Ch. 12 Signalling Flashcards
What does “cells are constantly changing” mean? (2)
They are sensing their environment and effecting change inside the cell.
What are the six characteristics of signal transduction pathways?
Specificity, amplification, modularity, adaptation, integration, localization
What is specificity?
A signal molecule fits into the binding site of a specific receptor; other signals don’t fit.
Other than ligands, how else does specificity occur?
Not all cells have the same/all receptors, so the signal is specific for cell type too.
What is amplification?
When enzymes activate enzymes, the number of affected molecules rapidly increases in an enzyme cascade
What is an example of amplification using insulin?
one insulin peptide binds to one insulin receptor activating it, that one receptor phosphorylates 100 enzymes, those 100 enzymes each activate 100 more, 100,000 active enzymes from one insulin ligand.
What is modularity?
Proteins that can participate in many pathways form diverse signaling complexes from interchangeable parts; organize into units
What is a feature of modularity that is beneficial to biochemical signaling pathways?
Activation of a system may not activate all pathways that are within the system.
What is adaptation?
The sensitivity of a receptor can change if the signal concentration remains high after a long period of time.
Describe adaptation from the perspective of a receptor.
Signal concentration has been high for a long time, receptor desensitizes, number of receptors in p.m. decreases and they stop being expressed.
What is the flip side of adaptation (not high concentration)?
If there is no signal, receptors can increase in number and become very sensitive to small concentrations of signal; hypersensitivity.
What is integration?
When two or more signals have an effect on a metabolic characteristic, the regulatory outcome is the integration of input from all receptors involved.
What is integration also termed?
“cross-talk”
What is localization?
When the enzyme that destroys an intracellular message is clustered with the message producer, the message is degraded before it can travel very far; localized and brief response.
What is an example of localization that is very prevalent in biochemistry?
lipid rafts
What are the four main types of signal transduction pathways?
GPCR, RTK, Gated Ion Channels, and Nuclear Hormone Receptors
What is a GPCR?
G-Protein Coupled Receptor: receptor that binds a protein, and that protein binds GTP
What are the hallmarks of a GPCR? (4)
- 7 membrane spanning ⍺ helices
- It is heterotrimeric
- It has to hydrolyze GTP to make GDP (causing conformational change!)
- Effector enzyme or ion channel involved is ALWAYS downstream from the G-protein
What is one of the most common effector enzymes involved with GPCRs?
Adenyl Cyclase: a lipid anchored protein on the cytosolic face of a p.m. that takes ATP in the cytosol and makes cAMP
What is cAMP?
A second messenger that can bind to many enzymes and effect change; small molecule.
What is the β-adrenergic receptor?
A GPCR that binds to epinephrine and shuts off energy storage pathways while turning on energy production pathways.
What are the subunits of the β-adrenergic receptor?
Gₐ
Gᵦ
Gᵧ
What is special about G alpha?
It binds to GDP and GTP. The other subunits do not.
Why doesn’t epinephrine for weight loss work long term?
The receptors desensitize.
Describe the GPCR pathway specifically using the β-adrenergic receptor.
- Epinephrine binds to the β-adrenergic receptor causing conformation change
- The conformation change is transferred to the Gₐ subunit
- Conformation change causes the alpha subunit to release GDP, allowing GTP to bind
- GTP-bound alpha subunit undergoes conformation change and is active
- Active alpha separates from the Gᵦᵧ subunits and moves along cytosolic face of p.m. to adenyl cyclase
- Adenyl cyclase is activated by GTP-bound Gₐ (conformation change)
- Adenyl cyclase converts ATP to cAMP
- [cAMP] jumps up
- cAMP activates PKA
What is PKA?
Protein Kinase A: a kinase that phosphorylates many other proteins; turns on energy production proteins and turns off energy storage proteins
What activates PKA?
cAMP
What is the structure of PKA?
A homotetramer with two catalytic subunits that have an active site and two regulatory subunits.
What is the catalytic subunit of PKA?
Contains and active site where the kinase activity takes place.
What is the regulatory subunit of PKA?
Contains a ligand binding site that either inhibits or activates the catalytic subunits (allosteric effect).
Describe how PKA becomes active and what it does once activated.
- cAMP binds to the regulatory subunits of PKA
- binding causes conformation change and the regulatory subunits moves out of catalytic subunit
- catalytic subunit is active and free to phosphorylate
- PKA binds ATP and substrate protein
- removes the ɑ phosphate (outermost) off of ATP and places it on the substrate protein
How do you turn off the β-adrenergic receptor GPCR? (2)
- G alpha has very slow GTPase activity
- Phosphodiesterase
What does GTPase do?
An enzyme that converts GTP to GDP;
GTP-bound Gₐ -to- GDP-bound Gₐ -to- Gₐ moving from adenyl cyclase to Gᵦᵧ -to- system reset.
What does phosphodiesterase do?
It cleaves cAMP to AMP, which is not a second messenger.
When will [cAMP] rise in the cell; what conditions need to be met?
[cAMP] will only rise when adenyl cyclase produces more cAMP than phosphodiesterase cleaves, which produces a middle ground while [cAMP] rises and falls.
What are the two main types of Gₐ?
Stimulatory: Gₛₐ
Inhibitory: Gᵢₐ
Do cells express the same Gₛₐ and Gᵢₐ , and what does this mean?
No. Each cell can express different types of G alpha proteins which means that each ligand will have a different effect of different cell types.
What is Phospholipase C?
An effector enzyme for some GPCRs that converts PIP₂ to IP₃ and DAG.
What is IP₃?
A second messenger that binds to a Ca⁺² channel in the ER, releasing Ca⁺² into the cytosol and causing a rapid spike in [Ca⁺²].
What does a rapid spike in cytosolic [Ca⁺²] cause?
Many latent proteins become active when Ca⁺² binds to them; like PKC.
What is DAG?
An second messenger in the inner leaflet of the p.m. that activates PKC alongside Ca⁺².
What is PKC?
Protein Kinase C: a protein kinase that is strongly correlated with cancer (cell immortality) and is very well studied.
How can the GPCR-Phospholipase C pathway be turned off or dimmed? (2)
- Phosphorylation of DAG at carbon one to turn it into a phospholipid
- Removal of Ca⁺² by active transport pumps in the ER and closing of Ca⁺² channels (by lowering [IP₃])
What do the methods for turning off or dimming the GPCR-Phospholipase C have in common?
Both methods remove a second messenger necessary for PKC activation; inactivate PKC.
What is an RTK?
Receptor Tyrosine Kinase: receptors; kinases that only phosphorylate tyrosine residues.
Where are RTKs found?
In the p.m.
What domains do all receptors in the p.m. have? (3)
A membrane spanning domain, an extracellular domain that binds a ligand, and a catalytic domain in the cytosol (has kinase activity).
What is the insulin receptor?
An example of an RTK that is a homodimer.
What does the insulin receptor have in the cytosolic domain?
A loop in the cytosolic domain with three tyrosine residues on it.
Describe what happens to the loop of the insulin receptor when bound to insulin.
- When bound to insulin the receptor is active and the loop folds into the active site
- Autophosphorylation of all three tyrosines occurs
- Phosphorylation of the tyrosines on the loop causes the loop to move completely out of the way (repulsion from “-“ charges)
- Active site is now available for substrate binding
The insulin receptor both activates itself and ________________________________________________.
The insulin receptor both activates itself and serves as its own inhibitor.
The loop moves back into the active site when tyrosines are dephosphorylated.
Describe the insulin receptor pathway.
- Insulin binds to insulin receptor and undergoes autophosphorylation
- Active insulin receptor phosphorylates IRS-1 on its tyrosine residues
- Grb2 binds to the phosphorylated tyrosine residue of IRS-1 through its SH2 domain
- Grb2 brings IRS-1 together with Sos
- Sos binds to Ras, causing a conformation change that exchanges GDP for GTP, activating it
- Ras binds to and activates other proteins that eventually affect genes involved in lipid and carbon metabolism
What is IRS-1?
A protein that can bind many other proteins when phosphorylated.
What is Grb2?
An adapter protein that brings ℗-IRS-1 together with other proteins.
What is an SH2 domain?
A domain on many proteins that binds to a ℗-Tyr.
What is Ras?
A protein very similar to Gₐ in that it is lipid anchored, active when GTP-bound, inactive when GDP-bound, and has slow GTPase activity. It binds to other proteins and activates them.
How is amplification present in the Insulin Receptor mechanism?
One insulin molecule binding to a receptor phosphorylates MANY IRS-1 proteins, which each bind to MANY other proteins.
How is modularity present in the Insulin Receptor mechanism?
Grb2 and Sos are involved in many other pathways besides the insulin receptor.
How is cross talk present in the Insulin Receptor mechanism?
This pathway has MANY effects and can be turned on in multiple ways.
Where are RTKs commonly found?
In lipid rafts in the membrane.
What can the insulin receptor phosphorylate in addition to IRS-1?
It can phosphorylate two tyrosines on the β-adrenergic receptor too.
What other protein is activated by the insulin receptor and what effect does it have regarding the β-adrenergic receptor?
Protein Kinase B (PKB) is also activated by the pathway and phosphorylates the β-adrenergic receptor on two different tyrosines.
What happens to a quadruply phosphorylated β-adrenergic receptor?
A quadruply phosphorylated β-adrenergic receptor is inactivated. Invagination of the membrane containing the receptor occurs, forming a vesicle, and the receptor can’t bind ligand.
How is the Insulin Receptor pathway reset?
Phosphotases reset the pathway by removing phosphates, which makes the proteins become latent.
What are adapter proteins?
Non-enzymatic proteins that bring specific proteins together in time and space; multifunctional (bind many proteins).
What is Src?
A tyrosine kinase that phosphorylates other proteins.
What is Glycogen Synthase Kinase Kinase Kinase (GSK3)?
A serine kinase.
What is a feature of both Src and GSK3?
They both autoinhibit themselves with broad conformation changes that block their active sites. Bind their own phosphorylated loop.
What are ion channels?
Protein channels that are always gated and are selective for the ion that passes through.
How do ions move through ion channels?
Ion move through channels rapidly.
What are excitable cells?
Cells that sense their environment and change their membrane potential creating a charge gradient across cell membranes.
What is membrane potiential?
The summation of all ions pumped out versus ions flowing in.
Total Membrane Potential = (Types and Copy # of Ion Channels) and (Types and Copy # of Opposing Pumps)
What does the Na⁺/K⁺ ATPase do?
It is an active transport protein pump that moves three Na⁺ out of the cells and moves two K⁺ into the cell by hydrolyzing ATP.
What does Na⁺/K⁺ ATPase do to the membrane potential?
Cell will be more negative inside than outside.
What else does the Na⁺/K⁺ ATPase pump do a cell?
Creates a chemical gradient of ions too. Charge and chemical gradient are present.
How does electrochemical gradient relate to ΔG?
The bigger the gradient, the more negative ΔG will be.
How does Na⁺ move in a cell and why?
Na⁺ will move INTO the cell because of the charge and chemical gradient (2 forces).
How does Ca²⁺ move in a cell and why?
Ca²⁺ will move INTO the cell because of the charge gradient (1 force).
How does K⁺ move in a cell and why?
K⁺ will move OUT of the cell AGAINST the charge gradient because the chemical gradient is stronger (~1 force).
How does Cl⁻ move in a cell and why?
Cl⁻ will move OUT of the cell because of the charge gradient (1 force).
What is a voltage-gated ion channel?
An ion channel whose gate position (open/closed) is dependent on membrane potential; can sense membrane potential.
What is an example of a voltage-gated ion channel in neurons?
Na⁺ channels along the length of nerve cells
What do these Na⁺ channels (and the cells they are within) have and why?
Have an electrochemical gradient because of the Na⁺/K⁺ ATPase pump.
Where is [Na⁺] highest? [K⁺]?
Sodium is higher outside the cell. Potassium is higher inside the cell.
What is the mechanism of an action potential along a neuron?
- Na⁺ channels open due to a stimulus
- Na⁺ floods into the cell wrecking the cell’s polarity (depolarization)
- K⁺ channels are closed when the cell is polarized, but will open in response to depolarization
- K⁺ flows out of the cell (repolarization)
- Repolarization moves along the neuron in a rapid wave
- Repolarization wave, coupled with Ca²⁺ centering through Ca²⁺ channels, causes vesicles with nts. to fuse with the p.m. at the synapse
- nts. bind to receptors on nearby cells and the process repeats
How long are the voltage-gated ion channels open?
The channels shut just as fast as they open and pumps return the cell to a “normal” state.
What are nuclear hormone receptors?
Receptors in the nucleus that work to change gene expression.
What is a hormone?
A hydrophobic molecule that can have a variety of effects on the body.
Track the movement of a hormone in reference to a nuclear hormone receptor pathway.
- hormone travels through the blood via a protein carrier
- passes through the cell’s p.m. (hydrophobic)
- traverses cytosol
- enters the nucleus
- binds to nuclear hormone receptor (specificity, induced fit, conf. Δ all at play here)
What does the active hormone/receptor complex do?
Hormone/receptor complexes help RNApol bind to DNA, therefore increasing the expression of mRNA.
What is an HRE?
Hormone response element (HRE) is a special set of sequences just upstream from the target genes. It is where the receptor/hormone complexes bind and recruit RNApol.
How is cancer described by a biochemist?
Unregulated cell growth; no “off” switch. Almost completely a signal transduction pathway malfunction.
What is the balance of cell growth and death in a healthy cell?
cell growth = cell death
How does cancer happen/occur?
Happens via mutations or environmental effects that cause some pathway to NOT turn off (“really successful cells”).
How does PKC lead to cancer?
Mutated PKC is active WITHOUT Ca²⁺ and DAG which causes all downstream protein kinases to be on and stimulating cell growth.
How does epidermal growth factor receptor lead to cancer?
A mutation causes the epidermal growth factor binding site to be gone and tyrosine kinase is stuck in the “on” position with NO stimulus (locked in the active state).
How does Ras lead to cancer?
Ras’ GTPase function is frequently mutated in cancer. Lack of GTPase function means that the pathway is always on.
What is an oncogene?
A cancer causing gene.
What danger does anything that loses its ability to turn off present?
Anything that loses its ability to turn the signal off is a potential cancerous event.
