparison to eukaryotes.
2. There are basically two systems of genes in bacteria, which are constitutive and regulated.
3. Constitutive genes are on all the time, because they are essential for life.
4. An example of a protein coded by a constitutive gene would be cytochrome C, which carries
oxygen. Living cells must always have it available.
5. Regulated genes are turned on and off, according to need.
6. Most genes involved with metabolism are regulated genes, since food is not always present.
7. Many such genes are individual, but others occur in clusters of related genes called operons.
8. An operon is a cluster of gene that turns on when the proteins coded by several genes are
needed for a related function.
9. The operon system was deduced through the study of the Lac Operon and the Trp operon in
E. Coli bacteria. The Lac Operon controls lactose metabolism, while the Trp operon controls
the production of the amino acid tryptophan.
10. An operon works almost like a series of switches, with several different parts.
11. Starting at the beginning, the first stretch of DNA ahead of the gene is called the promoter.
12. The promoter is a stretch of DNA that tells RNA polymerase “HEY!! Here is the start of the
gene! Get your butt over here and transcribe me!” It’s like runway lights at an airport.
13. There is a stretch of DNA directly in front of the promoter called the operator.
14. A protein called the repressor recognizes the sequence of the operator and binds to the
sequence, when the gene needs to be turned off.
15. What happens, effectively, is the repressor protein parks its butt in front of the RNA
polymerase and won’t move. Therefore, transcription won’t start.
16. Only when the repressor protein is moved by some trigger, will it get out of the way and let
transcription happen. Until then, no mRNA can be made, and therefore, no protein.
17. Let’s take a look at how the two operon systems first discovered in E. coli work.
18. The table and diagram below explain the components of the lac operon.
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20. The Lac Operon is what is called and induced operon. Unless a trigger molecule (lactose) is
present, it remains turned off.
21. It makes good sense as to why this is so. If there was no lactose available for consumption, the
cell would just be wasting energy making a useless protein that did nothing.
22. Most of the time, a bacteria will also use OTHER sugars besides lactose FIRST if given a choice,
because lactose is fairly difficult to break down and provides less energy than others.
23. So, lactose is pretty much a last resort fuel.
24. The lac operon, like many operons is actually a component of a larger circuit of genes called a
regulon. Regulons are clusters of operons that contain genes with common functions.
25. For instance, the lac operon is one of several operons that control sugar metabolism.
26. Each operon turns on in a hierarchy, according to what sort of food is available.
27. So how does the bacteria regulate the order that they turn on?
28. There is a second protein called CAP protein, which must be present and binding to the
promoter site, or otherwise the RNA polymerase can’t bind.
29. The CAP protein holds on to RNA polymerase the way a saddle lets someone stay on a horse.
Without it, transcription goes nowhere, because they enzyme falls off.
30. Most of the time, there is no CAP protein bound to any operon, other than the particular sugar
that is being consumed for energy.
31. When that sugar goes away, the cell sends out a cAMP signal saying “Hey I’m hungry! What else
is there to eat around here?”
32. In E. Coli, the
33. The cAMP then binds inactive CAP protein, changing it to its active conformation.
34. The active CAP protein then binds to the promoter, allowing the RNA polymerase to stick and
RNA transcription to go forward.
35. From there, the metabolic enzymes for the sugar’s metabolism are made.
36. A diagram of the entire thing is shown below.
37. So how did anyone ever figure this whole thing out anyway?
38. A couple of researchers named Francois Jacob and Jacques Monod mapped everything out by
back-tracking the map layout from studying mutant strains of E. Coli.
39. First, they X-rayed a ton of E. Coli cultures. This randomly created mutations. Some of these
cultures produced mutants specific to the genes for lactose metabolism.
40. From there, they found four general types of mutants, and were able to back-track and figure
out the function of the mutated proteins.
41. The first two types of mutants were repressor mutants.
42. The first type of repressor mutant could not use lactose at all, because a mutation to the
repressor protein caused it to bind so tightly that it would not let go.
43. As you might expect, the second type of repressor mutant did not bind at all, so the bacteria
made lactase enzymes all the time, in spite of the fact that they weren’t needed.
44. Operator mutants had a faulty operator sequence that the repressor protein did not recognize,
so these mutants also produced lactase constantly.
45. Finally, they found metabolic mutants, which had problems with Lac Y, Lac Z, or Lac A. They
were only able to partially metabolize the glucose.
46. On the surface (with modern technology), the premise doesn’t sound that hard, but for the
1960’s it was revolutionary. They both received the Nobel Prize.
47. Here are these two cat daddies in their lab and a schematic of the interaction of glucose and
lactose when E. coli encounters various concentrations.
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In addition to inducible operons, some genes are controlled by repressible operons.
Repressible operons are always ON unless something stops them.
An example of this is the Trp operon.
Bacterial cells will always make the amino acid tryptophan at low levels, since it is essential for
building proteins, as long as it remains unavailable.
However, should tryptophan become available, a system is needed to shut the genes off.
The Trp operon works in reverse of the way the Lac Operon works.
As long as tryptophan is unavailable, the repressor protein is unable to bind to the operator,
because it is in the wrong conformational shape.
In this case, the genes for making tryptophan remain on, and the cell cranks out the metabolic
enzymes needed to build it.
If the bacteria happens to find itself on easy street, hanging out on a spoiled bratwurst or taking
a trip to the Browns game in the Superbowl, then tryptophan is suddenly available.
Tryptophan, itself, binds to an allosteric site on the repressor protein, activating it.
The repressor then binds the operator, until all of the tryptophan has been metabolized.
Once all the tryptophan is gone, the repressor changes shape again, falls off, and the operon
starts up all over again.
A picture of the Trp operon is shown below.
61. Like the sugar metabolism system, a lot of the pathways that manufacture non-essential amino
acids are also controlled by regulons.
62. Regulons also control the metabolic reactions involving nitrogen compounds and phosphates.
63. While the controls we have discussed so far are pre-transcriptional, there are also posttranscriptional and post-translational controls that involve mRNA and proteins.
64. For instance, mRNA can be translated into proteins at different speeds, according to how many
ribosomes transcribe the sequence and how tightly the mRNA can bind.
65. In other cases, such as the repressible and inducible proteins we just talked about, some
proteins are made in an inactive state and must be activated via an allosteric site or cleaved by
enzymes to become active.
C) Eukaryotic Gene Control
1. Eukaryotes are extremely different from prokaryotes, genetically speaking.
2. In addition to having much more DNA divided across many chromosomes, along with large areas
of introns, eukaryotes usually regulate their genes differently.
3. While there are a few clusters of genes on operon systems, most eukaryote genes are not.
4. Most eukaryotic genes fit into one of three categories.
5. Temporal genes are usually involved with development. They only turn on once or a few times,
after which, they are completely inactivated.
6. For instance, the genes that control development of your eyes, arms, and legs are temporal.
7. If you lose your hand, you can’t just sprout another one, because the genes are turned off.
8. Usually, enzymes called methylases do the turning off. After some developmental cue triggers
them, they add methyl groups to the DNA bases after the gene has served its purpose.
9. This causes the cell to ignore the gene thereafter, since the methyl groups inhibit RNA
polymerase from accessing the DNA.
10. So, a number of your genes are permanently off. You can’t start them back up again.
11. However, some animals do not turn off their developmental genes.
12. This explains why a lizard can grow a new tail, but you can’t grow a new butt.
13. Here are pictures related to this notion. Sir Mix-A-Lot’s DNA is methylated and he cannot
regrow a butt, should he ever lose his ‘back’, while the skink is just fine and always has back.
14. Sir Mix A Lot likes genetics and he can’t deny. Those other brother can’t deny, that when a
scientist walks in with an itty bitty gel box and a DNA sequencer in his face, he gets sprung.
15. A number of other genes are constitutively regulated genes.
16. This means that they turn on or off as needed.
17. For instance, if you eat a meal, the gene that makes insulin is turned on by the presence of sugar
in the blood. However, when you are not eating, the gene shuts off to avoid waste.
18. Many of these genes are specific to tissues. For instance, the gene for insulin production NEVER
turns on in muscle cells or skin cells, because they lack the receptors to trigger this.
19. As you remember, hormones and signal molecules are used to turn on genes this way.
20. Protein hormones usually bind to receptor molecules on the cell’s surface.
21. Hormone proteins, on the other hand, diffuse right across the membrane and directly interact
with transcription factor proteins that control RNA transcription.
22. If you aren’t clear on this concept, you might want to go back and review the chapter on the
endocrine system. There are also refresher diagrams below.
23. Some genes, as they are in prokaryotes, are also constitutive in eukaryotes, particularly the
ones under the control of mitochondria or chloroplasts.
24. It’s not like you can ever afford to stop making cytochrome C or hemoglobin, for instance. That
is…unless you don’t value not suffocating to death.
25. Finally, other genes are for emergency only, and are triggered by such conditions.
26. Most of these genes produce chaperone proteins, heat shock proteins, or drought shock
proteins. These proteins are made to prevent other proteins from becoming denatured.
27. Chaperone proteins literally push back on proteins that are starting to denature and keep them
in their correct shape.
28. The three pictures below show the different scenarios with the different types of genes.
29. Development is temporal. Digesting food involves constitutive genes and avoiding death by
enzyme denaturation in the heat of the day involves emergency genes in the cactus.
30. As mentioned earlier, very few of these genes are under the control of operon systems.
31. Most eukaryotic genes are individually controlled, though they interact with other genes and
cause their transcription to be started, stopped, slowed, or speeded up.
32. To better understand the process, we will break down the regulation methods into pretranscriptional (before mRNA is made) and post-transcriptional/post-translational (after mRNA
or protein products have been made).
D) Pre-Transcriptional Control of Eukaryotic Genes
1. Transcription is the level where most eukaryotic genes are regulated.
2. Common sense says that if you don’t need a gene product, its best not to bother making it at all.
3. While the mechanisms are different than they are in prokaryotes, eukaryote genes also have
systems that allow them to be switched on and off.
4. To understand the regulation of eukaryotic genes, we will break down the parts of a typical
gene sequence. The box below describes each component and the schematic shows it.
Component
Function
Promoter
Region recognized by RNA polymerase that notes the start of a gene. Usually around 30 to 50 DNA bases
long.
Promoter elements
Most promoter sequences have regions of repeated DNA sequences in their content that bind the RNA
polymerase enzyme. The most common of these are the TATA box and the CAT box, which repeat over and
over.
RNA Polymerase
The enzyme that makes a complementary mRNA copy to the DNA gene.
Start Codon
The start codon of any eukaryote gene is always AUG, which codes for the amino acid methionine. This can
later be processed off if needed.
Gene Codons (Exons)
This is the main segment of DNA that codes for the protein. This segment can be anywhere from a few
dozen to hundreds of thousands of codons long.
Introns
Many genes are interrupted with junk sequences. However, these get transcribed right along with the
exons, and they must be processed out later.
Stop Codon
The sequences UGA, UAA, or UAG all tell the RNA polymerase that its at the end of the line and its time to
fall off. The end of the gene.
Upstream Promoter
Elements
These are sequences of DNA usually several hundred DNA bases upstream of the promoter. The more of
these that are present, the stronger the RNA polymerase binds, and the faster the gene is transcribed.
Enhancer Sequences
These sequences are found fairly far away upstream from the promoter region of the gene. These
sequences bind transcription factor proteins.
Transcription Factor
Proteins
There are many types of these. These proteins bind enhancer sequences and then bend until they find an
RNA polymerase enzyme. These regulate the speed of transcription. Generally, the more that are bound,
the faster the transcription goes, and the quicker the protein is made.
Repressors
If transcription factors are the gas, then these are the brakes. These slow down transcription when they
bind. Sometimes these are proteins, but sometimes they can be other chemical signals.
Proximal Region
This is a region of DNA this is fairly close to the promoter. This is where steroid hormones bind and interact
with transcription factors and RNA polymerase.
Steroid Hormones
Steroids bind at the proximal region and speed up or slow down the speed of transcription, depending on
what gene they interact with and the type of hormone. They do this by pushing or pulling on transcription
factors and RNA polymerase.
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As the table above outlines, there are several different types of proteins that interact with
varying speeds and intensities to control transcription.
This explains why certain genes are expressed in some cells and not in others.
Now let’s turn to how the proteins, themselves, grip the DNA and how they work.
Transcription factors and repressors, as well as the active domains of polymerase enzymes
usually contain domains (regions of the protein) that have common design functions.
There are three general motifs used for DNA-binding proteins.
Helix-turn-helix protein domains have two facing regions of alpha-helices in their secondary
structure. The amino acids that sit in these ridges have R-groups that interact with the side
chains of DNA bases, causing them to stick together with hydrogen bonds.
Zinc-finger protein domains have several small stretches of amino acids called fingers. Each
finger has R-groups that hydrogen bond to specific stretches of DNA. The fingers are all held
together by a zinc ion, which chelates them.
Leucine zipper protein domains occur as dimers (two parts) and are shaped like a Y.
They are called leucine zippers, because long stretches of repeating leucines interact with one
another and hold the Y together into shape.
The forks of the Y contain amino acids whose R-groups bind the DNA.
Pictures of the three types of DNA-binding protein domains are shown below.
Helix-turn-helix protein motif
Zinc finger protein motif
Leucine Zipper Protein Motif
16. Some proteins are needed in such great quantities (hemoglobin and other oxygen-carrying
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globulin proteins for instance), that transcription going really fast is not fast enough.
There are certain genes that may be present in multiple copies. Therefore, the same gene is
being transcribed several times at once. This is called gene amplification.
Genes that are extremely active are located in areas of the chromosome called euchromatin.
Euchromatin is very loosely packed, as compared to the rest of the chromosome, so
transcription factors and enzymes can easily access it.
In contrast, some DNA is located in densely packed areas called heterochromatin.
Most of the genes in heterochromatin are either rarely active, or more commonly, permanently
inactive developmental genes, which are methylated to preven them being turned on again.
In females, almost an entire X-chromosome becomes methylated and inactivated.
23. This extra chromosome is called a Barr body and is very conspicuous under a microscope. It
shows up well, because it’s so densely packed, it takes up lots of stain.
E) Post-Transcriptional and Post-Translational Genetic Regulation in Eukaryotes
1. As previously mentioned, most of the time, it is more efficient for a cell to pre-emptively control
protein production before a gene is ever transcribed into mRNA.
2. However, there is a need for processing after transcription for other reasons.
3. In most genes, introns are not edited out during transcription.
4. This means that left unattended, most proteins would have large areas of non-functional junk in
them that would ruin the protein.
5. Therefore, the cell must process this junk out.
6. Enzymes called sNRPs (small nuclear ribonuclear proteins) are complex enzymatic proteins that
are in charge of chopping out the superfluous mRNA and piecing it back together.
7. So the sNRPs cut out all of the junk mRNA and give the ribosome a usable transcript.
8. In this case, RNA polymerase is like a long-winded newspaper columnist like Dear Abby that just
won’t shut up. She sends in a transcript to be printed in the paper.
9. The sNRPs are like the editors who cut her crappy column down to a paragraph.
10. The ribosome, then, is analogous to the printing press that sends out finished papers (proteins).
11. Additionally, some proteins are modular, with a quaternary structure that must be put together
from multiple puzzle pieces.
12. Again, the sNRPs step in and cut out the modules and glue them together, as if they were
assembling cheap cardboard furniture from Wal-Mart, except understanding the complexities of
molecular biology is easier than assembling do-it-yourself furniture made in Hong Kong.
13. Sometimes, this means that the plans of the protein come from the mRNA from separate genes.
14. Other times, it means that different patterns of gene splicing can result in multiple
combinations of mRNAs that give you multiple different proteins.
15. An example of a real life protein that is spliced differently in different tissues is troponin.
16. You may remember that troponin is the protein in muscle fibers that acts like a lock on a bicycle
rack. Before you can contract a muscle, troponin must be removed.
17. Troponin happens to have slightly different structures in skeletal, cardiac, and smooth muscle.
18. However, there is only ONE gene for troponin in all cells. What makes it different in different
cells is the way that the mRNA is spliced up and glued back together by sNRPs.
19. sNRPs are also responsible for helping to advance the philosophies and ideologies of
communism, behind their red-hatted leader Papa sNRP. It is a mystery how sNRPs replicate
themselves, since sNRPette seems to be the only female sNRP in the village.
20. La-La…La-La-La-La….sing a happy song, Friedrich Engels.
21. By the way, Gargamel represents capitalism on the Smurfs, which is why he is depicted as evil. Is
it really a coincidence that he wanted to turn the smurfs into gold?
22. The snRPs also lived in a classless society, a la Karl Marx’s communist manifesto.
23. The diagram below simplifies the differential splicing idea.
24. Eventually, the mRNA makes its way over to the ribosome, where it is translated into protein.
25. However, mRNA can’t just be left lying around, or it will continue to go back through the loop
over and over again, and tons of waste proteins will be made.
26. For this reason, the cytoplasm is full of recycling enzymes called RNAses that chew up the RNA
and recycle it into A, C, G, and U.
27. There is, however, a happy medium between immediately destroying the new RNA with RNAses
and leaving it lying around forever.
28. Most eukaryote mRNAs are fairly long-lived, lasting for the better part of a day. The secret is in
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the poly-A tail. At the end of transcription in eukaryotes, RNA polymerase will add a long
stretch of meaningless adenines.
This sequence is ignored by the ribosome, since it comes after the stop codon.
However, this gives the angry RNAses something to chew on, before they finally start chomping
away at the useful part of the transcript. The poly-A tail works something like a timed fuse.
In some cases, RNAses are also inhibited by certain hormones.
For instance, vitellogenin is a protein that packs eggs full of stored proteins like albumen.
If a female animal is ovulating, this means that there are high estrogen levels.
In turn, the hormone estrogen triggers genes that cause RNAse enzymes to become inhibited
and slow down. This allows the RNA for vitellogenin protein to stick around, until the egg is full
of scrumptious protein goodness.
In addition to post-transcriptional processing, there are also some proteins which do not
become active until post-translational processing.
For instance, some proteins are made with included intron sequences that have been
translated into protein.
Enzymes in the golgi apparatus must splice out these junk segments, in order for the protein to
become active and useful.
Additionally, some proteins must be spliced in other ways, combined with other molecules, or
assembled into their quaternary structure from multiple pieces to become active.
An example of this would be the cyclin proteins used to control the cell cycle. These must be
phosphorylated by kinase enzymes, in order to be activated.
This is because the cell doesn’t want the protein doing its thing until it’s ready to divide. If the
cyclin proteins went around telling the cell to divide constantly, you would grow a tumor.
Insulin is an example of protein that must be activated by other enzymes. In its case, a piece of
the protein must be cut off, in order for it to activate.