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Gene Expression
Here is genetics in a nutshell: DNA RNA protein
DNA RNA is called Transcription, occurs in nucleus
RNA protein is called Translation, occurs in the cytoplasm, uses free or
bound ribosomes.
Proteins are the workhorses of the body. They are responsible for our physiology.
You should not denature them.
The primary structure of a protein is the string of amino acids.
All AA’s have the following things in common:
1. A central carbon
2. A carboxyl group (which is acidic, because it is an electron acceptor and
hydrogen donor)
3. An amine group (an electron buzzing around nitrogen. This means it can
donate an electron). Amine groups are basic since they remove hydrogen
and donate an electron.
4. They all have at least one hydrogen coming off the central carbon.
AAs differ in their R group (called the functional group). The R group dictates their
chemistry and is what makes each type of AA different from the others. The R
groups interact with each other as well as other things in the cell to create the
physiology. You make a protein by combining several AA’s in process called
dehydration synthesis. The monomer (individual AA) has now become a dimer
(two AAs). Keep combining AAs you get a polypeptide. They are linked by peptide
bonds.
There are 20 essential AA’s don’t memorize them. On each one, find their central
carbon, hydrogen, carboxyl group, and amine group.
Which one has an extra carboxyl group? Glutamic acid. If a protein is made up of
many Glutamic acids, it will be an acidic protein. Find two AAs with an R group
that has extra amines (Arginine and Lysine). These extra amine groups act like a
base because they bind with hydrogen in a solution.
AAs with benzyl rings, such as tyrosine, don’t like water, so tyrosine will be
hydrophobic. If a protein made of a lot of tyrosine is a hormone, it will be
secreted into the blood, where it dissolves in the water there. It will not be easy
for that protein to travel around in the plasma; it will need a carrier protein to
help it. An example of this type of hormone is thyroid hormone.
Histidine is a great AA. What does it have on its side chain? An amine group,
except the group is in a ring structure. A protein like this is critical to maintain
acid-base balance. They can both bind and release hydrogen in solutions, to
adjust the pH as needed.
Denaturing proteins leads to loss of function.
When a protein is properly folded in its tertiary structure, let’s say that three
particular AA are close to each other. Those three R groups need to do a
particular job on the substrate. For an analogy, say the substrate is an orange, and
the R group is the juicer. If the protein is unraveled, the orange cannot be turned
into orange juice. We need the tertiary structure of the protein to be intact.
Proteins can be denatured by heat, like egg yolk that goes from clear liquid to
solid white. As the proteins unravel, they get larger and precipitate out of
solution, so they solidify.
pH and salts can also denature proteins. When you cure meat with salt, it
eliminates bacteria proteins as well, so the meat stays preserved a long time.
A primary protein structure can be joined to itself by sulfide bridges, H bonds, and
hydrophobic interactions to help wrap it into a tertiary structure. A protein
cannot fold correctly if a single AA is changed. This defect is caused by a gene
defect.
Change a single AA and it cannot interact like it did before. If Glutamic acid
(acidic) was replaced by another acidic acid, the protein might work okay. It might
cause the protein to wrap around itself a little more loosely, and who knows? It
might work even faster. Even if it works slower, it still probably will work okay.
But if substituted by basic AA, can be a big problem. Valine causes a kink in a
protein. If the mutation substitution is Valine, the result is usually a big problem.
Loss of a Valine where there should be one is also a problem because a kink is not
where it should be.
A mutation can be harmful, beneficial, or cause no change. The more similar a
substitution, the less of a problem. But there is always a change in physiology.
Ten percent of all breast cancers are congenital genetic mutations (the woman is
born with it), the rest are from a spontaneous mutation of the gene. It gives us a
way to study that cancer. Brca 1 is a breast cancer genetic mutation. Genes code
for proteins that carry out functions, as well as proteins that regulate the
functional proteins. It tells the functional protein where to go or what to do. For
example, one type of protein that is made in the cytoplasm is supposed to return
immediately to the nucleus to perform its function. It knows to do this because its
regulatory protein gives it instructions. If a mutation occurs in the gene so the
functional protein is made but the regulatory gene is not, the functional protein
will be there, but it will not know return to the nucleus to perform its job. The
functional protein is there, but not in the right place.
Genes code for proteins, and are the functional units of DNA. DNA is a double
stranded string of nucleic acids, twisted together in a helix, like a twisted ribbon.
Take a cheek cell out of your mouth and add salt to it, and it will thicken up and
look like snot. This is because the salt ruptured cell and released the DNA and you
are now handling the DNA. Magnify it and can see billions of base pairs of DNA
nucleotides in one cell. How do they come together to make a gene? You have 27
thousand genes with known functions, the rest are called junk, but we just don’t
know what they do (they probably regulate the other proteins).
A cookbook is like a genome. A cookbook is a collection of recipes, an index, plus
tips on how to measure, convert to metric, etc. In the DNA you also have a series
of recipes, or genes. There are other things in a cookbook too, including blank
spaces, or other junk. If you delete junk genes from a mouse, there should be no
change in the mouse, but in experiments, they found that the mouse did have
problems. Cookbooks have recipes for chocolate chips, marinara sauce, fish
dishes, pies, but each cookbook has different recipes. We all have a recipe for hair
color, but we each have different color hair. Some have strong fingernails, some
have weak. These different recipes are organized in the same way, with spaces
between recipes. If a section of a gene does not create a protein, they call it junk.
But it is not a good name, because those genes do something, we just don’t know
what they do. Likewise, if you stop after making just the cookie dough, there
would be no cookies. We need those genes to do things other than code for
proteins. A recipe tells you what order to apply the ingredients and how to mix
them. Some of these junk DNA segments do have a function: to regulate the gene
expression of other genes.
There are proteins whose job it is to monitor the cell size, and when the cell gets
too big, they race back to the nucleus to tell the cell to divide. A gene codes for
those proteins: proto-oncogenes. They are supposed to be there, maintained in
homeostasis by other proteins. Those genes come from genes too, tumorsuppressor genes. That means that we have genes that encourage cell division
(proto-oncogenes) and genes that discourage cell division (tumor-suppression
genes). Proto-oncogenes and tumor suppressor genes should be in same amount.
If the proto-oncogene is made but not the tumor suppressor, there will be more
cell growth and division. What if the mutation caused excess proto-oncogenes to
form, but the person had a normal amount of tumor suppressors? You would also
get a tumor.
In DNA, nucleotides pair with each other. When the DNA unravels to make an
RNA template, the DNA nucleotide “T” pairs to the RNA nucleotide “A”, etc. This
pairing process is transcription. When the newly formed RNA strand detaches
itself from the DNA template and floats out of the nucleus, a second RNA can pair
with the first RNA, blocking it from binding to the ribosome, so it cannot make a
protein. Therefore, in a patient that has a mutation in a proto-oncogene that
favors too much cell division, you can inject this special type of blocking RNA into
the patient, and the injected RNA blocker goes to the RNA of the proto-oncogene
and binds to it so the proto-oncogene cannot be made, and the cancer will stop!
How does the injected RNA know where to go in the body? Scorpion venom loves
RNA, and heads right to it in every cell, so we combine the venom with the
injected RNA and it takes it to the right place!
What if you want to turn on a tumor suppressor gene? Certain “egg RNA” will
bolster this. You can inject an RNA egg. Suppose that a good RNA has been shut
down by a bad RNA blocker. Inject the RNA egg to bind with the bad one so the
good one is left alone so that it can bind with the ribosome and make the protein.
This happens in the body naturally, but we are trying to make it in large amounts
to inject. Mitochondria have their own DNA, RNA, proteins, and there is more
research being done there, as well.
Brain surgeons want to take out tumors surgically before chemotherapy is begun.
They don’t want to take good tissue, so how much tissue do you take before you
accidentally scrape out 10 years of piano lessons? Sprinkle scorpion venom on the
patient’s brain during the surgery, when the skull bone has been removed, turn
on a black light overhead, and wherever it lights up, scrape that out. This can be
done for prostate and breast cancer, as long as the involved tissues are
superficial. This type of medicine is called Molecular medicine, very interesting.
The ultimate website (not Wikipedia or Web MD) to learn about the latest things
in molecular medicine is here:
www.nlm.nih.gov
CLASS DEMONSTRATION OF PROTEIN SYNTHESIS
Need four groups of students with 10 people in each group:
10 students with black shirts (represent the nucleotide Adenine “A”)
10 students with white shirts (represent the nucleotide Thymine “T”)
10 students with blue shirts (represent the nucleotide Cytosine “C”)
10 students with grey shirts (represent the nucleotide Guanine “G”)
The copying of the original chromosome is during transcription.
In this process, think of wanting to make a duplicate of your hand. You first take a
plaster impression of your hand print. This is transcription, but it does not give
you a copy of your hand, it just makes a negative cast of your hand. The negative
cast is the RNA strand.
During translation, the RNA is copied.
In this process, we take the negative cast of your hand and fill it will plaster. Then
we peel away the negative cast, and are left with the plaster positive cast, which
is the duplicate of your hand.
When the DNA unravels to make an RNA template, the DNA nucleotide “T” pairs
to the RNA nucleotide “A”, etc. This pairing process is transcription. The newly
formed RNA strand detaches itself from the DNA template and floats out of the
nucleus, into the cytoplasm. There, it binds to a ribosome, which reads the RNA
strand and attaches a "T" nucleotide to the RNA "A" nucleotide, etc, until the
entire RNA strand has been paired with nucleotides. This is translation. Then the
RNA strand is taken away, taken apart, and its nucleotides are recycled. The string
of nucleotides that is left is then read in a different way: Every three nucleotides
codes for one amino acid. When the ribosome finishes reading all the nucleotides
and forming a string of amino acids, that is the protein.
The first task in protein synthesis (gene expression) is to make a strand of DNA.
One of each of the students will stand next to each other in this sequence:
Grey, white, white, blue, black, blue, grey, grey, grey. Each nucleotide should be
bound to the next one by dehydration synthesis, so now hold hands. This
represents one of the DNA strands in one of our chromosomes. To make the
second strand of the double helix of DNA, a Black shirt (A) will base pair with a
white shirt (T) and a blue shirt (C) will base pair with a grey shirt (G).
Someone with a blue shirt must go and face the first person in out sequence, who
is wearing a grey shirt. Then 2 black shirts are needed, then a grey, etc. This
second strand also needs to be bound together by dehydration synthesis, so hold
hands. To complete the double-stranded DNA, we need hydrogen bonding
between the two strands, so those in the first strand should put their toes on the
toes of the person in the second strand, who are facing them. Now we have a
segment (gene) of our double stranded DNA chain, and we are still located in the
nucleus. If DNA leaves the nucleus, it will be targeted for destruction. Therefore, if
we want to make a copy of it, we have to leave it in the nucleus while we copy it.
This is like making a copy of a book from the Reserve shelf in the library. You are
not allowed to leave with the book, so you have to make your copy before you
leave the building. Now that we see our double strand of DNA, we want to have
gene expression, to make a protein.
The second task in protein synthesis (gene expression) is transcription
(Takes place in the nucleus)
First, unwind the gene by stepping apart from the second strand. One strand is
the sense strand, used to code for a protein. We want to make a copy of that
strand. Do I use this strand of my template? No. I use the other strand, the nonsense strand, called the antisense strand. If we used the sense strand, our protein
would come out as a mirror image of what we want. When a black shirt (A) is on
the antisense strand, it pairs with a white shirt (T), but we are going to use RNA to
copy the antisense strand of DNA, and RNA does not have thymine (T), so it uses
uracil (U) to bind to adenine (A), instead. I need some students with a brown shirt
to represent uracil.
Now, when I come across a black shirt on the antisense strand, I need a brown
shirt. Continue to pair blue and grey as usual. When everyone on the antisense
strand is paired up, the third strand needs to hold hands. Now we have made a
copy of the antisense strand. The third strand we just made is called Messenger
RNA (mRNA). We have just finished transcription. The mRNA must now leave the
nucleus and head out toward the cytoplasm. Now that the mRNA has left, the two
original strands of DNA come back together and bond. If someone lets go of a
hand, the effect would be lethal. Ok, students in the DNA strand can sit down.
The third task in protein synthesis (gene expression) is translation
(Takes place in the cytoplasm)
While the mRNA leaves the nucleus and enters the cytoplasm, it must stay in a
line, and not bend or fold, or it will be attacked, degraded, and recycled for parts.
Now we are in the cytoplasm with our single strand of mRNA, with Thymine
replaced by uracil. A ribosome encompasses the first part of the strand. It reads
the students in the strand, three at a time. Each set of three nucleotides
(students) is a codon. Each codon is a code for a particular amino acid. The order
of nucleotides of the first codon (first three students) codes for a particular amino
acid, let’s say Tyrosine. This means that tyrosine will come and attach to the
ribosome. The ribosome reads the next codon, which codes for the amino acid,
histidine. That means that histidine will come and bind to the ribosome, next to
tyrosine. Scientists have decoded the codon code…we know what amino acid is
represented by each possible codon. The ribosome continues down the mRNA
strand, reading three nucleotides at a time, and the amino acids line up in
sequence, holding hands for dehydration synthesis.
Before the ribosome is done reading the mRNA strand, another ribosome can
come and start at the beginning of the same strand to start making a copy of the
same mRNA strand. After all, you probably need more than one of the same
protein.
When the ribosome has finished reading the mRNA strand, and all of the amino
acids will be present, lined up in proper order. This sequence of amino acids is the
primary structure of the protein. If the AA’s bend into a staircase shape, that is
secondary structure. If one AA holds the leg of another AA, that’s the tertiary
structure. If there was another protein, and both proteins joined hands, that is
the quaternary structure of a protein. That’s how a protein is made!
Note that the mRNA left the nucleus as a single strand. That means that it was
exposed, and other nucleotides in the cytoplasm could come and bind with it,
inhibiting its ability to get to the ribosome to be read and make a protein. The
mRNA could also pair with another mRNA strand, or a DNA strand. Scientists take
advantage of the vulnerable mRNA strand to bind something onto it if the mRNA
plans on making proteins as part of a tumor. In the future, we will be able to give
a shot to someone with cancer, and it can cure them. It is already in clinical trials.
It is not normal for uracil to be found in a DNA strand. If we see it there, it
indicates a mutation has taken place. This occurs when cytosine undergoes a
spontaneous chemical reaction and changes into uracil. This is an example of DNA
damage.
There are proteins in your nucleus whose job it is to scan DNA and replace
appropriate nucleotides. Sun creates damage to the DNA strand by causing
hydrogen bonds to cross link into covalent bonds. When this happens, the DNA
strand cannot unwind to allow gene expression.
Why are some people more prone to MI, HIV, cancer, diabetes? Gene expression.
Certain receptors are expressed in the heart; when there is a mutation in that
gene, they are more likely to have an MI (myocardial infarct, or heart attack) by
age 50. You can have your DNA sequenced to see where your mutations are.
Doctors are having hard time educating the public now; patients figure out what
their problem might be, ask the doctor for medicine now, even though there is no
problem yet. If the doctor gets their patent’s gene sequence, they don’t know
what to do with it, need a molecular biologist to help them.
Your mood changes your gene expression. Lonely, detached people get sick a lot.
If attitude is everything, better pick a good one! How can you improve your
mood? A simple touch from someone can elevate mood. For coffee lovers, just
the smell of coffee wakes you up because it elevates your mood. Mood is
improved by an increase in oxitocin production. Oxitocin does more than cause
childbirth contractions and production of breast milk; men have oxytocin too, so
it has other jobs, such as increasing your ability to bond socially. Infatuation
causes oxytocin to increase. It is made in the hypothalamus, stored in the
posterior pituitary (neurohypophysis), where you can also find ADH. To remember
what these hormones do, ADH will make you swell, oxytocin you scream like hell.
Men in orgasm are secreting high amounts of oxytocin.
Mutation vs. DNA damage
DNA damage is when the gene sequence of a cell is not in proper condition, but
the daughter cells are normal. Mutation is an inheritable change in the gene
sequence, so the daughter cells have the same damage.
Stem cells can be pleuripotent or unipotent
Who is determined to go into nursing? Pharmacy school? Physical Therapy? I can’t
tell by looking at you what your determination is. With proper training in your
graduate program, you will become a different person than you are now. Right
now, you are determined. When you get your graduate degree, you will be
differentiated. The ultimate stem cell is the one-cell zygote. It is pleuripotent,
because it can turn into anything you direct it to be: blood, bone, muscle, nerve.
Once it becomes determined to turn into a blood cell, it can no longer turn into a
bone, muscle, or nerve cell. Now it is no longer pleuripotent. It is unipotent. Still,
it is not fully differentiated yet, because, with further training, it can become a
specific type of blood cell, like a white blood cell. Yet, it is still not fully
differentiated, because it needs more training to become a specific type of white
blood cell, say a B-cell. Differentiation is a process, from Pleuripotent to
unipotent, to differentiated. When a cell is fully differentiated, it cannot turn into
a T-cell or any other type of cell. Training makes you more and more special.