November 8, 2015:38 PM
We can think of small molecules as signals can be sent through one cell
to another cell. That barrier around the cell is a plams membrane. So
how does the signal go into the cell?
How does it pass across the membrane?
Property of the signaling molecules decides the way it goes through
We look through the classes of small molecules:
we have charged molecules, polarized molecules.
In the top we have hydrophobic molecules.
Different classes of small signalling
We know that the middle of the PM is
hydrophobic, so looking at a charge we
can tell that charge is not favorable to
go through the PM.
Hydrophobic molecules can pass
through to the cytoplasm.
BIO230 Page 1 NO: Extremely small molecule with two atoms. N and O.
NO is made from deamination if AA residue arginine by the enzyme
nitric oxide synthase. Once it is made its an example of a short range
signalling molecule. It's a short range signalling molecule because its
life time is short. It turns over very quickly and breaks down.
Acts on smooth muscle and other targets.
Example shown is smooth muscle:
Epithelium There are 3 cell types involved in the signalling process. Smooth muscle
cell surrounding a blood vessel.
1. Epithelial cells, most specifically endothelial cells because they are
covering a blood vessel
2. Surrounding the blood vesseil is Muscle cell: can contract and
control the flow of blood
3. Nerve - can send signals to the muscle and tell whether to contract
The way it works is indirect: we have three cell types. The end of the
neuron can secrete acetylcholine which candiffuse through the tissue
and bind to the end of the treceptor on endothelial cell. and activate
the NO synthase. this is made within the cell from arginine. As soon as
it is maade it can start to diffuse out of the cell. Nothing is stopping it
from diffusing and leaving across the PM of the muscle cell. Within 10
seconds it is going to diffuse and rapidly diffuse inside to the muscle.
Then it binds to a certain protein --> Binding leads to the
conformational change in the protein--> changes the activity of the
protein , this case it's an enzyme which drives the formation of gunanyl
cyclase. GTP Converts it into cyclic GMP which relases the muscle to
NO signaling is embedded with a singal transcutuon pathway where
multiple types of molecules are there. Acetylcholine, NO and then
Lumen is where the blood is. Blood vessels have a special kind of blood vessels. This is specialized epithelium specials. cGMP. There is another cyclic moelcule cAMP later.
Besides wpithlium cells there is a basal lamina. The neuro cells go cloe to the endothelial cells. It’s a very simple setup.
Endothelial cells. We are looking at the acitvated nerve cell signalling to an endothelial cell. (image 1) . Activated nerve Medical aspects: Nitroglycerine can be used to treat heartpain. It is
converted to NO by body, this relaxes blood vessels so it reduces the
cell is releasing acetylcholine, whole bunch of proteins are activated. NO is activated. It activates arginine. Oyu want the work load on the heart. You can take advantage of the singalling
blood vessels to relax, less work load on the heart
pathway to treat heart pain.
Small hydrophobic moelcules that pass through the membrane.
There are multiple characterists.
- Steroid hormones.
Structure of cholesterol is four rings in a row. Estradiol and
testosterone. All made from cholesterol.
All these are classes of steroid.
- Thyrid hormones: made from tyrosine. Includes metabloic rate.
- Retinoic acid:
- Vitamin D. - affects metabolism
These all are small hydrophobic molecules and diffuses into the blood
stream.and affects cells at a distance.
When they enter the PM passively. they bind to this molecule inside .
They are called as nuclear receptor super family mebers > they are
hydrophobic. They have carrier proteins which will get them through
the blood stream. Little bit if them are continuously released from the
carrier protein and they can pass through the PM interact with the
The receptores have a common organization to them. They have a
binding site for small hydrophobic molecules and dna. So they bind to
dna and change gene transcription.
Signalling is changing the gene trasncription
BIO230 Page 2 Based on those two characterists : binding site to hydrophobic
molecule and DNA, you can go through a sequnce from the genome
and identify that there are 48 of these in the genome.
You can identify the receptor, but only about half of these are the
ligands known. So for those that the ligands are not known is called as
orphan nuclear receptors. And so we suspect that they must be doimng
something important because they have a binding site for dna and
small moleucles. We don’t know what the signalling is for.
The thing is we can do dna sequcening and find the domains. But its
hard to isolate small hydrophobic moelcule do binding assay for
purified receptors, do gentics to dna moelcuesl and test the effect. So
we are mising lots of thes epairs.
Orphan nuclear receptors
To the pairs that we do know, there is an impact to the small molecule
binding on receptors basic principle, when we have binding there is an
conformational change in the protein which affects the binding
properties or the enzymatic activity. Thereceptors are not enzymatic
enzymes so it change is affecting the conformations property.
The long one is the inactivating domain it has is multiple folded
domains in the polypeptide chain.
Dna binding domain, ligand binding domain so on. Normally this is
bound by a inhibited proteind molecule so it wont interact with dna.
But when the ligand is present it will bind and the inhibitory protein is
expelled so dna binding site is poen and the conformational change is
optimal for dna binding.
Confomrational change effects wither the binding property or the
enzymatic proeprty. k
BIO230 Page 3 This is the crystal strucutre where the alpha helices with indivudal
receptors when the ligannd binds to the receptor there is a major
change in conformation.
These receptors are TF and in any transcrition response there is going
to be a primary effect on transcription and some of the genes that were
transcribed will encode the TF itself. So you change the expression of TF
and it can additionally change the transcription in a second wave of
We have seen this before in segmental pattern in early drosophila
embryo in a cascade of signal transduction
We have a primary effect on gene transcription and they have an effect
on other genes. Turning some on and off.
BIO230 Page 4 Those were examples of how signaling molecules can pass through the
lipid bilayer all by themselves. . Now lets look at where n small
moelcules need help snd cannor pass.cannot pass on its ow
We look at channels…
They open up the space and passes through the membrane. And its
water filled, and moelcules pass through it
This is where we are looking at the class of charged molecules. Ion
channels can function in a whole array of different activties. the
electrical excitability of muscle cells. Outside of that there is a leaf
closure response in plants, single celled paramecium can reverse their
reaction retract after bumping into something.
These hannels are present in all animal cell.s best known in nervous
system but present in many cells
BIO230 Page 5 Ion channels can function in a whole array of different activities.
Cartoon of ion channels themselves.
Have narrow selective pores. Selctive for specif ions.
Can open close rapidly.
Many ions can pass through them in little time.
The key point here is that the transport is passive. The channel when
its open, It's not grabbing a molecule and forcing it through.
It just opens the gate, and the moelcules wants to go through
because of a gradient.
The massive flow is because of the graident that is built up.
Moelcules will flow from high  to low .
BIO230 Page 6 These ion channels are regulated. They are controlled by the cell.
Can be regulated in multiple ways.
• Voltage gated channel:channel is closed or open based on
electrical charges on opposite sides if the membranes. Based on
• Binding of a ligand: you can have a small molecule or a protein
bind to the outside/ inside of the channel to open them up. Idea
is there is an molecular interaction and conformational change
and an opening of a channel pore.
The conformational change is the opneing oif the pore.
• Mechanically gated channel: physical force that opens the
- Previously Sterocillia: that is on top of the sound waves it will
move past each other, when sound waves moves the tether will
open mechaincally gated channels.
Those are how channels can be opoend and closed. So other half of the
equation is how the gradients of ions.
The cahrt shows the gradietns comparing the Shows how the gradients
goes from  inside the cell to the  outside the cell.
Na+ is higher outside. And its prone to go in.
K is high inside and prone to go out. So the channels are open and the
ions will flow down the gradient.
The asterisk: the cell does contain equal quantities of + / - molecules.
The cell is neutral. No net positive / - charge.
Chloride donest add up, the number of + charged moelcues donet ad
All of the macromoelcuesl are also charges , dna, etc and they will
equally contribute to the gradinet.
Lets focus o Na and K gradients.
BIO230 Page 7 It sets up the potential for an action potential. We can have vboltage
gated na channels responding to action potential
The first step invovles leakage of K ions outside of the cell.
Left: we can see where there is no leakage of K+ ions. We have an equal
mix of + and - charges. In both sides. Exact balance of charges. No
In excitable cells: there is a slight leak of K going out of the membrane
the channels allow a slight leak of K. the leak can occur but its restricted
because of the difficulty in separating charges. You start to pull the
cahrges to that side, from inside and that will leave the + ions close to
the membrane. +/- don’t want to be far apart. They are pulled down
bvy the  gradient but they are pulled back from the electrical gradient.
This is the ground state for the exiftable cells.
The prioteins along the membrane will be in a specific confomration.
What happens for a sginal to occur is there is much more Na outside
So Na will go nto the cell, and distrupt the region of + charge. So the
charge is altered and protein will chnge its conformation.
This is how signals are sent.
The change can sent a travelling wave of depolarization.
BIO230 Page 8 The first step is to open one of the Na + channels. When you open them
there is a rush of + ions in.