Free Life Ain't A Fairy Tale by Miguel Rivera

am familiar with.
The long list of proteins in this pathway is intimidating. They
become less scary if you think of them as different people's names
involved in an assembly line that produces more cell growth.
    In general, signaling pathways are highly
similar. They are best understood as stories than as a long series
of proteins interacting with other molecules to carry out a
molecular process. From a storyline perspective, whether it is cell
division, cell growth, cell death, and wound healing to name a few,
a protein binds to another protein called a receptor at the cell's
boundary, the plasma membrane. After the protein binds to the
receptor, molecular processes inside the cell will occur. This
interaction will either increase or decrease a particular molecular
process.
    The difference between signaling pathways are
the molecules and their interactions with each other in a
particular molecular process. When a molecular process needs to
increase, the molecular interactions' end result is the secretion
of another protein out of the cell. The secreted protein binds
again to the receptor. This will encourage more of the same
molecular process. When a molecular process needs to decrease, the
end result is that translation from RNA to a protein does not occur
in the cell's nucleus. This negates the protein's secretion out of
the cell. This causes a decrease of any molecular process.
    Tumor growth leading to cancer is a magically
harmful process. Cells need oxygen to survive. What do cancerous
cells do? These cells secrete angiogenic proteins. They cause
vascular endothelial cells found on nearby blood vessels' surfaces
to grow and become another small blood vessel.
    This newly formed blood vessel branches out
towards the cancerous cells. This allows the feeding of cancerous
cells with oxygenated blood to grow more. It also allows cancerous
cells secrete angiogenic proteins. These proteins can travel into
the body's circulatory system to promote cancer growth in other
body parts. As I studied this topic in college, it felt like I was
reading science fiction.
    In Krishna's case, she is trying to
understand the Ras/Raf/Mek/Erk Pathway. This pathway is often
studied in cancer models.
    "James, this is what I understand so far. I
understand that proteins are translated to take part in the cell
cycle's regulation. I am having problems with what happens before
the proteins are translated in the nucleus. Make sure if I am
saying this right. The Epidermal Growth Factor (EGF), a protein,
binds to the receptor at the plasma membrane."
    "Yes. This receptor is also a protein. Its
name is a receptor tyrosine kinase."
    "What exactly happens at the receptor?"
    "This receptor adds phosphate groups to the
tyrosine (amino acid) portions of its own structure. The phosphates
attached to the tyrosine portions act as docking stations to
attract two other proteins, GRB and SOS, from the cytoplasm."
    "Okay, before moving on, let me get this
straight. An EGF binds to a receptor tyrosine kinase. This causes
that receptor to trans-phosphorylate itself. The phosphate groups
act as docking stations to attract GRB and SOS. Gotcha. Now, what's
next?"
    "Yes, Krishna, that is right. When GRB and
SOS are together, SOS becomes a nucleotide exchange factor. What
this means is that SOS can do something to Ras, which is a protein
that is an intracellular transducer."
    "Wait, hold on. Ras is an intracellular
transducer. What does SOS do to Ras, and what is an intracellular
transducer?"
    "Okay. Intracellular transducer is just a
term that describes Ras. Remember that SOS is a nucleotide exchange
factor. This is an important point. Ras is not active all the time.
When Ras has a GDP molecule attached to it, it is off. When Ras has
a GTP molecule attached to it, it is on. What SOS does is change
the GDP molecule into a GTP molecule on Ras."
    "So SOS turns Ras on, right?"
    "Yes. You are correct, Krishna." Krishna
cheers for being correct. "Now, this is what happens next,