Chapter 4: Growth factor signaling and oncogenes (Lecture) Flashcards
What are two general statements describing the molecular basis (origin) of cancer?
- Cancer arises by the accumulation of genetic and epigenetic changes in DNA.
- Cancer arises by deregulation of signal transduction pathways.
Why is signal transduction important (name three reasons)?
- Through signal transduction neighboring cells can communicate.
- Through signal transduction cells can react to a changing environment.
- Signals lead to cellular responses
Name cellular responses (for illustration).
Proliferation, differentiation, motility, apoptosis, kill something, metabolism, protein production and secretion, depolarization and contraction.
Changes in cellular activities are governed by changes in…
protein activity.
How can protein activity be changed on RNA level? And how on protein level?
RNA level: gene transcription regulation, transcript degradation regulation by miRNAs, differential splicing.
Protein level: protein production, modification, degradation and translocation.
Name three “actions” that act as “molecular switches” and enable protein modification.
Chemical modification, interaction, binding to small molecules (GTP, Ca2+, cAMP, PIP3, IP3, DAG).
Name different types of chemical modification.
Phosphorylation, acetylation, mono-ubiquitination, methylation, sumoylation.
What protein is responsible for phosphorylation?
The protein kinase
How can the protein kinase phosphorylate other molecules?
It can phosphorylate a protein or an amino acid with a free -OH through the use of ATP (amino acid/protein-OH + ATP -> amino acid/protein-O-P + ADP).
What are amino acids with free -OH?
Tyrosine, serine and threonine.
On what classifications are protein kinases based?
- Function classification (tyrosine kinases (PTKs), serine/threonine kinases (PSKs) or dual specificity kinases).
- Homology classification
What is the counterpart of the protein kinases?
The protein phosphatases (tyrosine phosphatases (PTPs), protein serine/threonine phosphatases (PSPs), dual specificity phosphatases).
What is the kinome?
The complete set of protein kinases encoded in the genome.
Why are there more protein kinases (n=518) than protein phosphatases (n=50-100)?
Because protein kinases have a higher specificity than protein phosphatases.
How can kinase inhibitors inhibit protein phosphorylation?
They are analogs of ATP. They can inhibit kinases through the use of ATP-like molecules (that don’t have the same function as ATP and thus cannot activate).
What is meant by dirty spectrum kinase inhibitors (KIs)?
Broad spectrum KIs (you also have small spectrum KIs).
What is the effect of protein phosphorylation?
Change in conformation or a creation of a docking site.
Name an example of the creation of a docking site as an effect of phosphorylation.
Phosphorylation of tyrosine is recognized by SH2-domain (Src homology 2-domain).
Onto the second “action” that acts as a “molecular switch” and can enable protein modification: protein interaction. With what kind of proteins can other proteins interact and what does it do?
- With an inhibiting protein -> the modification releases an inhibitor. - With an activating protein -> the modifcation stimulates activation or active complex formation.
Name examples of protein binding domains.
- SH2 domains (binds to phosphorylated tyrosine (phosphotyrosines).
- SH3 domains (binds to proline rich domains)
- WW domain
- Pleckstrin Homology domain
- Leucine zipper domain
Just know from this picture that several different molecules (enzymes, adaptors, docking proteins etc.) can have multiple protein binding domains combined.
This makes that the enzyme depicted in this picture is able to bind proline rich domains (SH3) and to phosphotyrosine (SH2) etc.
Onto the third “action” that acts as a “molecular switch” and can enable protein modification: binding to small molecules. GTP is always present in cells, what proteins can bind GTP?
Heterotrimeric G-proteins and most importantly Ras-like GTPases (important in cancer).
Ras is important in signal transduction and is located on the plasma membrane of cells. There, it is either found in an active or inactive state. Describe the active state of Ras.
Ras is bound by GTP (with three phosphate groups bound).
Ras is important in signal transduction and is located on the plasma membrane of cells. There, it is either found in an active or inactive state. How is Ras turned off (and also think of the protein which is involved in this process)?
GTP is switched for GDP through GTP hydrolysis (phosphate group is removed from GTP). GTP hydrolysis is stimulated by GTPase Activating Proteins (GAPs).
Ras is important in signal transduction and is located on the plasma membrane of cells. There, it is either found in an active or inactive state. How is Ras turned on (and also think of the protein which is involved in this process)?
Ras is converted to the active GTP-bound state by exchange of GTP for bound GDP, which is stimulated by guanine nucleotide exhange factors (GEFs).
What are other second messengers (which are freely diffusing small molecules formed or released)?
- cAMP, cGMP
- Ca2+
- Lipid derivatives (DAG, PIP, IP3).
What are important second messengers?
Phospholipids in the cell membrane
PIP2 is a minor phospholipid component of cell membranes. Which kinase can interact with PIP2?
PI3-kinase (phoshatidylinositol 3-kinase or PI3K). It exchanges ADP for ATP, so that PIP2 changes into PIP3 (which then can act as a second messenger).
Name an example of a relay system.
Steroid hormones
What is typical for steroid hormones?
They work through nuclear receptors, which results in transcription of certain proteins. These proteins are translocated to the cytoplasm, where they can change cell function.
In short: what is EGFR signaling?
EGFR stands for Epidermal Growth Factor Receptor. It’s a tyrosine kinase receptor that consists of two dimers. Depending on its activation, it can alter e.g. cell function.
Please remember that the classical example of EGFR signaling is the pathway mentioned above. Here, the first receptor discovered is described, which is the EGFR called ErBB1 or HER1.
But know that there are multiple receptors and ligands with different downstream effects (also dependent on the different phosphorylation sites). For example you have ErbB2 (HER2), ErbB3 (HER3) and ErbB4 (HER4).
Also look at this picture to have an idea of the different pleiotrophic effects of RAS.
Okay
Describe PI3K signaling after activation of RAS.
RAS interacts directly with the catalytic structure of PI3K. Here, lipid PIP2 changes into PIP3 with the help of PI3K. PIP3 recruits kinase PDK-1 to the membrane. Kinase Akt is also recruited and phosphorylated and activated by PDK-1. Active Akt is important in anti-apoptotic and survival roles by phosphorylating distinct target proteins.
What is a photon receptor?
A receptor in the retina of your eyes that uses light (or a photon) as a ligand. This pathway contains a G protein-coupled receptor. (I think the most important think here is to realize that receptors can work in different ways).
What will a nonsense mutation in a kinase receptor result in?
The mutation causes a premature stopcodon to be formed, which results in an incomplete protein. The kinase receptor will be incomplete, which causes loss of regulation. The receptor kinase is always on.
What will translocation of a gene result in?
It leads to a weird fusion protein with aberrant functions.
What is interesting about the RET oncogene?
The gene has many phosphorylation sites, all these sites can be altered which can have downstream effects.
What happens when there’s a nonsense or truncating mutation of p53?
There’s less p53, but it’s stil active. It produces a mild effect.
